-- dump date 20120504_155339 -- class Genbank::misc_feature -- table misc_feature_note -- id note 557722000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 557722000002 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 557722000003 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722000004 Walker A motif; other site 557722000005 ATP binding site [chemical binding]; other site 557722000006 Walker B motif; other site 557722000007 arginine finger; other site 557722000008 C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple...; Region: Bac_DnaA_C; cd06571 557722000009 DnaA box-binding interface [nucleotide binding]; other site 557722000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 557722000011 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 557722000012 putative DNA binding surface [nucleotide binding]; other site 557722000013 dimer interface [polypeptide binding]; other site 557722000014 beta-clamp/clamp loader binding surface; other site 557722000015 beta-clamp/translesion DNA polymerase binding surface; other site 557722000016 recombination protein F; Reviewed; Region: recF; PRK00064 557722000017 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000018 Walker A/P-loop; other site 557722000019 ATP binding site [chemical binding]; other site 557722000020 Q-loop/lid; other site 557722000021 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000022 ABC transporter signature motif; other site 557722000023 Walker B; other site 557722000024 D-loop; other site 557722000025 H-loop/switch region; other site 557722000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 557722000027 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722000028 Mg2+ binding site [ion binding]; other site 557722000029 G-X-G motif; other site 557722000030 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 557722000031 anchoring element; other site 557722000032 dimer interface [polypeptide binding]; other site 557722000033 ATP binding site [chemical binding]; other site 557722000034 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 557722000035 active site 557722000036 putative metal-binding site [ion binding]; other site 557722000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 557722000038 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 557722000039 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 557722000040 putative acyl-acceptor binding pocket; other site 557722000041 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 557722000042 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722000043 active site 557722000044 motif I; other site 557722000045 motif II; other site 557722000046 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 557722000047 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 557722000048 dimer interface [polypeptide binding]; other site 557722000049 motif 1; other site 557722000050 active site 557722000051 motif 2; other site 557722000052 motif 3; other site 557722000053 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 557722000054 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 557722000055 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722000056 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 557722000057 putative acyl-acceptor binding pocket; other site 557722000058 PilZ domain; Region: PilZ; cl01260 557722000059 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 557722000060 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722000061 TPR motif; other site 557722000062 TPR repeat; Region: TPR_11; pfam13414 557722000063 binding surface 557722000064 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 557722000065 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000066 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722000067 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000068 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722000069 16S rRNA methyltransferase B; Provisional; Region: PRK10901 557722000070 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 557722000071 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722000072 S-adenosylmethionine binding site [chemical binding]; other site 557722000073 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 557722000074 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 557722000075 putative active site [active] 557722000076 substrate binding site [chemical binding]; other site 557722000077 putative cosubstrate binding site; other site 557722000078 catalytic site [active] 557722000079 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 557722000080 substrate binding site [chemical binding]; other site 557722000081 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 557722000082 active site 557722000083 catalytic residues [active] 557722000084 metal binding site [ion binding]; metal-binding site 557722000085 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 557722000086 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722000087 putative peptidoglycan binding site; other site 557722000088 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 557722000089 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 557722000090 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 557722000091 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 557722000092 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 557722000093 NADP binding site [chemical binding]; other site 557722000094 dimer interface [polypeptide binding]; other site 557722000095 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 557722000096 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 557722000097 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 557722000098 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 557722000099 shikimate binding site; other site 557722000100 NAD(P) binding site [chemical binding]; other site 557722000101 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; cl03005 557722000102 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722000103 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 557722000104 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722000105 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722000106 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 557722000107 NMT1-like family; Region: NMT1_2; cl15260 557722000108 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 557722000109 choline-sulfatase; Region: chol_sulfatase; TIGR03417 557722000110 Sulfatase; Region: Sulfatase; cl10460 557722000111 Choline sulfatase enzyme C terminal; Region: Choline_sulf_C; pfam12411 557722000112 putative choline sulfate-utilization transcription factor; Region: chol_sulf_TF; TIGR03418 557722000113 Helix-turn-helix domains; Region: HTH; cl00088 557722000114 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 557722000115 dimerization interface [polypeptide binding]; other site 557722000116 substrate binding pocket [chemical binding]; other site 557722000117 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722000118 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722000119 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722000120 active site 557722000121 phosphorylation site [posttranslational modification] 557722000122 intermolecular recognition site; other site 557722000123 dimerization interface [polypeptide binding]; other site 557722000124 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722000125 DNA binding residues [nucleotide binding] 557722000126 dimerization interface [polypeptide binding]; other site 557722000127 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 557722000128 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 557722000129 substrate binding site [chemical binding]; other site 557722000130 active site 557722000131 catalytic residues [active] 557722000132 heterodimer interface [polypeptide binding]; other site 557722000133 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 557722000134 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 557722000135 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000136 catalytic residue [active] 557722000137 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722000138 Helix-turn-helix domains; Region: HTH; cl00088 557722000139 The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold; Region: PBP2_TrpI; cd08482 557722000140 putative dimerization interface [polypeptide binding]; other site 557722000141 putative substrate binding pocket [chemical binding]; other site 557722000142 Dodecin; Region: Dodecin; cl01328 557722000143 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 557722000144 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722000145 Surface antigen; Region: Bac_surface_Ag; cl03097 557722000146 haemagglutination activity domain; Region: Haemagg_act; cl05436 557722000147 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 557722000148 adhesin HecA family 20-residue repeat (two copies); Region: fil_hemag_20aa; TIGR01731 557722000149 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 557722000150 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 557722000151 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 557722000152 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 557722000153 Transposase IS200 like; Region: Y1_Tnp; cl00848 557722000154 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 557722000155 NAD+--asparagine ADP-ribosyltransferase [Signal transduction mechanisms]; Region: COG5585 557722000156 GTPase-activating protein (GAP) domain found in bacterial cytotoxins, ExoS, SptP, and YopE. Part of protein secretion system; stimulates Rac1- dependent cytoskeletal changes that promote bacterial internalization; Region: ToxGAP; cd00219 557722000157 switch II binding region; other site 557722000158 Rac1 P-loop interaction site [polypeptide binding]; other site 557722000159 GTP binding residues [chemical binding]; other site 557722000160 switch I binding region; other site 557722000161 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of...; Region: VIP2; cl00173 557722000162 active site 557722000163 conformational flexibility of ligand binding pocket; other site 557722000164 ADP-ribosylating toxin turn-turn motif; other site 557722000165 TolB amino-terminal domain; Region: TolB_N; cl00639 557722000166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 557722000167 Putative bacterial lipoprotein (DUF799); Region: DUF799; cl01813 557722000168 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722000169 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557722000170 active site 557722000171 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 557722000172 dimer interface [polypeptide binding]; other site 557722000173 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557722000174 Ligand Binding Site [chemical binding]; other site 557722000175 Molecular Tunnel; other site 557722000176 Cupin domain; Region: Cupin_2; cl09118 557722000177 Domain of unknown function (DUF1993); Region: DUF1993; cl01567 557722000178 transcriptional regulator; Provisional; Region: PRK10632 557722000179 Helix-turn-helix domains; Region: HTH; cl00088 557722000180 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722000181 putative effector binding pocket; other site 557722000182 dimerization interface [polypeptide binding]; other site 557722000183 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722000184 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 557722000185 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 557722000186 catalytic residues [active] 557722000187 OsmC-like protein; Region: OsmC; cl00767 557722000188 Protein of unknown function (DUF1161); Region: DUF1161; pfam06649 557722000189 Predicted aminopeptidase [General function prediction only]; Region: COG4324 557722000190 Predicted aminopeptidase (DUF2265); Region: DUF2265; pfam10023 557722000191 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 557722000192 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722000193 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722000194 motif II; other site 557722000195 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 557722000196 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 557722000197 trimer interface [polypeptide binding]; other site 557722000198 putative metal binding site [ion binding]; other site 557722000199 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 557722000200 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 557722000201 active site 557722000202 Zn binding site [ion binding]; other site 557722000203 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 557722000204 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 557722000205 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 557722000206 FeS/SAM binding site; other site 557722000207 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 557722000208 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 557722000209 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000210 Walker A/P-loop; other site 557722000211 ATP binding site [chemical binding]; other site 557722000212 Q-loop/lid; other site 557722000213 ABC transporter signature motif; other site 557722000214 Walker B; other site 557722000215 D-loop; other site 557722000216 H-loop/switch region; other site 557722000217 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 557722000218 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722000219 active site 557722000220 ATP binding site [chemical binding]; other site 557722000221 substrate binding site [chemical binding]; other site 557722000222 activation loop (A-loop); other site 557722000223 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 557722000224 metal ion-dependent adhesion site (MIDAS); other site 557722000225 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 557722000226 active site 557722000227 Protein phosphatase 2C; Region: PP2C; pfam00481 557722000228 Uncharacterized protein conserved in bacteria (DUF2094); Region: DUF2094; cl01611 557722000229 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 557722000230 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 557722000231 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 557722000232 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 557722000233 hypothetical protein; Provisional; Region: PRK07033 557722000234 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 557722000235 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722000236 ligand binding site [chemical binding]; other site 557722000237 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 557722000238 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 557722000239 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 557722000240 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 557722000241 phosphopeptide binding site; other site 557722000242 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 557722000243 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 557722000244 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 557722000245 Protein of unknown function (DUF770); Region: DUF770; cl01402 557722000246 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 557722000247 Protein of unknown function (DUF877); Region: DUF877; pfam05943 557722000248 Protein of unknown function (DUF796); Region: DUF796; cl01226 557722000249 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 557722000250 ImpE protein; Region: ImpE; pfam07024 557722000251 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557722000252 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 557722000253 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 557722000254 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 557722000255 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 557722000256 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722000257 Walker A motif; other site 557722000258 ATP binding site [chemical binding]; other site 557722000259 Walker B motif; other site 557722000260 arginine finger; other site 557722000261 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722000262 Walker A motif; other site 557722000263 ATP binding site [chemical binding]; other site 557722000264 Walker B motif; other site 557722000265 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722000266 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722000267 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722000268 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722000269 PAAR motif; Region: PAAR_motif; cl15808 557722000270 Domain of unknown function (DUF1795); Region: DUF1795; cl02256 557722000271 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722000272 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722000273 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722000274 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 557722000275 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 557722000276 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 557722000277 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 557722000278 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 557722000279 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 557722000280 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722000281 Uncharacterized protein conserved in bacteria (DUF2169); Region: DUF2169; cl02212 557722000282 3-oxoacyl-(acyl carrier protein) synthase; Validated; Region: PRK06147 557722000283 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 557722000284 active site 557722000285 PAAR motif; Region: PAAR_motif; cl15808 557722000286 conserved hypothetical protein; Region: TIGR02270 557722000287 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 557722000288 active site clefts [active] 557722000289 zinc binding site [ion binding]; other site 557722000290 dimer interface [polypeptide binding]; other site 557722000291 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 557722000292 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722000293 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722000294 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 557722000295 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 557722000296 cytochrome c oxidase, subunit II; Region: CoxB; TIGR02866 557722000297 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722000298 Cytochrome c; Region: Cytochrom_C; cl11414 557722000299 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 557722000300 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 557722000301 Subunit I/III interface [polypeptide binding]; other site 557722000302 D-pathway; other site 557722000303 Subunit I/VIIc interface [polypeptide binding]; other site 557722000304 Subunit I/IV interface [polypeptide binding]; other site 557722000305 Subunit I/II interface [polypeptide binding]; other site 557722000306 Low-spin heme (heme a) binding site [chemical binding]; other site 557722000307 Subunit I/VIIa interface [polypeptide binding]; other site 557722000308 Subunit I/VIa interface [polypeptide binding]; other site 557722000309 Dimer interface; other site 557722000310 Putative water exit pathway; other site 557722000311 Binuclear center (heme a3/CuB) [ion binding]; other site 557722000312 K-pathway; other site 557722000313 Subunit I/Vb interface [polypeptide binding]; other site 557722000314 Putative proton exit pathway; other site 557722000315 Subunit I/VIb interface; other site 557722000316 Subunit I/VIc interface [polypeptide binding]; other site 557722000317 Electron transfer pathway; other site 557722000318 Subunit I/VIIIb interface [polypeptide binding]; other site 557722000319 Subunit I/VIIb interface [polypeptide binding]; other site 557722000320 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 557722000321 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 557722000322 Subunit III/VIIa interface [polypeptide binding]; other site 557722000323 Phospholipid binding site [chemical binding]; other site 557722000324 Subunit I/III interface [polypeptide binding]; other site 557722000325 Subunit III/VIb interface [polypeptide binding]; other site 557722000326 Subunit III/VIa interface; other site 557722000327 Subunit III/Vb interface [polypeptide binding]; other site 557722000328 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 557722000329 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 557722000330 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 557722000331 UbiA prenyltransferase family; Region: UbiA; cl00337 557722000332 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 557722000333 Cu(I) binding site [ion binding]; other site 557722000334 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 557722000335 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722000336 Coenzyme A binding pocket [chemical binding]; other site 557722000337 Helix-turn-helix domains; Region: HTH; cl00088 557722000338 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 557722000339 classical (c) SDR, subgroup 10; Region: SDR_c10; cd05373 557722000340 putative NAD(P) binding site [chemical binding]; other site 557722000341 active site 557722000342 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 557722000343 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 557722000344 putative catalytic residue [active] 557722000345 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 557722000346 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557722000347 Transcriptional regulators [Transcription]; Region: FadR; COG2186 557722000348 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722000349 DNA-binding site [nucleotide binding]; DNA binding site 557722000350 FCD domain; Region: FCD; cl11656 557722000351 Helix-turn-helix domains; Region: HTH; cl00088 557722000352 DNA-binding site [nucleotide binding]; DNA binding site 557722000353 FCD domain; Region: FCD; cl11656 557722000354 Aegerolysin; Region: Aegerolysin; pfam06355 557722000355 transcriptional regulator; Provisional; Region: PRK10632 557722000356 Helix-turn-helix domains; Region: HTH; cl00088 557722000357 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722000358 putative effector binding pocket; other site 557722000359 dimerization interface [polypeptide binding]; other site 557722000360 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 557722000361 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 557722000362 Late embryogenesis abundant protein; Region: LEA_2; cl12118 557722000363 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 557722000364 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 557722000365 PhnA protein; Region: PhnA; pfam03831 557722000366 gamma-aminobutyrate permease; Region: GABAperm; TIGR01773 557722000367 Spore germination protein; Region: Spore_permease; cl15802 557722000368 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 557722000369 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722000370 tetrameric interface [polypeptide binding]; other site 557722000371 NAD binding site [chemical binding]; other site 557722000372 catalytic residues [active] 557722000373 Cupin domain; Region: Cupin_2; cl09118 557722000374 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 557722000375 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722000376 inhibitor-cofactor binding pocket; inhibition site 557722000377 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000378 catalytic residue [active] 557722000379 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000380 Helix-turn-helix domains; Region: HTH; cl00088 557722000381 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000382 guanine deaminase; Provisional; Region: PRK09228 557722000383 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 557722000384 active site 557722000385 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 557722000386 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 557722000387 Walker A/P-loop; other site 557722000388 ATP binding site [chemical binding]; other site 557722000389 Q-loop/lid; other site 557722000390 ABC transporter signature motif; other site 557722000391 Walker B; other site 557722000392 D-loop; other site 557722000393 H-loop/switch region; other site 557722000394 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 557722000395 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 557722000396 TM-ABC transporter signature motif; other site 557722000397 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 557722000398 TM-ABC transporter signature motif; other site 557722000399 peroxiredoxin; Region: AhpC; TIGR03137 557722000400 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 557722000401 dimer interface [polypeptide binding]; other site 557722000402 decamer (pentamer of dimers) interface [polypeptide binding]; other site 557722000403 catalytic triad [active] 557722000404 peroxidatic and resolving cysteines [active] 557722000405 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 557722000406 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 557722000407 catalytic residue [active] 557722000408 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 557722000409 catalytic residues [active] 557722000410 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722000411 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000412 active site 557722000413 hydroxydechloroatrazine ethylaminohydrolase; Reviewed; Region: PRK08203 557722000414 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 557722000415 active site 557722000416 putative substrate binding pocket [chemical binding]; other site 557722000417 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 557722000418 active site 557722000419 tetramer interface [polypeptide binding]; other site 557722000420 TIR domain; Region: TIR_2; cl15770 557722000421 TIR domain; Region: TIR_2; cl15770 557722000422 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 557722000423 putative ligand binding site [chemical binding]; other site 557722000424 oxidase reductase; Provisional; Region: PTZ00273 557722000425 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 557722000426 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722000427 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 557722000428 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 557722000429 active site 557722000430 purine riboside binding site [chemical binding]; other site 557722000431 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 557722000432 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722000433 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722000434 DNA binding residues [nucleotide binding] 557722000435 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722000436 FecR protein; Region: FecR; pfam04773 557722000437 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722000438 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722000439 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722000440 N-terminal plug; other site 557722000441 ligand-binding site [chemical binding]; other site 557722000442 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 557722000443 Helix-turn-helix domains; Region: HTH; cl00088 557722000444 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000445 dimerization interface [polypeptide binding]; other site 557722000446 Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_beta; cd03464 557722000447 multimer interface [polypeptide binding]; other site 557722000448 heterodimer interface [polypeptide binding]; other site 557722000449 protocatechuate 3,4-dioxygenase, beta subunit; Region: protocat_beta; TIGR02422 557722000450 active site 557722000451 Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_alpha; cd03463 557722000452 heterodimer interface [polypeptide binding]; other site 557722000453 active site 557722000454 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 557722000455 Helix-turn-helix domains; Region: HTH; cl00088 557722000456 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722000457 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722000458 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722000459 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722000460 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722000461 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722000462 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722000463 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 557722000464 transcriptional regulator; Provisional; Region: PRK10632 557722000465 Helix-turn-helix domains; Region: HTH; cl00088 557722000466 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722000467 putative effector binding pocket; other site 557722000468 dimerization interface [polypeptide binding]; other site 557722000469 outer membrane porin, OprD family; Region: OprD; pfam03573 557722000470 Cupin domain; Region: Cupin_2; cl09118 557722000471 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722000472 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722000473 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 557722000474 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 557722000475 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 557722000476 xanthine permease; Region: pbuX; TIGR03173 557722000477 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 557722000478 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 557722000479 Helix-turn-helix domains; Region: HTH; cl00088 557722000480 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 557722000481 Uncharacterized conserved protein [Function unknown]; Region: COG1739 557722000482 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 557722000483 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 557722000484 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722000485 metal binding site [ion binding]; metal-binding site 557722000486 active site 557722000487 I-site; other site 557722000488 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 557722000489 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722000490 dimerization interface [polypeptide binding]; other site 557722000491 two component system sensor kinase SsrA; Provisional; Region: PRK15347 557722000492 Sigma factor PP2C-like phosphatases; Region: PP2C_SIG; smart00331 557722000493 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 557722000494 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 557722000495 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722000496 active site 557722000497 phosphorylation site [posttranslational modification] 557722000498 intermolecular recognition site; other site 557722000499 dimerization interface [polypeptide binding]; other site 557722000500 CheB methylesterase; Region: CheB_methylest; pfam01339 557722000501 CheD chemotactic sensory transduction; Region: CheD; cl00810 557722000502 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 557722000503 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 557722000504 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000505 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722000506 PAS domain; Region: PAS_9; pfam13426 557722000507 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722000508 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722000509 dimer interface [polypeptide binding]; other site 557722000510 putative CheW interface [polypeptide binding]; other site 557722000511 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 557722000512 putative CheA interaction surface; other site 557722000513 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 557722000514 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 557722000515 putative binding surface; other site 557722000516 active site 557722000517 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 557722000518 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 557722000519 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722000520 ATP binding site [chemical binding]; other site 557722000521 G-X-G motif; other site 557722000522 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 557722000523 Response regulator receiver domain; Region: Response_reg; pfam00072 557722000524 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722000525 active site 557722000526 phosphorylation site [posttranslational modification] 557722000527 intermolecular recognition site; other site 557722000528 dimerization interface [polypeptide binding]; other site 557722000529 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557722000530 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722000531 putative CheW interface [polypeptide binding]; other site 557722000532 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000533 Helix-turn-helix domains; Region: HTH; cl00088 557722000534 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722000535 putative effector binding pocket; other site 557722000536 dimerization interface [polypeptide binding]; other site 557722000537 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 557722000538 classical (c) SDRs; Region: SDR_c; cd05233 557722000539 NAD(P) binding site [chemical binding]; other site 557722000540 active site 557722000541 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 557722000542 Sulfatase; Region: Sulfatase; cl10460 557722000543 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557722000544 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557722000545 Walker A/P-loop; other site 557722000546 ATP binding site [chemical binding]; other site 557722000547 Q-loop/lid; other site 557722000548 ABC transporter signature motif; other site 557722000549 Walker B; other site 557722000550 D-loop; other site 557722000551 H-loop/switch region; other site 557722000552 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722000553 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722000554 NMT1-like family; Region: NMT1_2; cl15260 557722000555 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 557722000556 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cd00250 557722000557 substrate binding pocket [chemical binding]; other site 557722000558 active site 557722000559 iron coordination sites [ion binding]; other site 557722000560 Membrane transport protein; Region: Mem_trans; cl09117 557722000561 outer membrane porin, OprD family; Region: OprD; pfam03573 557722000562 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 557722000563 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000564 Helix-turn-helix domains; Region: HTH; cl00088 557722000565 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722000566 dimerization interface [polypeptide binding]; other site 557722000567 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 557722000568 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722000569 N-terminal plug; other site 557722000570 ligand-binding site [chemical binding]; other site 557722000571 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 557722000572 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 557722000573 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 557722000574 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 557722000575 active site 557722000576 iron coordination sites [ion binding]; other site 557722000577 substrate binding pocket [chemical binding]; other site 557722000578 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 557722000579 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 557722000580 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000581 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 557722000582 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 557722000583 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557722000584 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722000585 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557722000586 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 557722000587 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722000588 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 557722000589 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 557722000590 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722000591 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722000592 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 557722000593 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 557722000594 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722000595 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722000596 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; cl07913 557722000597 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 557722000598 Acyl transferase domain; Region: Acyl_transf_1; cl08282 557722000599 Malonate transporter MadL subunit; Region: MadL; cl04273 557722000600 Malonate/sodium symporter MadM subunit; Region: MadM; cl04274 557722000601 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000602 Helix-turn-helix domains; Region: HTH; cl00088 557722000603 The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; Region: PBP2_MdcR; cd08416 557722000604 putative dimerization interface [polypeptide binding]; other site 557722000605 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000606 Helix-turn-helix domains; Region: HTH; cl00088 557722000607 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 557722000608 putative substrate binding pocket [chemical binding]; other site 557722000609 dimerization interface [polypeptide binding]; other site 557722000610 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722000611 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 557722000612 NAD(P) binding site [chemical binding]; other site 557722000613 catalytic residues [active] 557722000614 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 557722000615 Spore germination protein; Region: Spore_permease; cl15802 557722000616 putative aminotransferase; Provisional; Region: PRK12403 557722000617 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722000618 inhibitor-cofactor binding pocket; inhibition site 557722000619 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000620 catalytic residue [active] 557722000621 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557722000622 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000623 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 557722000624 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 557722000625 inhibitor site; inhibition site 557722000626 active site 557722000627 dimer interface [polypeptide binding]; other site 557722000628 catalytic residue [active] 557722000629 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 557722000630 intersubunit interface [polypeptide binding]; other site 557722000631 active site 557722000632 Zn2+ binding site [ion binding]; other site 557722000633 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722000634 sequence-specific DNA binding site [nucleotide binding]; other site 557722000635 salt bridge; other site 557722000636 Cupin domain; Region: Cupin_2; cl09118 557722000637 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722000638 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722000639 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 557722000640 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722000641 dimer interface [polypeptide binding]; other site 557722000642 active site 557722000643 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 557722000644 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000645 putative substrate translocation pore; other site 557722000646 3-carboxy-cis,cis-muconate cycloisomerase; Provisional; Region: PRK09053 557722000647 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 557722000648 tetramer interface [polypeptide binding]; other site 557722000649 active site 557722000650 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 557722000651 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557722000652 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000653 Helix-turn-helix domains; Region: HTH; cl00088 557722000654 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000655 dimerization interface [polypeptide binding]; other site 557722000656 benzoate transport; Region: 2A0115; TIGR00895 557722000657 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000658 putative substrate translocation pore; other site 557722000659 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000660 Helix-turn-helix domains; Region: HTH; cl00088 557722000661 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722000662 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722000663 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 557722000664 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000665 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 557722000666 EamA-like transporter family; Region: EamA; cl01037 557722000667 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557722000668 outer membrane porin, OprD family; Region: OprD; pfam03573 557722000669 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000670 D-galactonate transporter; Region: 2A0114; TIGR00893 557722000671 putative substrate translocation pore; other site 557722000672 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 557722000673 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 557722000674 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 557722000675 dimer interface [polypeptide binding]; other site 557722000676 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 557722000677 active site 557722000678 Fe binding site [ion binding]; other site 557722000679 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722000680 Helix-turn-helix domains; Region: HTH; cl00088 557722000681 shikimate 5-dehydrogenase; Reviewed; Region: PRK12549 557722000682 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 557722000683 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 557722000684 shikimate binding site; other site 557722000685 NAD(P) binding site [chemical binding]; other site 557722000686 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 557722000687 active site 557722000688 trimer interface [polypeptide binding]; other site 557722000689 dimer interface [polypeptide binding]; other site 557722000690 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000691 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722000692 putative substrate translocation pore; other site 557722000693 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000694 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 557722000695 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000696 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000697 Cupin domain; Region: Cupin_2; cl09118 557722000698 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722000699 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722000700 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557722000701 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722000702 Coenzyme A binding pocket [chemical binding]; other site 557722000703 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722000704 FOG: CBS domain [General function prediction only]; Region: COG0517 557722000705 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 557722000706 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 557722000707 Helix-turn-helix domains; Region: HTH; cl00088 557722000708 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 557722000709 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 557722000710 Protein of unknown function (DUF2875); Region: DUF2875; pfam11394 557722000711 Protein of unknown function (DUF3274); Region: DUF3274; pfam11678 557722000712 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722000713 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722000714 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722000715 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 557722000716 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 557722000717 Protein of unknown function (DUF796); Region: DUF796; cl01226 557722000718 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722000719 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 557722000720 tetramerization interface [polypeptide binding]; other site 557722000721 NAD(P) binding site [chemical binding]; other site 557722000722 catalytic residues [active] 557722000723 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 557722000724 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722000725 inhibitor-cofactor binding pocket; inhibition site 557722000726 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000727 catalytic residue [active] 557722000728 Response regulator receiver domain; Region: Response_reg; pfam00072 557722000729 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722000730 active site 557722000731 phosphorylation site [posttranslational modification] 557722000732 intermolecular recognition site; other site 557722000733 dimerization interface [polypeptide binding]; other site 557722000734 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 557722000735 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722000736 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722000737 DNA-binding site [nucleotide binding]; DNA binding site 557722000738 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722000739 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000740 homodimer interface [polypeptide binding]; other site 557722000741 catalytic residue [active] 557722000742 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557722000743 Cupin domain; Region: Cupin_2; cl09118 557722000744 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722000745 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000746 Helix-turn-helix domains; Region: HTH; cl00088 557722000747 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 557722000748 substrate binding pocket [chemical binding]; other site 557722000749 dimerization interface [polypeptide binding]; other site 557722000750 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 557722000751 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000752 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722000753 ligand binding site [chemical binding]; other site 557722000754 flexible hinge region; other site 557722000755 Helix-turn-helix domains; Region: HTH; cl00088 557722000756 Protein of unknown function (DUF962); Region: DUF962; cl01879 557722000757 Peptidase family M48; Region: Peptidase_M48; cl12018 557722000758 Domain of unknown function DUF81; Region: DUF81; cl00498 557722000759 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722000760 dimerization interface [polypeptide binding]; other site 557722000761 putative DNA binding site [nucleotide binding]; other site 557722000762 putative Zn2+ binding site [ion binding]; other site 557722000763 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 557722000764 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a...; Region: ABC_CysA_sulfate_importer; cd03296 557722000765 Walker A/P-loop; other site 557722000766 ATP binding site [chemical binding]; other site 557722000767 Q-loop/lid; other site 557722000768 ABC transporter signature motif; other site 557722000769 Walker B; other site 557722000770 D-loop; other site 557722000771 H-loop/switch region; other site 557722000772 TOBE-like domain; Region: TOBE_3; pfam12857 557722000773 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000774 dimer interface [polypeptide binding]; other site 557722000775 conserved gate region; other site 557722000776 putative PBP binding loops; other site 557722000777 ABC-ATPase subunit interface; other site 557722000778 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 557722000779 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000780 dimer interface [polypeptide binding]; other site 557722000781 conserved gate region; other site 557722000782 putative PBP binding loops; other site 557722000783 ABC-ATPase subunit interface; other site 557722000784 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000785 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 557722000786 Uncharacterized small protein (DUF2292); Region: DUF2292; cl02371 557722000787 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722000788 PAS fold; Region: PAS_3; pfam08447 557722000789 putative active site [active] 557722000790 heme pocket [chemical binding]; other site 557722000791 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722000792 PAS domain; Region: PAS_9; pfam13426 557722000793 putative active site [active] 557722000794 heme pocket [chemical binding]; other site 557722000795 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722000796 metal binding site [ion binding]; metal-binding site 557722000797 active site 557722000798 I-site; other site 557722000799 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722000800 Fatty acid desaturase; Region: FA_desaturase; pfam00487 557722000801 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 557722000802 Di-iron ligands [ion binding]; other site 557722000803 Transposase; Region: DDE_Tnp_ISL3; pfam01610 557722000804 Sodium:solute symporter family; Region: SSF; cl00456 557722000805 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557722000806 Arginase family; Region: Arginase; cl00306 557722000807 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722000808 Helix-turn-helix domains; Region: HTH; cl00088 557722000809 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722000810 dimerization interface [polypeptide binding]; other site 557722000811 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722000812 PAS fold; Region: PAS_3; pfam08447 557722000813 putative active site [active] 557722000814 heme pocket [chemical binding]; other site 557722000815 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722000816 metal binding site [ion binding]; metal-binding site 557722000817 active site 557722000818 I-site; other site 557722000819 outer membrane porin, OprD family; Region: OprD; pfam03573 557722000820 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 557722000821 agmatine deiminase; Region: agmatine_aguA; TIGR03380 557722000822 N-carbamolyputrescine amidase; Region: PLN02747 557722000823 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 557722000824 putative active site; other site 557722000825 catalytic triad [active] 557722000826 putative dimer interface [polypeptide binding]; other site 557722000827 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722000828 Helix-turn-helix domains; Region: HTH; cl00088 557722000829 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 557722000830 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000831 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722000832 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 557722000833 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722000834 Peptidase C26; Region: Peptidase_C26; pfam07722 557722000835 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 557722000836 catalytic triad [active] 557722000837 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722000838 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722000839 putative aminotransferase; Validated; Region: PRK07480 557722000840 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722000841 inhibitor-cofactor binding pocket; inhibition site 557722000842 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000843 catalytic residue [active] 557722000844 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 557722000845 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000846 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 557722000847 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000848 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 557722000849 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000850 Walker A/P-loop; other site 557722000851 ATP binding site [chemical binding]; other site 557722000852 Q-loop/lid; other site 557722000853 ABC transporter signature motif; other site 557722000854 Walker B; other site 557722000855 D-loop; other site 557722000856 H-loop/switch region; other site 557722000857 TOBE domain; Region: TOBE_2; cl01440 557722000858 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000859 dimer interface [polypeptide binding]; other site 557722000860 conserved gate region; other site 557722000861 putative PBP binding loops; other site 557722000862 ABC-ATPase subunit interface; other site 557722000863 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000864 dimer interface [polypeptide binding]; other site 557722000865 conserved gate region; other site 557722000866 putative PBP binding loops; other site 557722000867 ABC-ATPase subunit interface; other site 557722000868 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 557722000869 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 557722000870 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 557722000871 active site 557722000872 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722000873 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722000874 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722000875 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 557722000876 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722000877 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 557722000878 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 557722000879 DAK2 domain; Region: Dak2; cl03685 557722000880 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722000881 Protein of unknown function (DUF523); Region: DUF523; cl00733 557722000882 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722000883 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000884 dimer interface [polypeptide binding]; other site 557722000885 conserved gate region; other site 557722000886 putative PBP binding loops; other site 557722000887 ABC-ATPase subunit interface; other site 557722000888 cystine transporter subunit; Provisional; Region: PRK11260 557722000889 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722000890 substrate binding pocket [chemical binding]; other site 557722000891 membrane-bound complex binding site; other site 557722000892 hinge residues; other site 557722000893 Domain of unknown function (DUF4399); Region: DUF4399; pfam14347 557722000894 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 557722000895 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000896 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 557722000897 L-serine binding site [chemical binding]; other site 557722000898 ACT domain interface; other site 557722000899 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557722000900 FAD binding domain; Region: FAD_binding_4; pfam01565 557722000901 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722000902 SdiA-regulated; Region: SdiA-regulated; pfam06977 557722000903 SdiA-regulated; Region: SdiA-regulated; cd09971 557722000904 putative active site [active] 557722000905 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 557722000906 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 557722000907 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 557722000908 Spore germination protein; Region: Spore_permease; cl15802 557722000909 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557722000910 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722000911 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 557722000912 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000913 dimer interface [polypeptide binding]; other site 557722000914 conserved gate region; other site 557722000915 putative PBP binding loops; other site 557722000916 ABC-ATPase subunit interface; other site 557722000917 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722000918 dimer interface [polypeptide binding]; other site 557722000919 conserved gate region; other site 557722000920 putative PBP binding loops; other site 557722000921 ABC-ATPase subunit interface; other site 557722000922 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557722000923 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000924 Walker A/P-loop; other site 557722000925 ATP binding site [chemical binding]; other site 557722000926 Q-loop/lid; other site 557722000927 ABC transporter signature motif; other site 557722000928 Walker B; other site 557722000929 D-loop; other site 557722000930 H-loop/switch region; other site 557722000931 TOBE domain; Region: TOBE_2; cl01440 557722000932 SdiA-regulated; Region: SdiA-regulated; pfam06977 557722000933 SdiA-regulated; Region: SdiA-regulated; cd09971 557722000934 putative active site [active] 557722000935 alkaline phosphatase isozyme conversion aminopeptidase; Provisional; Region: PRK10199 557722000936 M28 Zn-peptidases include aminopeptidases and carboxypeptidases; Region: M28; cd02690 557722000937 metal binding site [ion binding]; metal-binding site 557722000938 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722000939 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 557722000940 trimer interface [polypeptide binding]; other site 557722000941 active site 557722000942 substrate binding site [chemical binding]; other site 557722000943 CoA binding site [chemical binding]; other site 557722000944 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 557722000945 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 557722000946 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 557722000947 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557722000948 active site 557722000949 dimer interface [polypeptide binding]; other site 557722000950 threonine dehydratase; Reviewed; Region: PRK09224 557722000951 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 557722000952 tetramer interface [polypeptide binding]; other site 557722000953 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722000954 catalytic residue [active] 557722000955 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 557722000956 putative Ile/Val binding site [chemical binding]; other site 557722000957 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 557722000958 putative Ile/Val binding site [chemical binding]; other site 557722000959 Predicted integral membrane protein (DUF2269); Region: DUF2269; cl02335 557722000960 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 557722000961 NADH(P)-binding; Region: NAD_binding_10; pfam13460 557722000962 putative NAD(P) binding site [chemical binding]; other site 557722000963 active site 557722000964 DoxX-like family; Region: DoxX_3; pfam13781 557722000965 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722000966 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 557722000967 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722000968 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 557722000969 putative active site [active] 557722000970 Ap4A binding site [chemical binding]; other site 557722000971 nudix motif; other site 557722000972 putative metal binding site [ion binding]; other site 557722000973 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 557722000974 GAF domain; Region: GAF; cl15785 557722000975 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 557722000976 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 557722000977 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722000978 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722000979 PAS fold; Region: PAS_3; pfam08447 557722000980 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722000981 metal binding site [ion binding]; metal-binding site 557722000982 active site 557722000983 I-site; other site 557722000984 NRDE protein; Region: NRDE; cl01315 557722000985 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557722000986 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 557722000987 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 557722000988 dimerization interface [polypeptide binding]; other site 557722000989 active site 557722000990 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722000991 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722000992 G1 box; other site 557722000993 GTP/Mg2+ binding site [chemical binding]; other site 557722000994 G2 box; other site 557722000995 Switch I region; other site 557722000996 G3 box; other site 557722000997 Switch II region; other site 557722000998 G4 box; other site 557722000999 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 557722001000 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 557722001001 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 557722001002 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 557722001003 putative active site [active] 557722001004 catalytic site [active] 557722001005 putative metal binding site [ion binding]; other site 557722001006 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 557722001007 folate binding site [chemical binding]; other site 557722001008 NADP+ binding site [chemical binding]; other site 557722001009 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 557722001010 active site 557722001011 metal binding site [ion binding]; metal-binding site 557722001012 homotetramer interface [polypeptide binding]; other site 557722001013 xanthine permease; Region: pbuX; TIGR03173 557722001014 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 557722001015 Dehydratase family; Region: ILVD_EDD; cl00340 557722001016 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 557722001017 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001018 S-adenosylmethionine binding site [chemical binding]; other site 557722001019 intracellular protease, PfpI family; Region: PfpI; TIGR01382 557722001020 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 557722001021 proposed catalytic triad [active] 557722001022 conserved cys residue [active] 557722001023 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 557722001024 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722001025 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 557722001026 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 557722001027 DNA binding site [nucleotide binding] 557722001028 catalytic residue [active] 557722001029 H2TH interface [polypeptide binding]; other site 557722001030 putative catalytic residues [active] 557722001031 turnover-facilitating residue; other site 557722001032 intercalation triad [nucleotide binding]; other site 557722001033 8OG recognition residue [nucleotide binding]; other site 557722001034 putative reading head residues; other site 557722001035 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 557722001036 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 557722001037 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 557722001038 putative acyl-acceptor binding pocket; other site 557722001039 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722001040 Sel1 repeat; Region: Sel1; cl02723 557722001041 Sel1 repeat; Region: Sel1; cl02723 557722001042 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 557722001043 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 557722001044 ferredoxin; Validated; Region: PRK07118 557722001045 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 557722001046 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 557722001047 active site 557722001048 (T/H)XGH motif; other site 557722001049 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 557722001050 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557722001051 Tat-translocated enzyme; Region: tat_substr_1; TIGR01412 557722001052 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 557722001053 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 557722001054 NAD(P) binding site [chemical binding]; other site 557722001055 catalytic residues [active] 557722001056 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722001057 Helix-turn-helix domains; Region: HTH; cl00088 557722001058 Bacterial transcriptional repressor; Region: TetR; pfam13972 557722001059 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 557722001060 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 557722001061 nucleophilic elbow; other site 557722001062 catalytic triad; other site 557722001063 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001064 S-adenosylmethionine binding site [chemical binding]; other site 557722001065 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 557722001066 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557722001067 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 557722001068 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 557722001069 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557722001070 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 557722001071 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 557722001072 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 557722001073 P loop; other site 557722001074 GTP binding site [chemical binding]; other site 557722001075 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 557722001076 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722001077 Walker A/P-loop; other site 557722001078 ATP binding site [chemical binding]; other site 557722001079 Q-loop/lid; other site 557722001080 ABC transporter signature motif; other site 557722001081 Walker B; other site 557722001082 D-loop; other site 557722001083 H-loop/switch region; other site 557722001084 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 557722001085 FtsX-like permease family; Region: FtsX; cl15850 557722001086 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 557722001087 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557722001088 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722001089 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722001090 DNA binding residues [nucleotide binding] 557722001091 Transglycosylase; Region: Transgly; cl07896 557722001092 Protein of unknown function (DUF423); Region: DUF423; cl01008 557722001093 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 557722001094 thiS-thiF/thiG interaction site; other site 557722001095 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 557722001096 ThiS interaction site; other site 557722001097 putative active site [active] 557722001098 tetramer interface [polypeptide binding]; other site 557722001099 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001100 S-adenosylmethionine binding site [chemical binding]; other site 557722001101 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 557722001102 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 557722001103 HemN family oxidoreductase; Provisional; Region: PRK05660 557722001104 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722001105 FeS/SAM binding site; other site 557722001106 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 557722001107 active site 557722001108 dimerization interface [polypeptide binding]; other site 557722001109 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 557722001110 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 557722001111 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001112 S-adenosylmethionine binding site [chemical binding]; other site 557722001113 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 557722001114 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722001115 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722001116 G1 box; other site 557722001117 GTP/Mg2+ binding site [chemical binding]; other site 557722001118 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 557722001119 G2 box; other site 557722001120 Switch I region; other site 557722001121 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 557722001122 G3 box; other site 557722001123 Switch II region; other site 557722001124 GTP/Mg2+ binding site [chemical binding]; other site 557722001125 G4 box; other site 557722001126 G5 box; other site 557722001127 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 557722001128 YGGT family; Region: YGGT; cl00508 557722001129 YGGT family; Region: YGGT; cl00508 557722001130 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 557722001131 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001132 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 557722001133 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722001134 catalytic residue [active] 557722001135 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 557722001136 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 557722001137 Walker A motif; other site 557722001138 ATP binding site [chemical binding]; other site 557722001139 Walker B motif; other site 557722001140 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 557722001141 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722001142 Walker A motif; other site 557722001143 ATP binding site [chemical binding]; other site 557722001144 Walker B motif; other site 557722001145 Cation efflux family; Region: Cation_efflux; cl00316 557722001146 TM2 domain; Region: TM2; cl00984 557722001147 TM2 domain; Region: TM2; cl00984 557722001148 cystathionine beta-synthase; Region: cysta_beta; TIGR01137 557722001149 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 557722001150 dimer interface [polypeptide binding]; other site 557722001151 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722001152 catalytic residue [active] 557722001153 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well...; Region: CBS_pair_PALP_assoc2; cd04609 557722001154 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 557722001155 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 557722001156 homodimer interface [polypeptide binding]; other site 557722001157 substrate-cofactor binding pocket; other site 557722001158 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722001159 catalytic residue [active] 557722001160 dihydroorotase; Validated; Region: pyrC; PRK09357 557722001161 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 557722001162 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 557722001163 active site 557722001164 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 557722001165 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557722001166 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001167 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722001168 active site 557722001169 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 557722001170 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 557722001171 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 557722001172 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557722001173 glutathione synthetase; Provisional; Region: PRK05246 557722001174 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 557722001175 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722001176 Response regulator receiver domain; Region: Response_reg; pfam00072 557722001177 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722001178 active site 557722001179 phosphorylation site [posttranslational modification] 557722001180 intermolecular recognition site; other site 557722001181 dimerization interface [polypeptide binding]; other site 557722001182 Response regulator receiver domain; Region: Response_reg; pfam00072 557722001183 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722001184 active site 557722001185 phosphorylation site [posttranslational modification] 557722001186 intermolecular recognition site; other site 557722001187 dimerization interface [polypeptide binding]; other site 557722001188 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 557722001189 putative CheA interaction surface; other site 557722001190 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 557722001191 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722001192 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722001193 dimer interface [polypeptide binding]; other site 557722001194 putative CheW interface [polypeptide binding]; other site 557722001195 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 557722001196 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 557722001197 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001198 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 557722001199 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 557722001200 putative binding surface; other site 557722001201 active site 557722001202 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722001203 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722001204 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 557722001205 putative binding surface; other site 557722001206 active site 557722001207 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 557722001208 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 557722001209 putative binding surface; other site 557722001210 active site 557722001211 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722001212 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 557722001213 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 557722001214 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722001215 ATP binding site [chemical binding]; other site 557722001216 Mg2+ binding site [ion binding]; other site 557722001217 G-X-G motif; other site 557722001218 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 557722001219 Response regulator receiver domain; Region: Response_reg; pfam00072 557722001220 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722001221 active site 557722001222 phosphorylation site [posttranslational modification] 557722001223 intermolecular recognition site; other site 557722001224 dimerization interface [polypeptide binding]; other site 557722001225 Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]; Region: CheB; COG2201 557722001226 CheB methylesterase; Region: CheB_methylest; pfam01339 557722001227 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 557722001228 Cupin domain; Region: Cupin_2; cl09118 557722001229 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722001230 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722001231 LysE type translocator; Region: LysE; cl00565 557722001232 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 557722001233 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 557722001234 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK07030 557722001235 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722001236 inhibitor-cofactor binding pocket; inhibition site 557722001237 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722001238 catalytic residue [active] 557722001239 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 557722001240 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557722001241 YceI-like domain; Region: YceI; cl01001 557722001242 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557722001243 Helix-turn-helix domains; Region: HTH; cl00088 557722001244 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 557722001245 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722001246 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722001247 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 557722001248 Protein export membrane protein; Region: SecD_SecF; cl14618 557722001249 Protein export membrane protein; Region: SecD_SecF; cl14618 557722001250 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722001251 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 557722001252 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 557722001253 ATP binding site [chemical binding]; other site 557722001254 Mg++ binding site [ion binding]; other site 557722001255 motif III; other site 557722001256 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722001257 nucleotide binding region [chemical binding]; other site 557722001258 ATP-binding site [chemical binding]; other site 557722001259 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 557722001260 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 557722001261 FAD binding site [chemical binding]; other site 557722001262 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722001263 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 557722001264 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001265 oligomerization interface [polypeptide binding]; other site 557722001266 active site 557722001267 NAD+ binding site [chemical binding]; other site 557722001268 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722001269 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722001270 N-terminal plug; other site 557722001271 ligand-binding site [chemical binding]; other site 557722001272 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722001273 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722001274 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722001275 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 557722001276 Helix-turn-helix domains; Region: HTH; cl00088 557722001277 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 557722001278 cytosine deaminase; Provisional; Region: PRK09230 557722001279 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 557722001280 active site 557722001281 Sodium:solute symporter family; Region: SSF; cl00456 557722001282 dihydropyrimidine dehydrogenase subunit B; Validated; Region: PRK08318 557722001283 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 557722001284 homodimer interface [polypeptide binding]; other site 557722001285 active site 557722001286 FMN binding site [chemical binding]; other site 557722001287 substrate binding site [chemical binding]; other site 557722001288 4Fe-4S binding domain; Region: Fer4; cl02805 557722001289 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 557722001290 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001291 phenylhydantoinase; Validated; Region: PRK08323 557722001292 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine...; Region: D-HYD; cd01314 557722001293 tetramer interface [polypeptide binding]; other site 557722001294 active site 557722001295 Sodium:solute symporter family; Region: SSF; cl00456 557722001296 allantoate amidohydrolase; Reviewed; Region: PRK09290 557722001297 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 557722001298 active site 557722001299 metal binding site [ion binding]; metal-binding site 557722001300 dimer interface [polypeptide binding]; other site 557722001301 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 557722001302 CoA-transferase family III; Region: CoA_transf_3; pfam02515 557722001303 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 557722001304 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722001305 FAD binding site [chemical binding]; other site 557722001306 substrate binding pocket [chemical binding]; other site 557722001307 catalytic base [active] 557722001308 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722001309 Helix-turn-helix domains; Region: HTH; cl00088 557722001310 The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_like; cd08481 557722001311 dimerization interface [polypeptide binding]; other site 557722001312 substrate binding pocket [chemical binding]; other site 557722001313 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 557722001314 Phosphate transporter family; Region: PHO4; cl00396 557722001315 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 557722001316 Phosphate transporter family; Region: PHO4; cl00396 557722001317 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 557722001318 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 557722001319 dimer interface [polypeptide binding]; other site 557722001320 active site residues [active] 557722001321 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 557722001322 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 557722001323 integral membrane protein, YccS/YhfK family; Region: YCCS_YHJK; TIGR01667 557722001324 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 557722001325 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 557722001326 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 557722001327 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 557722001328 ATP binding site [chemical binding]; other site 557722001329 Mg++ binding site [ion binding]; other site 557722001330 motif III; other site 557722001331 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722001332 nucleotide binding region [chemical binding]; other site 557722001333 ATP-binding site [chemical binding]; other site 557722001334 DbpA RNA binding domain; Region: DbpA; pfam03880 557722001335 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557722001336 DNA-binding site [nucleotide binding]; DNA binding site 557722001337 RNA-binding motif; other site 557722001338 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 557722001339 putative transporter; Provisional; Region: PRK10504 557722001340 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722001341 putative substrate translocation pore; other site 557722001342 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722001343 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 557722001344 Clp amino terminal domain; Region: Clp_N; pfam02861 557722001345 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722001346 Walker A motif; other site 557722001347 ATP binding site [chemical binding]; other site 557722001348 Walker B motif; other site 557722001349 arginine finger; other site 557722001350 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722001351 Walker A motif; other site 557722001352 ATP binding site [chemical binding]; other site 557722001353 Walker B motif; other site 557722001354 arginine finger; other site 557722001355 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722001356 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 557722001357 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 557722001358 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 557722001359 putative acyl-acceptor binding pocket; other site 557722001360 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 557722001361 DNA-binding response regulator CreB; Provisional; Region: PRK11083 557722001362 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722001363 active site 557722001364 phosphorylation site [posttranslational modification] 557722001365 intermolecular recognition site; other site 557722001366 dimerization interface [polypeptide binding]; other site 557722001367 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722001368 DNA binding site [nucleotide binding] 557722001369 sensory histidine kinase CreC; Provisional; Region: PRK11100 557722001370 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722001371 dimer interface [polypeptide binding]; other site 557722001372 phosphorylation site [posttranslational modification] 557722001373 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722001374 ATP binding site [chemical binding]; other site 557722001375 G-X-G motif; other site 557722001376 Inner membrane protein CreD; Region: CreD; cl01844 557722001377 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722001378 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 557722001379 putative C-terminal domain interface [polypeptide binding]; other site 557722001380 putative GSH binding site (G-site) [chemical binding]; other site 557722001381 putative dimer interface [polypeptide binding]; other site 557722001382 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 557722001383 N-terminal domain interface [polypeptide binding]; other site 557722001384 dimer interface [polypeptide binding]; other site 557722001385 Streptogramin lyase [Defense mechanisms]; Region: Vgb; COG4257 557722001386 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 557722001387 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722001388 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 557722001389 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722001390 N-terminal plug; other site 557722001391 ligand-binding site [chemical binding]; other site 557722001392 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722001393 FecR protein; Region: FecR; pfam04773 557722001394 RNA polymerase sigma factor; Reviewed; Region: PRK12523 557722001395 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722001396 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722001397 DNA binding residues [nucleotide binding] 557722001398 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 557722001399 C-terminal domain interface [polypeptide binding]; other site 557722001400 GSH binding site (G-site) [chemical binding]; other site 557722001401 dimer interface [polypeptide binding]; other site 557722001402 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 557722001403 N-terminal domain interface [polypeptide binding]; other site 557722001404 dimer interface [polypeptide binding]; other site 557722001405 substrate binding pocket (H-site) [chemical binding]; other site 557722001406 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722001407 CoenzymeA binding site [chemical binding]; other site 557722001408 subunit interaction site [polypeptide binding]; other site 557722001409 PHB binding site; other site 557722001410 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722001411 Helix-turn-helix domains; Region: HTH; cl00088 557722001412 Sodium:solute symporter family; Region: SSF; cl00456 557722001413 Helix-turn-helix domains; Region: HTH; cl00088 557722001414 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold; Region: PBP2_Pa0477; cd08468 557722001415 putative substrate binding pocket [chemical binding]; other site 557722001416 dimerization interface [polypeptide binding]; other site 557722001417 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722001418 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722001419 Helix-turn-helix domains; Region: HTH; cl00088 557722001420 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722001421 dimerization interface [polypeptide binding]; other site 557722001422 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 557722001423 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 557722001424 active site 557722001425 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557722001426 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722001427 Coenzyme A binding pocket [chemical binding]; other site 557722001428 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 557722001429 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 557722001430 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 557722001431 Predicted permeases [General function prediction only]; Region: RarD; COG2962 557722001432 EamA-like transporter family; Region: EamA; cl01037 557722001433 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722001434 Helix-turn-helix domains; Region: HTH; cl00088 557722001435 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 557722001436 TOBE domain; Region: TOBE_2; cl01440 557722001437 TOBE domain; Region: TOBE_2; cl01440 557722001438 Predicted periplasmic lipoprotein (DUF2279); Region: DUF2279; cl11574 557722001439 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 557722001440 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722001441 active site 557722001442 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722001443 Helix-turn-helix domains; Region: HTH; cl00088 557722001444 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 557722001445 putative substrate binding pocket [chemical binding]; other site 557722001446 dimerization interface [polypeptide binding]; other site 557722001447 LamB/YcsF family; Region: LamB_YcsF; cl00664 557722001448 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 557722001449 carboxyltransferase (CT) interaction site; other site 557722001450 biotinylation site [posttranslational modification]; other site 557722001451 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional; Region: PRK12833 557722001452 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722001453 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722001454 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557722001455 Allophanate hydrolase subunit 1; Region: AHS1; smart00796 557722001456 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 557722001457 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 557722001458 Fimbrial protein; Region: Fimbrial; cl01416 557722001459 Fimbrial protein; Region: Fimbrial; cl01416 557722001460 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 557722001461 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722001462 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 557722001463 biotin synthase; Provisional; Region: PRK15108 557722001464 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722001465 FeS/SAM binding site; other site 557722001466 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 557722001467 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 557722001468 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 557722001469 substrate-cofactor binding pocket; other site 557722001470 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722001471 catalytic residue [active] 557722001472 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 557722001473 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 557722001474 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001475 S-adenosylmethionine binding site [chemical binding]; other site 557722001476 AAA domain; Region: AAA_26; pfam13500 557722001477 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722001478 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722001479 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722001480 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722001481 active site 557722001482 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722001483 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722001484 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722001485 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722001486 active site 557722001487 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722001488 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722001489 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722001490 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722001491 active site 557722001492 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722001493 Cytochrome c; Region: Cytochrom_C; cl11414 557722001494 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 557722001495 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 557722001496 structural tetrad; other site 557722001497 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722001498 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 557722001499 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 557722001500 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722001501 FeS/SAM binding site; other site 557722001502 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722001503 Helix-turn-helix domains; Region: HTH; cl00088 557722001504 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722001505 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722001506 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722001507 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 557722001508 Cytochrome c; Region: Cytochrom_C; cl11414 557722001509 Cytochrome c; Region: Cytochrom_C; cl11414 557722001510 Cytochrome c; Region: Cytochrom_C; cl11414 557722001511 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 557722001512 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722001513 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 557722001514 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of...; Region: NorE_like; cd02862 557722001515 Subunit I/III interface [polypeptide binding]; other site 557722001516 Cytochrome c; Region: Cytochrom_C; cl11414 557722001517 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 557722001518 Low-spin heme binding site [chemical binding]; other site 557722001519 D-pathway; other site 557722001520 Putative water exit pathway; other site 557722001521 Binuclear center (active site) [active] 557722001522 K-pathway; other site 557722001523 Putative proton exit pathway; other site 557722001524 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 557722001525 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 557722001526 metal ion-dependent adhesion site (MIDAS); other site 557722001527 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 557722001528 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722001529 ligand binding site [chemical binding]; other site 557722001530 flexible hinge region; other site 557722001531 Helix-turn-helix domains; Region: HTH; cl00088 557722001532 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722001533 Helix-turn-helix domains; Region: HTH; cl00088 557722001534 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722001535 dimerization interface [polypeptide binding]; other site 557722001536 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 557722001537 MOSC domain; Region: MOSC; pfam03473 557722001538 3-alpha domain; Region: 3-alpha; pfam03475 557722001539 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 557722001540 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722001541 inhibitor-cofactor binding pocket; inhibition site 557722001542 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722001543 catalytic residue [active] 557722001544 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 557722001545 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 557722001546 catalytic triad [active] 557722001547 PAS domain; Region: PAS_9; pfam13426 557722001548 PAS domain S-box; Region: sensory_box; TIGR00229 557722001549 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722001550 putative active site [active] 557722001551 heme pocket [chemical binding]; other site 557722001552 PAS domain S-box; Region: sensory_box; TIGR00229 557722001553 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722001554 putative active site [active] 557722001555 heme pocket [chemical binding]; other site 557722001556 DNA-binding transcriptional activator UhpA; Provisional; Region: PRK10360 557722001557 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722001558 DNA binding residues [nucleotide binding] 557722001559 dimerization interface [polypeptide binding]; other site 557722001560 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001561 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722001562 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722001563 non-specific DNA binding site [nucleotide binding]; other site 557722001564 salt bridge; other site 557722001565 sequence-specific DNA binding site [nucleotide binding]; other site 557722001566 Cupin domain; Region: Cupin_2; cl09118 557722001567 Repair protein; Region: Repair_PSII; cl01535 557722001568 LemA family; Region: LemA; cl00742 557722001569 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 557722001570 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 557722001571 EamA-like transporter family; Region: EamA; cl01037 557722001572 MAPEG family; Region: MAPEG; cl09190 557722001573 Cytochrome C'; Region: Cytochrom_C_2; cl01610 557722001574 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 557722001575 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 557722001576 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722001577 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557722001578 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 557722001579 active site 557722001580 metal binding site [ion binding]; metal-binding site 557722001581 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 557722001582 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 557722001583 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 557722001584 FAD binding pocket [chemical binding]; other site 557722001585 FAD binding motif [chemical binding]; other site 557722001586 phosphate binding motif [ion binding]; other site 557722001587 beta-alpha-beta structure motif; other site 557722001588 NAD binding pocket [chemical binding]; other site 557722001589 S-adenosylmethionine synthetase; Validated; Region: PRK05250 557722001590 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 557722001591 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 557722001592 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 557722001593 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722001594 putative DNA binding site [nucleotide binding]; other site 557722001595 dimerization interface [polypeptide binding]; other site 557722001596 putative Zn2+ binding site [ion binding]; other site 557722001597 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001598 S-adenosylmethionine binding site [chemical binding]; other site 557722001599 transketolase; Reviewed; Region: PRK12753 557722001600 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 557722001601 TPP-binding site [chemical binding]; other site 557722001602 dimer interface [polypeptide binding]; other site 557722001603 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 557722001604 PYR/PP interface [polypeptide binding]; other site 557722001605 dimer interface [polypeptide binding]; other site 557722001606 TPP binding site [chemical binding]; other site 557722001607 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557722001608 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 557722001609 erythrose-4-phosphate dehydrogenase; Region: E4PD_g-proteo; TIGR01532 557722001610 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001611 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 557722001612 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 557722001613 Phosphoglycerate kinase; Region: PGK; pfam00162 557722001614 substrate binding site [chemical binding]; other site 557722001615 hinge regions; other site 557722001616 ADP binding site [chemical binding]; other site 557722001617 catalytic site [active] 557722001618 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 557722001619 hypothetical protein; Provisional; Region: PRK08185 557722001620 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 557722001621 intersubunit interface [polypeptide binding]; other site 557722001622 active site 557722001623 zinc binding site [ion binding]; other site 557722001624 Na+ binding site [ion binding]; other site 557722001625 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722001626 hypothetical protein; Provisional; Region: PRK08317 557722001627 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722001628 S-adenosylmethionine binding site [chemical binding]; other site 557722001629 HI0933-like protein; Region: HI0933_like; pfam03486 557722001630 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001631 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001632 Protein of unknown function DUF45; Region: DUF45; cl00636 557722001633 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 557722001634 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722001635 motif II; other site 557722001636 Protein of unknown function (DUF805); Region: DUF805; cl01224 557722001637 Cupin domain; Region: Cupin_2; cl09118 557722001638 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722001639 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722001640 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557722001641 Proteolipid membrane potential modulator; Region: Pmp3; cl00431 557722001642 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 557722001643 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 557722001644 Peptidase M60-like family; Region: M60-like; pfam13402 557722001645 Restriction endonuclease; Region: Mrr_cat; cl00516 557722001646 Fic family protein [Function unknown]; Region: COG3177 557722001647 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 557722001648 Fic/DOC family; Region: Fic; cl00960 557722001649 Helix-turn-helix domains; Region: HTH; cl00088 557722001650 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722001651 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722001652 substrate binding pocket [chemical binding]; other site 557722001653 membrane-bound complex binding site; other site 557722001654 hinge residues; other site 557722001655 PAS domain S-box; Region: sensory_box; TIGR00229 557722001656 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722001657 putative active site [active] 557722001658 heme pocket [chemical binding]; other site 557722001659 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722001660 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 557722001661 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722001662 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722001663 putative active site [active] 557722001664 heme pocket [chemical binding]; other site 557722001665 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722001666 metal binding site [ion binding]; metal-binding site 557722001667 active site 557722001668 I-site; other site 557722001669 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722001670 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 557722001671 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 557722001672 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557722001673 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 557722001674 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722001675 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557722001676 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722001677 DNA binding residues [nucleotide binding] 557722001678 DNA primase, catalytic core; Region: dnaG; TIGR01391 557722001679 CHC2 zinc finger; Region: zf-CHC2; cl15369 557722001680 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 557722001681 TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_DnaG_primases; cd03364 557722001682 active site 557722001683 metal binding site [ion binding]; metal-binding site 557722001684 interdomain interaction site; other site 557722001685 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 557722001686 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 557722001687 GatB domain; Region: GatB_Yqey; cl11497 557722001688 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 557722001689 UGMP family protein; Validated; Region: PRK09604 557722001690 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 557722001691 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 557722001692 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 557722001693 homooctamer interface [polypeptide binding]; other site 557722001694 active site 557722001695 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 557722001696 catalytic center binding site [active] 557722001697 ATP binding site [chemical binding]; other site 557722001698 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 557722001699 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 557722001700 active site 557722001701 NTP binding site [chemical binding]; other site 557722001702 metal binding triad [ion binding]; metal-binding site 557722001703 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 557722001704 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557722001705 Zn2+ binding site [ion binding]; other site 557722001706 Mg2+ binding site [ion binding]; other site 557722001707 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 557722001708 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 557722001709 SpoVR family protein; Provisional; Region: PRK11767 557722001710 Uncharacterized conserved protein [Function unknown]; Region: COG2718 557722001711 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722001712 PrkA family serine protein kinase; Provisional; Region: PRK15455 557722001713 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 557722001714 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 557722001715 active site residue [active] 557722001716 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 557722001717 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 557722001718 active site 557722001719 metal binding site [ion binding]; metal-binding site 557722001720 Protein of unknown function (DUF525); Region: DUF525; cl01119 557722001721 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001722 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 557722001723 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 557722001724 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 557722001725 SurA N-terminal domain; Region: SurA_N_3; cl07813 557722001726 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722001727 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722001728 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 557722001729 OstA-like protein; Region: OstA; cl00844 557722001730 Organic solvent tolerance protein; Region: OstA_C; pfam04453 557722001731 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722001732 Phosphotransferase enzyme family; Region: APH; pfam01636 557722001733 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 557722001734 Substrate binding site; other site 557722001735 metal-binding site 557722001736 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 557722001737 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 557722001738 putative metal binding site [ion binding]; other site 557722001739 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 557722001740 HSP70 interaction site [polypeptide binding]; other site 557722001741 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 557722001742 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722001743 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722001744 substrate binding pocket [chemical binding]; other site 557722001745 membrane-bound complex binding site; other site 557722001746 hinge residues; other site 557722001747 PAS domain S-box; Region: sensory_box; TIGR00229 557722001748 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722001749 putative active site [active] 557722001750 heme pocket [chemical binding]; other site 557722001751 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722001752 PAS fold; Region: PAS_3; pfam08447 557722001753 putative active site [active] 557722001754 heme pocket [chemical binding]; other site 557722001755 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 557722001756 Histidine kinase; Region: HisKA_3; pfam07730 557722001757 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722001758 ATP binding site [chemical binding]; other site 557722001759 Mg2+ binding site [ion binding]; other site 557722001760 G-X-G motif; other site 557722001761 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722001762 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722001763 active site 557722001764 phosphorylation site [posttranslational modification] 557722001765 intermolecular recognition site; other site 557722001766 dimerization interface [polypeptide binding]; other site 557722001767 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722001768 DNA binding residues [nucleotide binding] 557722001769 dimerization interface [polypeptide binding]; other site 557722001770 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557722001771 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722001772 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557722001773 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required...; Region: ABC_PotA_N; cd03300 557722001774 Walker A/P-loop; other site 557722001775 ATP binding site [chemical binding]; other site 557722001776 Q-loop/lid; other site 557722001777 ABC transporter signature motif; other site 557722001778 Walker B; other site 557722001779 D-loop; other site 557722001780 H-loop/switch region; other site 557722001781 TOBE domain; Region: TOBE_2; cl01440 557722001782 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557722001783 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722001784 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722001785 dimer interface [polypeptide binding]; other site 557722001786 conserved gate region; other site 557722001787 putative PBP binding loops; other site 557722001788 ABC-ATPase subunit interface; other site 557722001789 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722001790 dimer interface [polypeptide binding]; other site 557722001791 conserved gate region; other site 557722001792 putative PBP binding loops; other site 557722001793 ABC-ATPase subunit interface; other site 557722001794 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 557722001795 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 557722001796 substrate binding site [chemical binding]; other site 557722001797 hexamer interface [polypeptide binding]; other site 557722001798 metal binding site [ion binding]; metal-binding site 557722001799 phosphoglycolate phosphatase; Provisional; Region: PRK13223 557722001800 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722001801 motif II; other site 557722001802 anthranilate synthase component I; Provisional; Region: PRK13565 557722001803 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 557722001804 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557722001805 Pyocin activator protein PrtN; Region: PyocinActivator; pfam11112 557722001806 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722001807 non-specific DNA binding site [nucleotide binding]; other site 557722001808 Predicted transcriptional regulator [Transcription]; Region: COG2932 557722001809 salt bridge; other site 557722001810 sequence-specific DNA binding site [nucleotide binding]; other site 557722001811 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722001812 Catalytic site [active] 557722001813 LES prophage 1 557722001814 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557722001815 Phage P2 baseplate assembly protein gpV [General function prediction only]; Region: gpV; COG4540 557722001816 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722001817 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557722001818 Baseplate J-like protein; Region: Baseplate_J; cl01294 557722001819 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 557722001820 Phage-related tail fibre protein [General function prediction only]; Region: COG5301 557722001821 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 557722001822 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 557722001823 Phage tail tube protein FII; Region: Phage_tube; cl01390 557722001824 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 557722001825 Mu-like prophage protein [General function prediction only]; Region: COG3941 557722001826 Mu-like prophage protein [General function prediction only]; Region: COG3941 557722001827 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 557722001828 Phage Tail Protein X; Region: Phage_tail_X; cl02088 557722001829 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722001830 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722001831 catalytic residue [active] 557722001832 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 557722001833 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557722001834 glutamine binding [chemical binding]; other site 557722001835 catalytic triad [active] 557722001836 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 557722001837 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 557722001838 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 557722001839 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 557722001840 active site 557722001841 ribulose/triose binding site [chemical binding]; other site 557722001842 phosphate binding site [ion binding]; other site 557722001843 substrate (anthranilate) binding pocket [chemical binding]; other site 557722001844 product (indole) binding pocket [chemical binding]; other site 557722001845 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 557722001846 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722001847 ligand binding site [chemical binding]; other site 557722001848 flexible hinge region; other site 557722001849 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 557722001850 putative switch regulator; other site 557722001851 non-specific DNA interactions [nucleotide binding]; other site 557722001852 DNA binding site [nucleotide binding] 557722001853 sequence specific DNA binding site [nucleotide binding]; other site 557722001854 putative cAMP binding site [chemical binding]; other site 557722001855 OsmC-like protein; Region: OsmC; cl00767 557722001856 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 557722001857 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 557722001858 diiron binding motif [ion binding]; other site 557722001859 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 557722001860 nucleotide binding site/active site [active] 557722001861 HIT family signature motif; other site 557722001862 catalytic residue [active] 557722001863 Ycf46; Provisional; Region: ycf46; CHL00195 557722001864 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722001865 Walker A motif; other site 557722001866 ATP binding site [chemical binding]; other site 557722001867 Walker B motif; other site 557722001868 arginine finger; other site 557722001869 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 557722001870 classical (c) SDRs; Region: SDR_c; cd05233 557722001871 NAD(P) binding site [chemical binding]; other site 557722001872 active site 557722001873 Protein of unknown function (DUF805); Region: DUF805; cl01224 557722001874 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 557722001875 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 557722001876 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 557722001877 FMN binding site [chemical binding]; other site 557722001878 substrate binding site [chemical binding]; other site 557722001879 putative catalytic residue [active] 557722001880 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 557722001881 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 557722001882 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722001883 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 557722001884 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 557722001885 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557722001886 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 557722001887 putative peptidase; Provisional; Region: PRK11649 557722001888 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 557722001889 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 557722001890 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 557722001891 active site 557722001892 HIGH motif; other site 557722001893 dimer interface [polypeptide binding]; other site 557722001894 KMSKS motif; other site 557722001895 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 557722001896 Helix-turn-helix domains; Region: HTH; cl00088 557722001897 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 557722001898 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 557722001899 Type III pantothenate kinase; Region: Pan_kinase; cl09130 557722001900 Sporulation related domain; Region: SPOR; cl10051 557722001901 Sporulation related domain; Region: SPOR; cl10051 557722001902 Sporulation related domain; Region: SPOR; cl10051 557722001903 elongation factor Tu; Reviewed; Region: PRK00049 557722001904 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 557722001905 G1 box; other site 557722001906 GEF interaction site [polypeptide binding]; other site 557722001907 GTP/Mg2+ binding site [chemical binding]; other site 557722001908 Switch I region; other site 557722001909 G2 box; other site 557722001910 G3 box; other site 557722001911 Switch II region; other site 557722001912 G4 box; other site 557722001913 G5 box; other site 557722001914 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 557722001915 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 557722001916 Antibiotic Binding Site [chemical binding]; other site 557722001917 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 557722001918 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 557722001919 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 557722001920 putative homodimer interface [polypeptide binding]; other site 557722001921 KOW motif; Region: KOW; cl00354 557722001922 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 557722001923 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal...; Region: Ribosomal_L11; cd00349 557722001924 23S rRNA interface [nucleotide binding]; other site 557722001925 L7/L12 interface [polypeptide binding]; other site 557722001926 putative thiostrepton binding site; other site 557722001927 L25 interface [polypeptide binding]; other site 557722001928 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 557722001929 mRNA/rRNA interface [nucleotide binding]; other site 557722001930 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 557722001931 23S rRNA interface [nucleotide binding]; other site 557722001932 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 557722001933 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of...; Region: Ribosomal_L7_L12; cd00387 557722001934 core dimer interface [polypeptide binding]; other site 557722001935 peripheral dimer interface [polypeptide binding]; other site 557722001936 L10 interface [polypeptide binding]; other site 557722001937 L11 interface [polypeptide binding]; other site 557722001938 putative EF-Tu interaction site [polypeptide binding]; other site 557722001939 putative EF-G interaction site [polypeptide binding]; other site 557722001940 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 557722001941 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 557722001942 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 557722001943 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 557722001944 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 557722001945 RPB11 interaction site [polypeptide binding]; other site 557722001946 RPB12 interaction site [polypeptide binding]; other site 557722001947 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 557722001948 RPB3 interaction site [polypeptide binding]; other site 557722001949 RPB1 interaction site [polypeptide binding]; other site 557722001950 RPB11 interaction site [polypeptide binding]; other site 557722001951 RPB10 interaction site [polypeptide binding]; other site 557722001952 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 557722001953 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 557722001954 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 557722001955 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 557722001956 DNA-directed RNA polymerase, beta'' subunit; Region: rpoC2_cyan; TIGR02388 557722001957 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 557722001958 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 557722001959 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 557722001960 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 557722001961 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 557722001962 DNA binding site [nucleotide binding] 557722001963 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 557722001964 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 557722001965 S17 interaction site [polypeptide binding]; other site 557722001966 S8 interaction site; other site 557722001967 16S rRNA interaction site [nucleotide binding]; other site 557722001968 streptomycin interaction site [chemical binding]; other site 557722001969 23S rRNA interaction site [nucleotide binding]; other site 557722001970 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 557722001971 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 557722001972 elongation factor G; Reviewed; Region: PRK00007 557722001973 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 557722001974 G1 box; other site 557722001975 putative GEF interaction site [polypeptide binding]; other site 557722001976 GTP/Mg2+ binding site [chemical binding]; other site 557722001977 Switch I region; other site 557722001978 G2 box; other site 557722001979 G3 box; other site 557722001980 Switch II region; other site 557722001981 G4 box; other site 557722001982 G5 box; other site 557722001983 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 557722001984 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 557722001985 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 557722001986 elongation factor Tu; Reviewed; Region: PRK00049 557722001987 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 557722001988 G1 box; other site 557722001989 GEF interaction site [polypeptide binding]; other site 557722001990 GTP/Mg2+ binding site [chemical binding]; other site 557722001991 Switch I region; other site 557722001992 G2 box; other site 557722001993 G3 box; other site 557722001994 Switch II region; other site 557722001995 G4 box; other site 557722001996 G5 box; other site 557722001997 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 557722001998 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 557722001999 Antibiotic Binding Site [chemical binding]; other site 557722002000 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 557722002001 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 557722002002 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 557722002003 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 557722002004 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 557722002005 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 557722002006 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 557722002007 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 557722002008 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper...; Region: Ribosomal_L22; cd00336 557722002009 protein-rRNA interface [nucleotide binding]; other site 557722002010 putative translocon binding site; other site 557722002011 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 557722002012 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 557722002013 G-X-X-G motif; other site 557722002014 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 557722002015 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 557722002016 23S rRNA interface [nucleotide binding]; other site 557722002017 5S rRNA interface [nucleotide binding]; other site 557722002018 putative antibiotic binding site [chemical binding]; other site 557722002019 L25 interface [polypeptide binding]; other site 557722002020 L27 interface [polypeptide binding]; other site 557722002021 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 557722002022 23S rRNA interface [nucleotide binding]; other site 557722002023 putative translocon interaction site; other site 557722002024 signal recognition particle (SRP54) interaction site; other site 557722002025 L23 interface [polypeptide binding]; other site 557722002026 trigger factor interaction site; other site 557722002027 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 557722002028 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 557722002029 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 557722002030 KOW motif; Region: KOW; cl00354 557722002031 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 557722002032 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 557722002033 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 557722002034 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 557722002035 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 557722002036 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 557722002037 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 557722002038 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 557722002039 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 557722002040 5S rRNA interface [nucleotide binding]; other site 557722002041 23S rRNA interface [nucleotide binding]; other site 557722002042 L5 interface [polypeptide binding]; other site 557722002043 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 557722002044 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 557722002045 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 557722002046 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 557722002047 23S rRNA binding site [nucleotide binding]; other site 557722002048 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 557722002049 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 557722002050 SecY translocase; Region: SecY; pfam00344 557722002051 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 557722002052 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 557722002053 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 557722002054 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 557722002055 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 557722002056 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722002057 RNA binding surface [nucleotide binding]; other site 557722002058 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 557722002059 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 557722002060 alphaNTD homodimer interface [polypeptide binding]; other site 557722002061 alphaNTD - beta interaction site [polypeptide binding]; other site 557722002062 alphaNTD - beta' interaction site [polypeptide binding]; other site 557722002063 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 557722002064 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 557722002065 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 557722002066 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 557722002067 tetramer interface [polypeptide binding]; other site 557722002068 heme binding pocket [chemical binding]; other site 557722002069 NADPH binding site [chemical binding]; other site 557722002070 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 557722002071 Ferritin-like domain; Region: Ferritin; pfam00210 557722002072 heme binding site [chemical binding]; other site 557722002073 ferroxidase pore; other site 557722002074 ferroxidase diiron center [ion binding]; other site 557722002075 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 557722002076 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 557722002077 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 557722002078 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 557722002079 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722002080 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722002081 putative substrate translocation pore; other site 557722002082 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 557722002083 dimer interface [polypeptide binding]; other site 557722002084 ssDNA binding site [nucleotide binding]; other site 557722002085 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557722002086 salicylate biosynthesis isochorismate synthase; Validated; Region: PRK07054 557722002087 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557722002088 Chorismate mutase type II; Region: CM_2; cl00693 557722002089 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 557722002090 Peptide arylation enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntE; COG1021 557722002091 AMP-binding enzyme; Region: AMP-binding; cl15778 557722002092 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722002093 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722002094 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722002095 Condensation domain; Region: Condensation; pfam00668 557722002096 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 557722002097 Nonribosomal peptide synthase; Region: NRPS; pfam08415 557722002098 AMP-binding enzyme; Region: AMP-binding; cl15778 557722002099 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 557722002100 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722002101 Condensation domain; Region: Condensation; pfam00668 557722002102 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 557722002103 Nonribosomal peptide synthase; Region: NRPS; pfam08415 557722002104 AMP-binding enzyme; Region: AMP-binding; cl15778 557722002105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002106 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK07824 557722002107 peptide synthase; Provisional; Region: PRK12467 557722002108 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722002109 thiazolinyl imide reductase; Region: thiaz-red; TIGR01761 557722002110 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002111 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 557722002112 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722002113 Walker A/P-loop; other site 557722002114 ATP binding site [chemical binding]; other site 557722002115 Q-loop/lid; other site 557722002116 ABC transporter signature motif; other site 557722002117 Walker B; other site 557722002118 D-loop; other site 557722002119 H-loop/switch region; other site 557722002120 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 557722002121 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722002122 Walker A/P-loop; other site 557722002123 ATP binding site [chemical binding]; other site 557722002124 Q-loop/lid; other site 557722002125 ABC transporter signature motif; other site 557722002126 Walker B; other site 557722002127 D-loop; other site 557722002128 H-loop/switch region; other site 557722002129 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 557722002130 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722002131 N-terminal plug; other site 557722002132 ligand-binding site [chemical binding]; other site 557722002133 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722002134 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 557722002135 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 557722002136 hypothetical protein; Provisional; Region: PRK07538 557722002137 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002138 Pyridoxamine-phosphate oxidase [Coenzyme metabolism]; Region: PdxH; COG0259 557722002139 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557722002140 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 557722002141 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722002142 Phenazine biosynthesis-like protein; Region: PhzC-PhzF; pfam02567 557722002143 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557722002144 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557722002145 Glutamine amidotransferase class-I; Region: GATase; pfam00117 557722002146 glutamine binding [chemical binding]; other site 557722002147 catalytic triad [active] 557722002148 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological...; Region: isochorismatase; cd01013 557722002149 hydrophobic substrate binding pocket; other site 557722002150 Isochorismatase family; Region: Isochorismatase; pfam00857 557722002151 active site 557722002152 conserved cis-peptide bond; other site 557722002153 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 557722002154 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722002155 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722002156 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722002157 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722002158 multidrug efflux protein; Reviewed; Region: PRK09579 557722002159 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722002160 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722002161 DoxX; Region: DoxX; cl00976 557722002162 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 557722002163 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722002164 Helix-turn-helix domains; Region: HTH; cl00088 557722002165 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 557722002166 putative dimerization interface [polypeptide binding]; other site 557722002167 Nitronate monooxygenase; Region: NMO; pfam03060 557722002168 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 557722002169 FMN binding site [chemical binding]; other site 557722002170 substrate binding site [chemical binding]; other site 557722002171 putative catalytic residue [active] 557722002172 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 557722002173 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 557722002174 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722002175 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722002176 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722002177 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722002178 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722002179 active site 557722002180 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722002181 acyl-CoA synthetase; Validated; Region: PRK08162 557722002182 AMP-binding enzyme; Region: AMP-binding; cl15778 557722002183 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722002184 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722002185 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 557722002186 putative active site [active] 557722002187 heme pocket [chemical binding]; other site 557722002188 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722002189 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722002190 putative active site [active] 557722002191 heme pocket [chemical binding]; other site 557722002192 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722002193 dimer interface [polypeptide binding]; other site 557722002194 phosphorylation site [posttranslational modification] 557722002195 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722002196 ATP binding site [chemical binding]; other site 557722002197 Mg2+ binding site [ion binding]; other site 557722002198 G-X-G motif; other site 557722002199 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 557722002200 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722002201 active site 557722002202 phosphorylation site [posttranslational modification] 557722002203 intermolecular recognition site; other site 557722002204 dimerization interface [polypeptide binding]; other site 557722002205 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722002206 DNA binding residues [nucleotide binding] 557722002207 dimerization interface [polypeptide binding]; other site 557722002208 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722002209 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722002210 substrate binding pocket [chemical binding]; other site 557722002211 membrane-bound complex binding site; other site 557722002212 hinge residues; other site 557722002213 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722002214 dimer interface [polypeptide binding]; other site 557722002215 conserved gate region; other site 557722002216 putative PBP binding loops; other site 557722002217 ABC-ATPase subunit interface; other site 557722002218 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722002219 dimer interface [polypeptide binding]; other site 557722002220 conserved gate region; other site 557722002221 putative PBP binding loops; other site 557722002222 ABC-ATPase subunit interface; other site 557722002223 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557722002224 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722002225 Walker A/P-loop; other site 557722002226 ATP binding site [chemical binding]; other site 557722002227 Q-loop/lid; other site 557722002228 ABC transporter signature motif; other site 557722002229 Walker B; other site 557722002230 D-loop; other site 557722002231 H-loop/switch region; other site 557722002232 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 557722002233 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 557722002234 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722002235 putative monooxygenase; Reviewed; Region: PRK07045 557722002236 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002237 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 557722002238 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722002239 NAD(P) binding site [chemical binding]; other site 557722002240 catalytic residues [active] 557722002241 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 557722002242 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 557722002243 inhibitor site; inhibition site 557722002244 active site 557722002245 dimer interface [polypeptide binding]; other site 557722002246 catalytic residue [active] 557722002247 benzoate transport; Region: 2A0115; TIGR00895 557722002248 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722002249 putative substrate translocation pore; other site 557722002250 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002251 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722002252 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557722002253 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722002254 DNA-binding site [nucleotide binding]; DNA binding site 557722002255 FCD domain; Region: FCD; cl11656 557722002256 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 557722002257 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 557722002258 conserved cys residue [active] 557722002259 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722002260 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 557722002261 active site 557722002262 metal binding site [ion binding]; metal-binding site 557722002263 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557722002264 B3/4 domain; Region: B3_4; cl11458 557722002265 acetolactate synthase; Reviewed; Region: PRK08322 557722002266 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722002267 PYR/PP interface [polypeptide binding]; other site 557722002268 dimer interface [polypeptide binding]; other site 557722002269 TPP binding site [chemical binding]; other site 557722002270 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722002271 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 557722002272 TPP-binding site [chemical binding]; other site 557722002273 dimer interface [polypeptide binding]; other site 557722002274 outer membrane porin, OprD family; Region: OprD; pfam03573 557722002275 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 557722002276 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002277 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 557722002278 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722002279 transcriptional regulator; Provisional; Region: PRK10632 557722002280 Helix-turn-helix domains; Region: HTH; cl00088 557722002281 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 557722002282 putative effector binding pocket; other site 557722002283 putative dimerization interface [polypeptide binding]; other site 557722002284 YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgH_like; cd02198 557722002285 homotrimer interaction site [polypeptide binding]; other site 557722002286 putative active site [active] 557722002287 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 557722002288 putative phosphate binding site [ion binding]; other site 557722002289 putative catalytic site [active] 557722002290 active site 557722002291 metal binding site A [ion binding]; metal-binding site 557722002292 DNA binding site [nucleotide binding] 557722002293 putative AP binding site [nucleotide binding]; other site 557722002294 putative metal binding site B [ion binding]; other site 557722002295 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 557722002296 intracellular protease, PfpI family; Region: PfpI; TIGR01382 557722002297 proposed catalytic triad [active] 557722002298 conserved cys residue [active] 557722002299 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002300 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 557722002301 Helix-turn-helix domains; Region: HTH; cl00088 557722002302 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 557722002303 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722002304 N-terminal plug; other site 557722002305 ligand-binding site [chemical binding]; other site 557722002306 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722002307 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 557722002308 active site 557722002309 catalytic tetrad [active] 557722002310 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 557722002311 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722002312 Coenzyme A binding pocket [chemical binding]; other site 557722002313 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722002314 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722002315 DNA-binding site [nucleotide binding]; DNA binding site 557722002316 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722002317 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722002318 homodimer interface [polypeptide binding]; other site 557722002319 catalytic residue [active] 557722002320 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 557722002321 putative active site pocket [active] 557722002322 dimerization interface [polypeptide binding]; other site 557722002323 putative catalytic residue [active] 557722002324 amidase; Validated; Region: PRK06565 557722002325 Amidase; Region: Amidase; cl11426 557722002326 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 557722002327 classical (c) SDRs; Region: SDR_c; cd05233 557722002328 NAD(P) binding site [chemical binding]; other site 557722002329 active site 557722002330 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 557722002331 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 557722002332 ABC-ATPase subunit interface; other site 557722002333 dimer interface [polypeptide binding]; other site 557722002334 putative PBP binding regions; other site 557722002335 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 557722002336 ABC-ATPase subunit interface; other site 557722002337 dimer interface [polypeptide binding]; other site 557722002338 putative PBP binding regions; other site 557722002339 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 557722002340 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 557722002341 siderophore binding site; other site 557722002342 iron-enterobactin transporter ATP-binding protein; Provisional; Region: PRK10253 557722002343 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 557722002344 Walker A/P-loop; other site 557722002345 ATP binding site [chemical binding]; other site 557722002346 Q-loop/lid; other site 557722002347 ABC transporter signature motif; other site 557722002348 Walker B; other site 557722002349 D-loop; other site 557722002350 H-loop/switch region; other site 557722002351 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722002352 Helix-turn-helix domains; Region: HTH; cl00088 557722002353 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722002354 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722002355 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722002356 N-terminal plug; other site 557722002357 ligand-binding site [chemical binding]; other site 557722002358 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 557722002359 active site 557722002360 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 557722002361 non-prolyl cis peptide bond; other site 557722002362 SH3 domain protein [Signal transduction mechanisms]; Region: COG3103 557722002363 Bacterial SH3 domain; Region: SH3_3; cl02551 557722002364 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 557722002365 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 557722002366 putative NAD(P) binding site [chemical binding]; other site 557722002367 catalytic Zn binding site [ion binding]; other site 557722002368 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional; Region: PRK14875 557722002369 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722002370 E3 interaction surface; other site 557722002371 lipoyl attachment site [posttranslational modification]; other site 557722002372 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 557722002373 nucleophilic elbow; other site 557722002374 catalytic triad; other site 557722002375 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 557722002376 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 557722002377 alpha subunit interface [polypeptide binding]; other site 557722002378 TPP binding site [chemical binding]; other site 557722002379 heterodimer interface [polypeptide binding]; other site 557722002380 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557722002381 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 557722002382 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 557722002383 tetramer interface [polypeptide binding]; other site 557722002384 TPP-binding site [chemical binding]; other site 557722002385 heterodimer interface [polypeptide binding]; other site 557722002386 phosphorylation loop region [posttranslational modification] 557722002387 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 557722002388 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722002389 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002390 NAD(P) binding site [chemical binding]; other site 557722002391 active site 557722002392 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 557722002393 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722002394 Walker A motif; other site 557722002395 ATP binding site [chemical binding]; other site 557722002396 Walker B motif; other site 557722002397 arginine finger; other site 557722002398 Helix-turn-helix domains; Region: HTH; cl00088 557722002399 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722002400 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722002401 putative effector binding pocket; other site 557722002402 dimerization interface [polypeptide binding]; other site 557722002403 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 557722002404 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 557722002405 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39C; cd02419 557722002406 putative active site [active] 557722002407 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722002408 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722002409 Walker A/P-loop; other site 557722002410 ATP binding site [chemical binding]; other site 557722002411 Q-loop/lid; other site 557722002412 ABC transporter signature motif; other site 557722002413 Walker B; other site 557722002414 D-loop; other site 557722002415 H-loop/switch region; other site 557722002416 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 557722002417 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722002418 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722002419 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557722002420 FAD binding domain; Region: FAD_binding_4; pfam01565 557722002421 Cholesterol oxidase, substrate-binding; Region: Chol_subst-bind; pfam09129 557722002422 LES prophage 2 557722002423 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722002424 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722002425 DNA binding site [nucleotide binding] 557722002426 Int/Topo IB signature motif; other site 557722002427 active site 557722002428 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722002429 DNA binding residues [nucleotide binding] 557722002430 dimerization interface [polypeptide binding]; other site 557722002431 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722002432 salt bridge; other site 557722002433 non-specific DNA binding site [nucleotide binding]; other site 557722002434 sequence-specific DNA binding site [nucleotide binding]; other site 557722002435 Predicted transcriptional regulator [Transcription]; Region: COG2932 557722002436 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722002437 Catalytic site [active] 557722002438 HNH endonuclease; Region: HNH_3; pfam13392 557722002439 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 557722002440 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722002441 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 557722002442 Walker A motif; other site 557722002443 ATP binding site [chemical binding]; other site 557722002444 Walker B motif; other site 557722002445 arginine finger; other site 557722002446 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 557722002447 replicative DNA helicase; Region: DnaB; TIGR00665 557722002448 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722002449 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 557722002450 Walker A motif; other site 557722002451 Walker A motif; other site 557722002452 ATP binding site [chemical binding]; other site 557722002453 Walker B motif; other site 557722002454 DNA binding loops [nucleotide binding] 557722002455 PrpA and PrpB, metallophosphatase domain; Region: MPP_PrpA_PrpB; cd07424 557722002456 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557722002457 active site 557722002458 metal binding site [ion binding]; metal-binding site 557722002459 Phage antitermination protein Q; Region: Phage_antitermQ; pfam06530 557722002460 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722002461 salt bridge; other site 557722002462 non-specific DNA binding site [nucleotide binding]; other site 557722002463 sequence-specific DNA binding site [nucleotide binding]; other site 557722002464 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 557722002465 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722002466 catalytic residue [active] 557722002467 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 557722002468 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 557722002469 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 557722002470 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 557722002471 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 557722002472 active site residues [active] 557722002473 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 557722002474 Duplication 1a 557722002475 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 557722002476 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 557722002477 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557722002478 Mu-like prophage protein [General function prediction only]; Region: COG3941 557722002479 tape measure domain; Region: tape_meas_nterm; TIGR02675 557722002480 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 557722002481 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 557722002482 active site 557722002483 HIGH motif; other site 557722002484 dimer interface [polypeptide binding]; other site 557722002485 KMSKS motif; other site 557722002486 outer membrane porin, OprD family; Region: OprD; pfam03573 557722002487 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 557722002488 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722002489 putative substrate translocation pore; other site 557722002490 Helix-turn-helix domains; Region: HTH; cl00088 557722002491 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 557722002492 Low-spin heme binding site [chemical binding]; other site 557722002493 Putative water exit pathway; other site 557722002494 Binuclear center (active site) [active] 557722002495 Putative proton exit pathway; other site 557722002496 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722002497 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722002498 DNA-binding site [nucleotide binding]; DNA binding site 557722002499 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722002500 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722002501 homodimer interface [polypeptide binding]; other site 557722002502 catalytic residue [active] 557722002503 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 557722002504 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557722002505 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 557722002506 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 557722002507 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557722002508 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557722002509 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 557722002510 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 557722002511 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722002512 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722002513 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 557722002514 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722002515 putative substrate translocation pore; other site 557722002516 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 557722002517 putative substrate binding pocket [chemical binding]; other site 557722002518 trimer interface [polypeptide binding]; other site 557722002519 The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate; Region: HPCD; cd07370 557722002520 putative active site [active] 557722002521 putative metal binding site [ion binding]; other site 557722002522 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722002523 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 557722002524 NAD binding site [chemical binding]; other site 557722002525 catalytic residues [active] 557722002526 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 557722002527 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722002528 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722002529 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 557722002530 Cupin domain; Region: Cupin_2; cl09118 557722002531 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722002532 Aminoglycoside 3'-phosphotransferase (APH). The APH subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase; Region: APH; cd05150 557722002533 Phosphotransferase enzyme family; Region: APH; pfam01636 557722002534 active site 557722002535 ATP binding site [chemical binding]; other site 557722002536 antibiotic binding site [chemical binding]; other site 557722002537 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 557722002538 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 557722002539 GAF domain; Region: GAF; cl15785 557722002540 Phytochrome region; Region: PHY; pfam00360 557722002541 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722002542 dimer interface [polypeptide binding]; other site 557722002543 phosphorylation site [posttranslational modification] 557722002544 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722002545 ATP binding site [chemical binding]; other site 557722002546 Mg2+ binding site [ion binding]; other site 557722002547 G-X-G motif; other site 557722002548 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 557722002549 heme binding pocket [chemical binding]; other site 557722002550 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 557722002551 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 557722002552 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722002553 putative arabinose transporter; Provisional; Region: PRK03545 557722002554 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722002555 putative substrate translocation pore; other site 557722002556 CHASE domain; Region: CHASE; cl01369 557722002557 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722002558 putative active site [active] 557722002559 heme pocket [chemical binding]; other site 557722002560 PAS domain; Region: PAS_9; pfam13426 557722002561 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722002562 putative active site [active] 557722002563 heme pocket [chemical binding]; other site 557722002564 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722002565 PAS fold; Region: PAS_3; pfam08447 557722002566 putative active site [active] 557722002567 heme pocket [chemical binding]; other site 557722002568 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722002569 dimer interface [polypeptide binding]; other site 557722002570 phosphorylation site [posttranslational modification] 557722002571 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722002572 ATP binding site [chemical binding]; other site 557722002573 Mg2+ binding site [ion binding]; other site 557722002574 G-X-G motif; other site 557722002575 Response regulator receiver domain; Region: Response_reg; pfam00072 557722002576 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722002577 active site 557722002578 phosphorylation site [posttranslational modification] 557722002579 intermolecular recognition site; other site 557722002580 dimerization interface [polypeptide binding]; other site 557722002581 Response regulator receiver domain; Region: Response_reg; pfam00072 557722002582 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722002583 active site 557722002584 phosphorylation site [posttranslational modification] 557722002585 intermolecular recognition site; other site 557722002586 dimerization interface [polypeptide binding]; other site 557722002587 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 557722002588 putative binding surface; other site 557722002589 active site 557722002590 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 557722002591 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722002592 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722002593 Helix-turn-helix domains; Region: HTH; cl00088 557722002594 The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_beta_lactamase; cd08484 557722002595 putative dimerization interface [polypeptide binding]; other site 557722002596 putative substrate binding pocket [chemical binding]; other site 557722002597 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 557722002598 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 557722002599 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557722002600 Zn2+ binding site [ion binding]; other site 557722002601 Mg2+ binding site [ion binding]; other site 557722002602 SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate...; Region: SPARC_EC; cd00252 557722002603 EF-hand Ca2+ binding loops [ion binding]; other site 557722002604 FS-domain interface [polypeptide binding]; other site 557722002605 Protein of unknown function (DUF692); Region: DUF692; cl01263 557722002606 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 557722002607 DoxX; Region: DoxX; cl00976 557722002608 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 557722002609 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 557722002610 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722002611 ATP binding site [chemical binding]; other site 557722002612 Mg2+ binding site [ion binding]; other site 557722002613 G-X-G motif; other site 557722002614 osmolarity response regulator; Provisional; Region: ompR; PRK09468 557722002615 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722002616 active site 557722002617 phosphorylation site [posttranslational modification] 557722002618 intermolecular recognition site; other site 557722002619 dimerization interface [polypeptide binding]; other site 557722002620 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722002621 DNA binding site [nucleotide binding] 557722002622 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 557722002623 choline dehydrogenase; Validated; Region: PRK02106 557722002624 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002625 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557722002626 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 557722002627 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722002628 classical (c) SDRs; Region: SDR_c; cd05233 557722002629 NAD(P) binding site [chemical binding]; other site 557722002630 active site 557722002631 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 557722002632 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 557722002633 putative NAD(P) binding site [chemical binding]; other site 557722002634 catalytic Zn binding site [ion binding]; other site 557722002635 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722002636 D-galactonate transporter; Region: 2A0114; TIGR00893 557722002637 putative substrate translocation pore; other site 557722002638 Cupin domain; Region: Cupin_2; cl09118 557722002639 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 557722002640 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722002641 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722002642 CoenzymeA binding site [chemical binding]; other site 557722002643 subunit interaction site [polypeptide binding]; other site 557722002644 PHB binding site; other site 557722002645 Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating...; Region: Rieske_RO_Alpha_VanA_DdmC; cd03532 557722002646 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 557722002647 hydrophobic ligand binding site; other site 557722002648 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 557722002649 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 557722002650 FMN-binding pocket [chemical binding]; other site 557722002651 flavin binding motif; other site 557722002652 phosphate binding motif [ion binding]; other site 557722002653 beta-alpha-beta structure motif; other site 557722002654 NAD binding pocket [chemical binding]; other site 557722002655 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722002656 catalytic loop [active] 557722002657 iron binding site [ion binding]; other site 557722002658 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722002659 DNA binding residues [nucleotide binding] 557722002660 dimerization interface [polypeptide binding]; other site 557722002661 Flavin Reductases; Region: FlaRed; cl00801 557722002662 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component; Region: HpaB-2; TIGR02310 557722002663 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 557722002664 Uncharacterized protein conserved in bacteria (DUF2218); Region: DUF2218; cl01424 557722002665 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 557722002666 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002667 NAD(P) binding site [chemical binding]; other site 557722002668 active site 557722002669 aminotransferase; Validated; Region: PRK07046 557722002670 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722002671 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722002672 catalytic residue [active] 557722002673 Molybdenum cofactor biosynthesis protein F; Region: MoaF; pfam10703 557722002674 Fimbrial protein; Region: Fimbrial; cl01416 557722002675 putative chaperone protein EcpD; Provisional; Region: PRK09926 557722002676 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722002677 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 557722002678 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 557722002679 PapC N-terminal domain; Region: PapC_N; pfam13954 557722002680 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 557722002681 PapC C-terminal domain; Region: PapC_C; pfam13953 557722002682 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722002683 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 557722002684 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 557722002685 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 557722002686 haemagglutination activity domain; Region: Haemagg_act; cl05436 557722002687 Fimbrial protein; Region: Fimbrial; cl01416 557722002688 transcriptional regulator RcsB; Provisional; Region: PRK10840 557722002689 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722002690 active site 557722002691 phosphorylation site [posttranslational modification] 557722002692 intermolecular recognition site; other site 557722002693 dimerization interface [polypeptide binding]; other site 557722002694 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722002695 DNA binding residues [nucleotide binding] 557722002696 dimerization interface [polypeptide binding]; other site 557722002697 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002698 NAD(P) binding site [chemical binding]; other site 557722002699 active site 557722002700 D-alanine--poly(phosphoribitol) ligase subunit 1; Provisional; Region: PRK04813 557722002701 AMP-binding enzyme; Region: AMP-binding; cl15778 557722002702 AMP-binding enzyme; Region: AMP-binding; cl15778 557722002703 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722002704 thioester reductase domain; Region: Thioester-redct; TIGR01746 557722002705 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002706 NAD(P) binding site [chemical binding]; other site 557722002707 active site 557722002708 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722002709 non-specific DNA binding site [nucleotide binding]; other site 557722002710 salt bridge; other site 557722002711 sequence-specific DNA binding site [nucleotide binding]; other site 557722002712 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722002713 DNA binding residues [nucleotide binding] 557722002714 dimerization interface [polypeptide binding]; other site 557722002715 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 557722002716 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722002717 NAD(P) binding site [chemical binding]; other site 557722002718 catalytic residues [active] 557722002719 Spore germination protein; Region: Spore_permease; cl15802 557722002720 Protein of unknown function (DUF3156); Region: DUF3156; pfam11354 557722002721 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 557722002722 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722002723 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 557722002724 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002725 NAD(P) binding site [chemical binding]; other site 557722002726 active site 557722002727 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002728 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 557722002729 NAD(P) binding site [chemical binding]; other site 557722002730 active site 557722002731 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 557722002732 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722002733 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 557722002734 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557722002735 FtsX-like permease family; Region: FtsX; cl15850 557722002736 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 557722002737 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 557722002738 Walker A/P-loop; other site 557722002739 ATP binding site [chemical binding]; other site 557722002740 Q-loop/lid; other site 557722002741 ABC transporter signature motif; other site 557722002742 Walker B; other site 557722002743 D-loop; other site 557722002744 H-loop/switch region; other site 557722002745 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 557722002746 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 557722002747 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 557722002748 Predicted methyltransferase [General function prediction only]; Region: COG3897 557722002749 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722002750 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 557722002751 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 557722002752 ATP cone domain; Region: ATP-cone; pfam03477 557722002753 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 557722002754 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 557722002755 catalytic motif [active] 557722002756 Zn binding site [ion binding]; other site 557722002757 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 557722002758 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 557722002759 Lumazine binding domain; Region: Lum_binding; pfam00677 557722002760 Lumazine binding domain; Region: Lum_binding; pfam00677 557722002761 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 557722002762 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 557722002763 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 557722002764 dimerization interface [polypeptide binding]; other site 557722002765 active site 557722002766 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 557722002767 homopentamer interface [polypeptide binding]; other site 557722002768 active site 557722002769 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 557722002770 thiamine monophosphate kinase; Provisional; Region: PRK05731 557722002771 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 557722002772 ATP binding site [chemical binding]; other site 557722002773 dimerization interface [polypeptide binding]; other site 557722002774 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 557722002775 tetramer interfaces [polypeptide binding]; other site 557722002776 binuclear metal-binding site [ion binding]; other site 557722002777 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl15306 557722002778 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722002779 substrate binding pocket [chemical binding]; other site 557722002780 membrane-bound complex binding site; other site 557722002781 hinge residues; other site 557722002782 Predicted aspartyl protease [General function prediction only]; Region: COG3577 557722002783 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 557722002784 catalytic motif [active] 557722002785 Catalytic residue [active] 557722002786 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 557722002787 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 557722002788 dimerization interface [polypeptide binding]; other site 557722002789 active site 557722002790 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 557722002791 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 557722002792 cobalamin binding residues [chemical binding]; other site 557722002793 putative BtuC binding residues; other site 557722002794 dimer interface [polypeptide binding]; other site 557722002795 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 557722002796 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 557722002797 TPP-binding site; other site 557722002798 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 557722002799 PYR/PP interface [polypeptide binding]; other site 557722002800 dimer interface [polypeptide binding]; other site 557722002801 TPP binding site [chemical binding]; other site 557722002802 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557722002803 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 557722002804 substrate binding pocket [chemical binding]; other site 557722002805 chain length determination region; other site 557722002806 substrate-Mg2+ binding site; other site 557722002807 catalytic residues [active] 557722002808 aspartate-rich region 1; other site 557722002809 active site lid residues [active] 557722002810 aspartate-rich region 2; other site 557722002811 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 557722002812 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 557722002813 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_1; cd03326 557722002814 putative active site pocket [active] 557722002815 metal binding site [ion binding]; metal-binding site 557722002816 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 557722002817 ABC-type uncharacterized transport system involved in gliding motility, auxiliary component [Cell motility and secretion]; Region: GldG; COG3225 557722002818 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722002819 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 557722002820 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722002821 Walker A/P-loop; other site 557722002822 ATP binding site [chemical binding]; other site 557722002823 Q-loop/lid; other site 557722002824 ABC transporter signature motif; other site 557722002825 Walker B; other site 557722002826 D-loop; other site 557722002827 H-loop/switch region; other site 557722002828 CHASE2 domain; Region: CHASE2; cl01732 557722002829 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557722002830 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722002831 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722002832 dimer interface [polypeptide binding]; other site 557722002833 phosphorylation site [posttranslational modification] 557722002834 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722002835 ATP binding site [chemical binding]; other site 557722002836 Mg2+ binding site [ion binding]; other site 557722002837 G-X-G motif; other site 557722002838 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 557722002839 FecR protein; Region: FecR; pfam04773 557722002840 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 557722002841 amphipathic channel; other site 557722002842 Asn-Pro-Ala signature motifs; other site 557722002843 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722002844 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722002845 active site 557722002846 phosphorylation site [posttranslational modification] 557722002847 intermolecular recognition site; other site 557722002848 dimerization interface [polypeptide binding]; other site 557722002849 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722002850 DNA binding site [nucleotide binding] 557722002851 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 557722002852 dimer interface [polypeptide binding]; other site 557722002853 substrate binding site [chemical binding]; other site 557722002854 metal binding sites [ion binding]; metal-binding site 557722002855 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 557722002856 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557722002857 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 557722002858 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722002859 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722002860 substrate binding pocket [chemical binding]; other site 557722002861 membrane-bound complex binding site; other site 557722002862 hinge residues; other site 557722002863 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722002864 Coenzyme A binding pocket [chemical binding]; other site 557722002865 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 557722002866 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 557722002867 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 557722002868 ethanolamine permease; Region: 2A0305; TIGR00908 557722002869 Spore germination protein; Region: Spore_permease; cl15802 557722002870 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 557722002871 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722002872 NAD(P) binding site [chemical binding]; other site 557722002873 catalytic residues [active] 557722002874 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 557722002875 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722002876 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722002877 Walker A motif; other site 557722002878 ATP binding site [chemical binding]; other site 557722002879 Walker B motif; other site 557722002880 arginine finger; other site 557722002881 Helix-turn-helix domains; Region: HTH; cl00088 557722002882 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 557722002883 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557722002884 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557722002885 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557722002886 aromatic acid decarboxylase; Validated; Region: PRK05920 557722002887 Flavoprotein; Region: Flavoprotein; cl08021 557722002888 Protein of unknown function (DUF1375); Region: DUF1375; cl11456 557722002889 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 557722002890 NAD binding site [chemical binding]; other site 557722002891 active site 557722002892 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 557722002893 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 557722002894 MORN repeat; Region: MORN; cl14787 557722002895 Peptidase C13 family; Region: Peptidase_C13; cl02159 557722002896 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 557722002897 putative active site [active] 557722002898 putative catalytic site [active] 557722002899 LrgB-like family; Region: LrgB; cl00596 557722002900 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 557722002901 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557722002902 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 557722002903 active site 557722002904 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 557722002905 active site 557722002906 DNA binding site [nucleotide binding] 557722002907 Leucine carboxyl methyltransferase; Region: LCM; cl01306 557722002908 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722002909 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 557722002910 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 557722002911 putative catalytic cysteine [active] 557722002912 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 557722002913 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 557722002914 active site 557722002915 (T/H)XGH motif; other site 557722002916 Oligomerisation domain; Region: Oligomerisation; cl00519 557722002917 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 557722002918 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 557722002919 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 557722002920 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557722002921 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722002922 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 557722002923 Transglycosylase SLT domain; Region: SLT_2; pfam13406 557722002924 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722002925 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722002926 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 557722002927 Sporulation related domain; Region: SPOR; cl10051 557722002928 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 557722002929 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722002930 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 557722002931 Protein of unknown function (DUF493); Region: DUF493; cl01102 557722002932 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 557722002933 lipoyl synthase; Provisional; Region: PRK05481 557722002934 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722002935 FeS/SAM binding site; other site 557722002936 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722002937 Helix-turn-helix domains; Region: HTH; cl00088 557722002938 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722002939 dimerization interface [polypeptide binding]; other site 557722002940 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722002941 Transglycosylase SLT domain; Region: SLT_2; pfam13406 557722002942 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722002943 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722002944 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 557722002945 Domain of unknown function; Region: DUF331; cl01149 557722002946 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 557722002947 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 557722002948 Lipopolysaccharide-assembly; Region: LptE; cl01125 557722002949 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 557722002950 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 557722002951 HIGH motif; other site 557722002952 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 557722002953 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722002954 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722002955 active site 557722002956 KMSKS motif; other site 557722002957 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 557722002958 tRNA binding surface [nucleotide binding]; other site 557722002959 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 557722002960 putative active site [active] 557722002961 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 557722002962 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 557722002963 putative active site [active] 557722002964 catalytic triad [active] 557722002965 putative dimer interface [polypeptide binding]; other site 557722002966 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 557722002967 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 557722002968 Transporter associated domain; Region: CorC_HlyC; cl08393 557722002969 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 557722002970 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 557722002971 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722002972 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 557722002973 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 557722002974 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722002975 FeS/SAM binding site; other site 557722002976 TRAM domain; Region: TRAM; cl01282 557722002977 Domain of unknown function (DUF1820); Region: DUF1820; cl11545 557722002978 Sel1 repeat; Region: Sel1; cl02723 557722002979 Sel1 repeat; Region: Sel1; cl02723 557722002980 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 557722002981 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722002982 inhibitor-cofactor binding pocket; inhibition site 557722002983 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722002984 catalytic residue [active] 557722002985 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 557722002986 thiamine phosphate binding site [chemical binding]; other site 557722002987 active site 557722002988 pyrophosphate binding site [ion binding]; other site 557722002989 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 557722002990 dimer interface [polypeptide binding]; other site 557722002991 substrate binding site [chemical binding]; other site 557722002992 ATP binding site [chemical binding]; other site 557722002993 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 557722002994 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 557722002995 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722002996 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722002997 dimer interface [polypeptide binding]; other site 557722002998 phosphorylation site [posttranslational modification] 557722002999 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722003000 ATP binding site [chemical binding]; other site 557722003001 Mg2+ binding site [ion binding]; other site 557722003002 G-X-G motif; other site 557722003003 Response regulator receiver domain; Region: Response_reg; pfam00072 557722003004 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003005 active site 557722003006 phosphorylation site [posttranslational modification] 557722003007 intermolecular recognition site; other site 557722003008 dimerization interface [polypeptide binding]; other site 557722003009 TetR family transcriptional regulator; Provisional; Region: PRK14996 557722003010 Helix-turn-helix domains; Region: HTH; cl00088 557722003011 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 557722003012 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722003013 active site 557722003014 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722003015 CoenzymeA binding site [chemical binding]; other site 557722003016 subunit interaction site [polypeptide binding]; other site 557722003017 PHB binding site; other site 557722003018 AMP nucleosidase; Provisional; Region: PRK08292 557722003019 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 557722003020 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 557722003021 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722003022 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 557722003023 pseudouridine synthase; Region: TIGR00093 557722003024 active site 557722003025 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 557722003026 heme-binding site [chemical binding]; other site 557722003027 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 557722003028 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 557722003029 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722003030 putative DNA binding site [nucleotide binding]; other site 557722003031 putative Zn2+ binding site [ion binding]; other site 557722003032 Helix-turn-helix domains; Region: HTH; cl00088 557722003033 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 557722003034 Cation efflux family; Region: Cation_efflux; cl00316 557722003035 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 557722003036 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722003037 ATP binding site [chemical binding]; other site 557722003038 putative Mg++ binding site [ion binding]; other site 557722003039 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722003040 nucleotide binding region [chemical binding]; other site 557722003041 ATP-binding site [chemical binding]; other site 557722003042 Helicase associated domain (HA2); Region: HA2; cl04503 557722003043 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 557722003044 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl15306 557722003045 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722003046 substrate binding pocket [chemical binding]; other site 557722003047 membrane-bound complex binding site; other site 557722003048 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 557722003049 short chain dehydrogenase; Provisional; Region: PRK06181 557722003050 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003051 NAD(P) binding site [chemical binding]; other site 557722003052 active site 557722003053 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 557722003054 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722003055 dimethyl sulfone monooxygenase SfnG; Region: LLM_DMSO2_sfnG; TIGR04021 557722003056 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 557722003057 active site 557722003058 dimer interface [polypeptide binding]; other site 557722003059 non-prolyl cis peptide bond; other site 557722003060 insertion regions; other site 557722003061 Isochorismatase family; Region: Isochorismatase; pfam00857 557722003062 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 557722003063 catalytic triad [active] 557722003064 conserved cis-peptide bond; other site 557722003065 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 557722003066 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 557722003067 putative metal binding site [ion binding]; other site 557722003068 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 557722003069 ATP binding site [chemical binding]; other site 557722003070 Mg++ binding site [ion binding]; other site 557722003071 motif III; other site 557722003072 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722003073 nucleotide binding region [chemical binding]; other site 557722003074 ATP-binding site [chemical binding]; other site 557722003075 HI0933-like protein; Region: HI0933_like; pfam03486 557722003076 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003077 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722003078 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003079 active site 557722003080 phosphorylation site [posttranslational modification] 557722003081 intermolecular recognition site; other site 557722003082 dimerization interface [polypeptide binding]; other site 557722003083 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722003084 DNA binding residues [nucleotide binding] 557722003085 dimerization interface [polypeptide binding]; other site 557722003086 Response regulator receiver domain; Region: Response_reg; pfam00072 557722003087 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003088 active site 557722003089 phosphorylation site [posttranslational modification] 557722003090 intermolecular recognition site; other site 557722003091 dimerization interface [polypeptide binding]; other site 557722003092 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722003093 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional; Region: PRK09959 557722003094 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722003095 substrate binding pocket [chemical binding]; other site 557722003096 membrane-bound complex binding site; other site 557722003097 hinge residues; other site 557722003098 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722003099 substrate binding pocket [chemical binding]; other site 557722003100 membrane-bound complex binding site; other site 557722003101 hinge residues; other site 557722003102 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722003103 putative active site [active] 557722003104 heme pocket [chemical binding]; other site 557722003105 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722003106 dimer interface [polypeptide binding]; other site 557722003107 phosphorylation site [posttranslational modification] 557722003108 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722003109 ATP binding site [chemical binding]; other site 557722003110 Mg2+ binding site [ion binding]; other site 557722003111 G-X-G motif; other site 557722003112 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003113 active site 557722003114 phosphorylation site [posttranslational modification] 557722003115 intermolecular recognition site; other site 557722003116 dimerization interface [polypeptide binding]; other site 557722003117 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722003118 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 557722003119 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 557722003120 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722003121 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 557722003122 NADPH bind site [chemical binding]; other site 557722003123 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 557722003124 NADPH bind site [chemical binding]; other site 557722003125 putative FMN binding site [chemical binding]; other site 557722003126 acyl-CoA thioesterase II; Provisional; Region: PRK10526 557722003127 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 557722003128 active site 557722003129 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 557722003130 catalytic triad [active] 557722003131 dimer interface [polypeptide binding]; other site 557722003132 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722003133 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 557722003134 active site 557722003135 motif I; other site 557722003136 motif II; other site 557722003137 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 557722003138 IHF dimer interface [polypeptide binding]; other site 557722003139 IHF - DNA interface [nucleotide binding]; other site 557722003140 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722003141 active site 557722003142 ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: TauA; COG4521 557722003143 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722003144 substrate binding pocket [chemical binding]; other site 557722003145 membrane-bound complex binding site; other site 557722003146 hinge residues; other site 557722003147 ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG4525 557722003148 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557722003149 Walker A/P-loop; other site 557722003150 ATP binding site [chemical binding]; other site 557722003151 Q-loop/lid; other site 557722003152 ABC transporter signature motif; other site 557722003153 Walker B; other site 557722003154 D-loop; other site 557722003155 H-loop/switch region; other site 557722003156 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722003157 dimer interface [polypeptide binding]; other site 557722003158 conserved gate region; other site 557722003159 putative PBP binding loops; other site 557722003160 ABC-ATPase subunit interface; other site 557722003161 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 557722003162 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 557722003163 OPT oligopeptide transporter protein; Region: OPT; cl14607 557722003164 BCCT family transporter; Region: BCCT; cl00569 557722003165 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722003166 Walker A motif; other site 557722003167 ATP binding site [chemical binding]; other site 557722003168 Walker B motif; other site 557722003169 NMT1-like family; Region: NMT1_2; cl15260 557722003170 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 557722003171 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 557722003172 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 557722003173 Protein of unknown function (DUF2474); Region: DUF2474; pfam10617 557722003174 Cupin domain; Region: Cupin_2; cl09118 557722003175 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722003176 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722003177 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722003178 putative substrate translocation pore; other site 557722003179 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 557722003180 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722003181 dimer interface [polypeptide binding]; other site 557722003182 active site 557722003183 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 557722003184 AMP-binding enzyme; Region: AMP-binding; cl15778 557722003185 AMP-binding enzyme; Region: AMP-binding; cl15778 557722003186 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 557722003187 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 557722003188 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722003189 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722003190 DNA binding residues [nucleotide binding] 557722003191 dimerization interface [polypeptide binding]; other site 557722003192 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722003193 metal-binding site [ion binding] 557722003194 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557722003195 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722003196 metal-binding site [ion binding] 557722003197 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722003198 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722003199 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 557722003200 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 557722003201 putative active site [active] 557722003202 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722003203 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 557722003204 trimer interface [polypeptide binding]; other site 557722003205 dimer interface [polypeptide binding]; other site 557722003206 putative active site [active] 557722003207 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 557722003208 MoaE interaction surface [polypeptide binding]; other site 557722003209 MoeB interaction surface [polypeptide binding]; other site 557722003210 thiocarboxylated glycine; other site 557722003211 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 557722003212 MoaE homodimer interface [polypeptide binding]; other site 557722003213 MoaD interaction [polypeptide binding]; other site 557722003214 active site residues [active] 557722003215 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 557722003216 MPT binding site; other site 557722003217 trimer interface [polypeptide binding]; other site 557722003218 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 557722003219 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 557722003220 dimer interface [polypeptide binding]; other site 557722003221 putative functional site; other site 557722003222 putative MPT binding site; other site 557722003223 Peptidase family U32; Region: Peptidase_U32; cl03113 557722003224 Peptidase family U32; Region: Peptidase_U32; cl03113 557722003225 SCP-2 sterol transfer family; Region: SCP2; cl01225 557722003226 Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]; Region: PhoD; COG3540 557722003227 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 557722003228 putative active site [active] 557722003229 putative metal binding site [ion binding]; other site 557722003230 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 557722003231 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 557722003232 Lamin Tail Domain; Region: LTD; pfam00932 557722003233 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 557722003234 generic binding surface I; other site 557722003235 generic binding surface II; other site 557722003236 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 557722003237 putative active site [active] 557722003238 putative catalytic site [active] 557722003239 putative Mg binding site IVb [ion binding]; other site 557722003240 putative phosphate binding site [ion binding]; other site 557722003241 putative DNA binding site [nucleotide binding]; other site 557722003242 putative Mg binding site IVa [ion binding]; other site 557722003243 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 557722003244 PAAR motif; Region: PAAR_motif; cl15808 557722003245 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 557722003246 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 557722003247 G1 box; other site 557722003248 putative GEF interaction site [polypeptide binding]; other site 557722003249 GTP/Mg2+ binding site [chemical binding]; other site 557722003250 Switch I region; other site 557722003251 G2 box; other site 557722003252 G3 box; other site 557722003253 Switch II region; other site 557722003254 G4 box; other site 557722003255 G5 box; other site 557722003256 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 557722003257 Inhibitor of vertebrate lysozyme (Ivy); Region: Ivy; cl07428 557722003258 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 557722003259 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722003260 N-terminal plug; other site 557722003261 ligand-binding site [chemical binding]; other site 557722003262 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722003263 FecR protein; Region: FecR; pfam04773 557722003264 RNA polymerase sigma factor; Provisional; Region: PRK12528 557722003265 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722003266 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722003267 DNA binding residues [nucleotide binding] 557722003268 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722003269 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722003270 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 557722003271 EamA-like transporter family; Region: EamA; cl01037 557722003272 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional; Region: PRK15409 557722003273 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003274 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722003275 Helix-turn-helix domains; Region: HTH; cl00088 557722003276 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722003277 putative effector binding pocket; other site 557722003278 dimerization interface [polypeptide binding]; other site 557722003279 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722003280 Fusaric acid resistance protein family; Region: FUSC; pfam04632 557722003281 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 557722003282 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 557722003283 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722003284 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722003285 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 557722003286 OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of...; Region: ABC_OpuCA_Osmoprotection; cd03295 557722003287 Walker A/P-loop; other site 557722003288 ATP binding site [chemical binding]; other site 557722003289 Q-loop/lid; other site 557722003290 ABC transporter signature motif; other site 557722003291 Walker B; other site 557722003292 D-loop; other site 557722003293 H-loop/switch region; other site 557722003294 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing...; Region: CBS_pair_ABC_OpuCA_assoc; cd04582 557722003295 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722003296 NMT1-like family; Region: NMT1_2; cl15260 557722003297 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 557722003298 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 557722003299 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722003300 ABC-ATPase subunit interface; other site 557722003301 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 557722003302 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557722003303 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 557722003304 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722003305 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722003306 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 557722003307 short chain dehydrogenase; Provisional; Region: PRK05693 557722003308 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003309 NAD(P) binding site [chemical binding]; other site 557722003310 active site 557722003311 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722003312 DGC domain; Region: DGC; cl01742 557722003313 transcriptional regulator NarL; Provisional; Region: PRK10651 557722003314 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003315 active site 557722003316 phosphorylation site [posttranslational modification] 557722003317 intermolecular recognition site; other site 557722003318 dimerization interface [polypeptide binding]; other site 557722003319 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722003320 DNA binding residues [nucleotide binding] 557722003321 dimerization interface [polypeptide binding]; other site 557722003322 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 557722003323 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 557722003324 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722003325 dimerization interface [polypeptide binding]; other site 557722003326 Histidine kinase; Region: HisKA_3; pfam07730 557722003327 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722003328 ATP binding site [chemical binding]; other site 557722003329 Mg2+ binding site [ion binding]; other site 557722003330 G-X-G motif; other site 557722003331 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 557722003332 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722003333 putative substrate translocation pore; other site 557722003334 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 557722003335 respiratory nitrate reductase, alpha subunit; Region: narG; TIGR01580 557722003336 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 557722003337 [4Fe-4S] binding site [ion binding]; other site 557722003338 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722003339 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722003340 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722003341 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722003342 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 557722003343 molybdopterin cofactor binding site; other site 557722003344 nitrate reductase, beta subunit; Region: narH; TIGR01660 557722003345 4Fe-4S binding domain; Region: Fer4; cl02805 557722003346 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 557722003347 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 557722003348 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722003349 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 557722003350 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722003351 FeS/SAM binding site; other site 557722003352 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 557722003353 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 557722003354 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722003355 substrate binding pocket [chemical binding]; other site 557722003356 membrane-bound complex binding site; other site 557722003357 hinge residues; other site 557722003358 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 557722003359 YheO-like PAS domain; Region: PAS_6; pfam08348 557722003360 Helix-turn-helix domains; Region: HTH; cl00088 557722003361 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722003362 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003363 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 557722003364 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003365 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 557722003366 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 557722003367 ATP binding site [chemical binding]; other site 557722003368 Mg++ binding site [ion binding]; other site 557722003369 motif III; other site 557722003370 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722003371 nucleotide binding region [chemical binding]; other site 557722003372 ATP-binding site [chemical binding]; other site 557722003373 AMP-binding domain protein; Validated; Region: PRK07529 557722003374 AMP-binding enzyme; Region: AMP-binding; cl15778 557722003375 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 557722003376 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722003377 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 557722003378 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722003379 substrate binding pocket [chemical binding]; other site 557722003380 membrane-bound complex binding site; other site 557722003381 hinge residues; other site 557722003382 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 557722003383 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722003384 GST_N family, Metaxin subfamily, Metaxin-like proteins; a heterogenous group of proteins, predominantly uncharacterized, with similarity to metaxins and GSTs. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It...; Region: GST_N_Metaxin_like; cd03080 557722003385 putative C-terminal domain interface [polypeptide binding]; other site 557722003386 putative GSH binding site [chemical binding]; other site 557722003387 putative dimer interface [polypeptide binding]; other site 557722003388 C-terminal, alpha helical domain of Metaxin and related proteins; Region: GST_C_Metaxin; cd03193 557722003389 putative N-terminal domain interface [polypeptide binding]; other site 557722003390 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 557722003391 GIY-YIG motif/motif A; other site 557722003392 putative active site [active] 557722003393 putative metal binding site [ion binding]; other site 557722003394 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 557722003395 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 557722003396 trimer interface [polypeptide binding]; other site 557722003397 active site 557722003398 substrate binding site [chemical binding]; other site 557722003399 CoA binding site [chemical binding]; other site 557722003400 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722003401 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 557722003402 C-terminal domain interface [polypeptide binding]; other site 557722003403 GSH binding site (G-site) [chemical binding]; other site 557722003404 dimer interface [polypeptide binding]; other site 557722003405 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 557722003406 substrate binding pocket (H-site) [chemical binding]; other site 557722003407 N-terminal domain interface [polypeptide binding]; other site 557722003408 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_2; cd02433 557722003409 Nucleoid-associated protein [General function prediction only]; Region: COG3081 557722003410 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 557722003411 NMT1-like family; Region: NMT1_2; cl15260 557722003412 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 557722003413 hydrophobic ligand binding site; other site 557722003414 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 557722003415 Isochorismatase family; Region: Isochorismatase; pfam00857 557722003416 catalytic triad [active] 557722003417 dimer interface [polypeptide binding]; other site 557722003418 conserved cis-peptide bond; other site 557722003419 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722003420 Helix-turn-helix domains; Region: HTH; cl00088 557722003421 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 557722003422 dimerization interface [polypeptide binding]; other site 557722003423 substrate binding pocket [chemical binding]; other site 557722003424 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722003425 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 557722003426 C-terminal domain interface [polypeptide binding]; other site 557722003427 GSH binding site (G-site) [chemical binding]; other site 557722003428 dimer interface [polypeptide binding]; other site 557722003429 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 557722003430 dimer interface [polypeptide binding]; other site 557722003431 N-terminal domain interface [polypeptide binding]; other site 557722003432 putative substrate binding pocket (H-site) [chemical binding]; other site 557722003433 Tir chaperone protein (CesT) family; Region: CesT; cl08444 557722003434 NAD+--asparagine ADP-ribosyltransferase [Signal transduction mechanisms]; Region: COG5585 557722003435 GTPase-activating protein (GAP) domain found in bacterial cytotoxins, ExoS, SptP, and YopE. Part of protein secretion system; stimulates Rac1- dependent cytoskeletal changes that promote bacterial internalization; Region: ToxGAP; cd00219 557722003436 switch II binding region; other site 557722003437 Rac1 P-loop interaction site [polypeptide binding]; other site 557722003438 GTP binding residues [chemical binding]; other site 557722003439 switch I binding region; other site 557722003440 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of...; Region: VIP2; cl00173 557722003441 active site 557722003442 conformational flexibility of ligand binding pocket; other site 557722003443 ADP-ribosylating toxin turn-turn motif; other site 557722003444 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722003445 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 557722003446 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 557722003447 transmembrane helices; other site 557722003448 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 557722003449 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722003450 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722003451 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 557722003452 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 557722003453 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722003454 Walker A/P-loop; other site 557722003455 ATP binding site [chemical binding]; other site 557722003456 Q-loop/lid; other site 557722003457 ABC transporter signature motif; other site 557722003458 Walker B; other site 557722003459 D-loop; other site 557722003460 H-loop/switch region; other site 557722003461 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 557722003462 TM-ABC transporter signature motif; other site 557722003463 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 557722003464 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 557722003465 zinc binding site [ion binding]; other site 557722003466 putative ligand binding site [chemical binding]; other site 557722003467 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 557722003468 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 557722003469 HIGH motif; other site 557722003470 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 557722003471 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 557722003472 active site 557722003473 KMSKS motif; other site 557722003474 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 557722003475 tRNA binding surface [nucleotide binding]; other site 557722003476 anticodon binding site; other site 557722003477 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 557722003478 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 557722003479 multifunctional aminopeptidase A; Provisional; Region: PRK00913 557722003480 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 557722003481 interface (dimer of trimers) [polypeptide binding]; other site 557722003482 Substrate-binding/catalytic site; other site 557722003483 Zn-binding sites [ion binding]; other site 557722003484 Cupin domain; Region: Cupin_2; cl09118 557722003485 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722003486 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 557722003487 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722003488 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722003489 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 557722003490 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 557722003491 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 557722003492 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 557722003493 RDD family; Region: RDD; cl00746 557722003494 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 557722003495 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 557722003496 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722003497 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 557722003498 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 557722003499 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 557722003500 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 557722003501 Preprotein translocase subunit; Region: YajC; cl00806 557722003502 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 557722003503 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 557722003504 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 557722003505 Protein export membrane protein; Region: SecD_SecF; cl14618 557722003506 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 557722003507 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 557722003508 Protein export membrane protein; Region: SecD_SecF; cl14618 557722003509 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 557722003510 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 557722003511 active site 557722003512 dimerization interface [polypeptide binding]; other site 557722003513 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 557722003514 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557722003515 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 557722003516 serine O-acetyltransferase; Region: cysE; TIGR01172 557722003517 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 557722003518 trimer interface [polypeptide binding]; other site 557722003519 active site 557722003520 substrate binding site [chemical binding]; other site 557722003521 CoA binding site [chemical binding]; other site 557722003522 phosphonate metabolim protein, transferase hexapeptide repeat family; Region: phn_thr-fam; TIGR03308 557722003523 Helix-turn-helix domains; Region: HTH; cl00088 557722003524 Rrf2 family protein; Region: rrf2_super; TIGR00738 557722003525 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722003526 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 557722003527 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722003528 catalytic residue [active] 557722003529 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 557722003530 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 557722003531 trimerization site [polypeptide binding]; other site 557722003532 active site 557722003533 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557722003534 co-chaperone HscB; Provisional; Region: hscB; PRK00294 557722003535 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 557722003536 HSP70 interaction site [polypeptide binding]; other site 557722003537 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 557722003538 chaperone protein HscA; Provisional; Region: hscA; PRK05183 557722003539 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722003540 catalytic loop [active] 557722003541 iron binding site [ion binding]; other site 557722003542 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 557722003543 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 557722003544 active site 557722003545 multimer interface [polypeptide binding]; other site 557722003546 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 557722003547 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722003548 FeS/SAM binding site; other site 557722003549 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 557722003550 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722003551 binding surface 557722003552 TPR motif; other site 557722003553 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722003554 binding surface 557722003555 TPR motif; other site 557722003556 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 557722003557 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722003558 non-specific DNA binding site [nucleotide binding]; other site 557722003559 salt bridge; other site 557722003560 sequence-specific DNA binding site [nucleotide binding]; other site 557722003561 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 557722003562 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 557722003563 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 557722003564 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 557722003565 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 557722003566 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 557722003567 dimer interface [polypeptide binding]; other site 557722003568 motif 1; other site 557722003569 active site 557722003570 motif 2; other site 557722003571 motif 3; other site 557722003572 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 557722003573 anticodon binding site; other site 557722003574 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 557722003575 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 557722003576 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 557722003577 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 557722003578 Trp docking motif [polypeptide binding]; other site 557722003579 active site 557722003580 GTP-binding protein Der; Reviewed; Region: PRK00093 557722003581 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 557722003582 G1 box; other site 557722003583 GTP/Mg2+ binding site [chemical binding]; other site 557722003584 Switch I region; other site 557722003585 G2 box; other site 557722003586 Switch II region; other site 557722003587 G3 box; other site 557722003588 G4 box; other site 557722003589 G5 box; other site 557722003590 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 557722003591 G1 box; other site 557722003592 GTP/Mg2+ binding site [chemical binding]; other site 557722003593 Switch I region; other site 557722003594 G2 box; other site 557722003595 G3 box; other site 557722003596 Switch II region; other site 557722003597 G4 box; other site 557722003598 G5 box; other site 557722003599 methionine aminotransferase; Validated; Region: PRK09082 557722003600 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722003601 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722003602 homodimer interface [polypeptide binding]; other site 557722003603 catalytic residue [active] 557722003604 Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases); Region: Xc-1258_like; cd07575 557722003605 Predicted amidohydrolase [General function prediction only]; Region: COG0388 557722003606 putative active site [active] 557722003607 catalytic triad [active] 557722003608 multimer interface [polypeptide binding]; other site 557722003609 dimer interface [polypeptide binding]; other site 557722003610 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 557722003611 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 557722003612 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722003613 active site 557722003614 catalytic tetrad [active] 557722003615 2-isopropylmalate synthase; Validated; Region: PRK03739 557722003616 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 557722003617 active site 557722003618 catalytic residues [active] 557722003619 metal binding site [ion binding]; metal-binding site 557722003620 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 557722003621 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 557722003622 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722003623 N-terminal plug; other site 557722003624 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 557722003625 ligand-binding site [chemical binding]; other site 557722003626 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722003627 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722003628 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 557722003629 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722003630 Peptidase family M23; Region: Peptidase_M23; pfam01551 557722003631 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 557722003632 Protein of unknown function (DUF461); Region: DUF461; cl01071 557722003633 AZL_007950 family protein; Region: AZL_007950_fam; cl14861 557722003634 Isochorismatase family; Region: Isochorismatase; pfam00857 557722003635 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 557722003636 catalytic triad [active] 557722003637 conserved cis-peptide bond; other site 557722003638 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 557722003639 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 557722003640 conserved cys residue [active] 557722003641 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722003642 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 557722003643 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 557722003644 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 557722003645 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722003646 Helix-turn-helix domains; Region: HTH; cl00088 557722003647 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722003648 dimerization interface [polypeptide binding]; other site 557722003649 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 557722003650 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 557722003651 generic binding surface II; other site 557722003652 generic binding surface I; other site 557722003653 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 557722003654 Helix-turn-helix domains; Region: HTH; cl00088 557722003655 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 557722003656 dimerization interface [polypeptide binding]; other site 557722003657 substrate binding pocket [chemical binding]; other site 557722003658 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 557722003659 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 557722003660 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557722003661 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722003662 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722003663 DNA binding residues [nucleotide binding] 557722003664 dimerization interface [polypeptide binding]; other site 557722003665 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 557722003666 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 557722003667 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 557722003668 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 557722003669 active site 557722003670 GMP synthase; Reviewed; Region: guaA; PRK00074 557722003671 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 557722003672 AMP/PPi binding site [chemical binding]; other site 557722003673 candidate oxyanion hole; other site 557722003674 catalytic triad [active] 557722003675 potential glutamine specificity residues [chemical binding]; other site 557722003676 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 557722003677 ATP Binding subdomain [chemical binding]; other site 557722003678 Dimerization subdomain; other site 557722003679 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 557722003680 active site 557722003681 cosubstrate binding site; other site 557722003682 substrate binding site [chemical binding]; other site 557722003683 catalytic site [active] 557722003684 Chordopoxvirus A20R protein; Region: Chordopox_A20R; pfam05941 557722003685 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 557722003686 oxidoreductase; Provisional; Region: PRK06196 557722003687 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003688 NAD(P) binding site [chemical binding]; other site 557722003689 active site 557722003690 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722003691 putative substrate translocation pore; other site 557722003692 Cupin domain; Region: Cupin_2; cl09118 557722003693 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722003694 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722003695 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 557722003696 Prostaglandin dehydrogenases; Region: PGDH; cd05288 557722003697 NAD(P) binding site [chemical binding]; other site 557722003698 substrate binding site [chemical binding]; other site 557722003699 dimer interface [polypeptide binding]; other site 557722003700 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 557722003701 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722003702 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722003703 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 557722003704 nucleoside/Zn binding site; other site 557722003705 dimer interface [polypeptide binding]; other site 557722003706 catalytic motif [active] 557722003707 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 557722003708 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 557722003709 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; cl01461 557722003710 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 557722003711 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722003712 substrate binding pocket [chemical binding]; other site 557722003713 membrane-bound complex binding site; other site 557722003714 hinge residues; other site 557722003715 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722003716 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722003717 catalytic residue [active] 557722003718 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 557722003719 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 557722003720 dimerization interface [polypeptide binding]; other site 557722003721 ATP binding site [chemical binding]; other site 557722003722 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 557722003723 dimerization interface [polypeptide binding]; other site 557722003724 ATP binding site [chemical binding]; other site 557722003725 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 557722003726 putative active site [active] 557722003727 catalytic triad [active] 557722003728 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 557722003729 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 557722003730 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cd00212 557722003731 active site turn [active] 557722003732 phosphorylation site [posttranslational modification] 557722003733 PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_glc; cl00162 557722003734 HPr interaction site; other site 557722003735 glycerol kinase (GK) interaction site [polypeptide binding]; other site 557722003736 active site 557722003737 phosphorylation site [posttranslational modification] 557722003738 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 557722003739 regulatory protein interface [polypeptide binding]; other site 557722003740 active site 557722003741 regulatory phosphorylation site [posttranslational modification]; other site 557722003742 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 557722003743 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 557722003744 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 557722003745 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722003746 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 557722003747 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 557722003748 dimer interface [polypeptide binding]; other site 557722003749 active site 557722003750 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 557722003751 dimer interface [polypeptide binding]; other site 557722003752 active site 557722003753 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 557722003754 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 557722003755 active site 557722003756 dimer interface [polypeptide binding]; other site 557722003757 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 557722003758 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722003759 DNA-binding site [nucleotide binding]; DNA binding site 557722003760 UTRA domain; Region: UTRA; cl01230 557722003761 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 557722003762 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 557722003763 nudix motif; other site 557722003764 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 557722003765 putative active site [active] 557722003766 putative CoA binding site [chemical binding]; other site 557722003767 nudix motif; other site 557722003768 metal binding site [ion binding]; metal-binding site 557722003769 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 557722003770 trimer interface [polypeptide binding]; other site 557722003771 putative metal binding site [ion binding]; other site 557722003772 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 557722003773 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 557722003774 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003775 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722003776 SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it...; Region: FeeA_FeeB_like; cd01836 557722003777 active site 557722003778 catalytic triad [active] 557722003779 oxyanion hole [active] 557722003780 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722003781 metabolite-proton symporter; Region: 2A0106; TIGR00883 557722003782 putative substrate translocation pore; other site 557722003783 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 557722003784 Domain of unknown function DUF21; Region: DUF21; pfam01595 557722003785 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 557722003786 Transporter associated domain; Region: CorC_HlyC; cl08393 557722003787 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557722003788 signal recognition particle protein; Provisional; Region: PRK10867 557722003789 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 557722003790 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 557722003791 P loop; other site 557722003792 GTP binding site [chemical binding]; other site 557722003793 Signal peptide binding domain; Region: SRP_SPB; pfam02978 557722003794 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 557722003795 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 557722003796 RimM N-terminal domain; Region: RimM; pfam01782 557722003797 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 557722003798 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 557722003799 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 557722003800 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 557722003801 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 557722003802 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 557722003803 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003804 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 557722003805 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 557722003806 Int/Topo IB signature motif; other site 557722003807 active site 557722003808 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 557722003809 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 557722003810 dimerization domain [polypeptide binding]; other site 557722003811 dimer interface [polypeptide binding]; other site 557722003812 catalytic residues [active] 557722003813 homoserine dehydrogenase; Provisional; Region: PRK06349 557722003814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003815 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 557722003816 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 557722003817 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 557722003818 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 557722003819 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722003820 catalytic residue [active] 557722003821 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 557722003822 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 557722003823 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 557722003824 CoA-transferase family III; Region: CoA_transf_3; pfam02515 557722003825 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 557722003826 nucleotide binding site [chemical binding]; other site 557722003827 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; cl01551 557722003828 PspA/IM30 family; Region: PspA_IM30; pfam04012 557722003829 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 557722003830 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 557722003831 ATPase involved in DNA repair; Region: DUF3686; pfam12458 557722003832 Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; Region: SPEC; cl02488 557722003833 linker region; other site 557722003834 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722003835 Walker A motif; other site 557722003836 ATP binding site [chemical binding]; other site 557722003837 Walker B motif; other site 557722003838 HOOK protein; Region: HOOK; pfam05622 557722003839 Catalytic domain of vertebrate phospholipase D6 and similar proteins; Region: PLDc_vPLD6_like; cd09171 557722003840 PLD-like domain; Region: PLDc_2; pfam13091 557722003841 putative active site [active] 557722003842 catalytic site [active] 557722003843 YaeQ protein; Region: YaeQ; cl01913 557722003844 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 557722003845 DHH family; Region: DHH; pfam01368 557722003846 DHHA1 domain; Region: DHHA1; pfam02272 557722003847 Zinc metalloprotease (elastase) [Amino acid transport and metabolism]; Region: LasB; COG3227 557722003848 Fungalysin/Thermolysin Propeptide Motif; Region: FTP; pfam07504 557722003849 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 557722003850 Peptidase M4 family includes thermolysin, protealysin, aureolysin and neutral protease; Region: M4_neutral_protease; cd09597 557722003851 active site 557722003852 Zn binding site [ion binding]; other site 557722003853 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 557722003854 active site 557722003855 FMN binding site [chemical binding]; other site 557722003856 substrate binding site [chemical binding]; other site 557722003857 homotetramer interface [polypeptide binding]; other site 557722003858 catalytic residue [active] 557722003859 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722003860 Helix-turn-helix domains; Region: HTH; cl00088 557722003861 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722003862 putative substrate translocation pore; other site 557722003863 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557722003864 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722003865 transcriptional regulator RcsB; Provisional; Region: PRK10840 557722003866 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003867 active site 557722003868 phosphorylation site [posttranslational modification] 557722003869 intermolecular recognition site; other site 557722003870 dimerization interface [polypeptide binding]; other site 557722003871 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722003872 DNA binding residues [nucleotide binding] 557722003873 dimerization interface [polypeptide binding]; other site 557722003874 trimethylamine N-oxide reductase I catalytic subunit; Provisional; Region: PRK15102 557722003875 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 557722003876 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003877 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 557722003878 putative metal binding site [ion binding]; other site 557722003879 Helix-turn-helix domains; Region: HTH; cl00088 557722003880 transcriptional activator TtdR; Provisional; Region: PRK09801 557722003881 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722003882 dimerization interface [polypeptide binding]; other site 557722003883 choline dehydrogenase; Validated; Region: PRK02106 557722003884 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003885 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557722003886 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722003887 putative substrate translocation pore; other site 557722003888 metabolite-proton symporter; Region: 2A0106; TIGR00883 557722003889 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557722003890 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722003891 dimerization interface [polypeptide binding]; other site 557722003892 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722003893 dimer interface [polypeptide binding]; other site 557722003894 putative CheW interface [polypeptide binding]; other site 557722003895 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 557722003896 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 557722003897 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003898 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 557722003899 Response regulator receiver domain; Region: Response_reg; pfam00072 557722003900 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722003901 active site 557722003902 phosphorylation site [posttranslational modification] 557722003903 intermolecular recognition site; other site 557722003904 dimerization interface [polypeptide binding]; other site 557722003905 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722003906 metal binding site [ion binding]; metal-binding site 557722003907 active site 557722003908 I-site; other site 557722003909 peptide chain release factor 2; Provisional; Region: PRK08787 557722003910 RF-1 domain; Region: RF-1; cl02875 557722003911 RF-1 domain; Region: RF-1; cl02875 557722003912 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 557722003913 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 557722003914 dimer interface [polypeptide binding]; other site 557722003915 putative anticodon binding site; other site 557722003916 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 557722003917 motif 1; other site 557722003918 active site 557722003919 motif 2; other site 557722003920 motif 3; other site 557722003921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3226 557722003922 Domain of unknown function (DUF1704); Region: DUF1704; cl06858 557722003923 conserved hypothetical protein; Region: QEGLA; TIGR02421 557722003924 Mitochondrial biogenesis AIM24; Region: AIM24; cl00884 557722003925 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722003926 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722003927 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722003928 Macro domain, Appr-1'-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 557722003929 putative ADP-ribose binding site [chemical binding]; other site 557722003930 putative active site [active] 557722003931 hypothetical protein; Validated; Region: PRK09039 557722003932 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722003933 ligand binding site [chemical binding]; other site 557722003934 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 557722003935 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557722003936 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722003937 metal-binding site [ion binding] 557722003938 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722003939 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722003940 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 557722003941 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 557722003942 DNA binding residues [nucleotide binding] 557722003943 dimer interface [polypeptide binding]; other site 557722003944 putative metal binding site [ion binding]; other site 557722003945 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 557722003946 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 557722003947 adenylate kinase; Reviewed; Region: adk; PRK00279 557722003948 Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for...; Region: ADK; cd01428 557722003949 AMP-binding site [chemical binding]; other site 557722003950 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 557722003951 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 557722003952 Protein of unknown function DUF72; Region: DUF72; cl00777 557722003953 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 557722003954 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 557722003955 tetramer interface [polypeptide binding]; other site 557722003956 active site 557722003957 Mg2+/Mn2+ binding site [ion binding]; other site 557722003958 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 557722003959 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722003960 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 557722003961 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722003962 Helix-turn-helix domains; Region: HTH; cl00088 557722003963 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 557722003964 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722003965 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722003966 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722003967 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 557722003968 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 557722003969 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 557722003970 Glycerol-3-phosphate O-acyltransferase [Lipid metabolism]; Region: PlsB; COG2937 557722003971 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 557722003972 putative acyl-acceptor binding pocket; other site 557722003973 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 557722003974 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722003975 Walker A/P-loop; other site 557722003976 ATP binding site [chemical binding]; other site 557722003977 Q-loop/lid; other site 557722003978 ABC transporter signature motif; other site 557722003979 Walker B; other site 557722003980 D-loop; other site 557722003981 H-loop/switch region; other site 557722003982 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722003983 ABC-type uncharacterized transport system involved in gliding motility, auxiliary component [Cell motility and secretion]; Region: GldG; COG3225 557722003984 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 557722003985 Fe-S metabolism associated domain; Region: SufE; cl00951 557722003986 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 557722003987 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 557722003988 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722003989 catalytic residue [active] 557722003990 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Region: DapD_gpp; TIGR03536 557722003991 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 557722003992 putative trimer interface [polypeptide binding]; other site 557722003993 putative CoA binding site [chemical binding]; other site 557722003994 LysE type translocator; Region: LysE; cl00565 557722003995 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 557722003996 ArsC family; Region: ArsC; pfam03960 557722003997 putative catalytic residues [active] 557722003998 LES prophage 3 557722003999 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722004000 Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They belong to the superfamily...; Region: INT_Lambda_C; cd00800 557722004001 dimer interface [polypeptide binding]; other site 557722004002 Int/Topo IB signature motif; other site 557722004003 active site 557722004004 Excisionase-like protein; Region: Exc; pfam07825 557722004005 Duplication 2a 557722004006 PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a...; Region: PLA2_like; cl05417 557722004007 primary metal binding site; other site 557722004008 TIR domain; Region: TIR_2; cl15770 557722004009 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004010 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722004011 DNA binding residues [nucleotide binding] 557722004012 dimerization interface [polypeptide binding]; other site 557722004013 ParB-like nuclease domain; Region: ParBc; cl02129 557722004014 KorB domain; Region: KorB; pfam08535 557722004015 Protein of unknown function (DUF1654); Region: DUF1654; pfam07867 557722004016 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722004017 Catalytic site [active] 557722004018 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 557722004019 Phage antirepressor protein KilAC domain; Region: ANT; cl01462 557722004020 Helix-turn-helix domains; Region: HTH; cl00088 557722004021 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 557722004022 Phage antitermination protein Q; Region: Phage_antitermQ; pfam06530 557722004023 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 557722004024 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722004025 YcfA-like protein; Region: YcfA; cl00752 557722004026 Phage holin family (Lysis protein S); Region: Phage_holin_3; cl04938 557722004027 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722004028 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 557722004029 Caudovirales tail fibre assembly protein; Region: Caudo_TAP; cl05448 557722004030 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 557722004031 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 557722004032 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 557722004033 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 557722004034 oligomer interface [polypeptide binding]; other site 557722004035 active site residues [active] 557722004036 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 557722004037 Duplication 1b 557722004038 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 557722004039 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 557722004040 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557722004041 Mu-like prophage protein [General function prediction only]; Region: COG3941 557722004042 tape measure domain; Region: tape_meas_nterm; TIGR02675 557722004043 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 557722004044 Flagellin N-methylase; Region: FliB; cl00497 557722004045 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557722004046 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 557722004047 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722004048 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722004049 homodimer interface [polypeptide binding]; other site 557722004050 catalytic residue [active] 557722004051 PII uridylyl-transferase; Provisional; Region: glnD; PRK00275 557722004052 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557722004053 metal binding triad; other site 557722004054 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557722004055 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722004056 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 557722004057 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 557722004058 methionine aminopeptidase; Provisional; Region: PRK08671 557722004059 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 557722004060 active site 557722004061 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of...; Region: RPS2; cd01425 557722004062 rRNA interaction site [nucleotide binding]; other site 557722004063 S8 interaction site; other site 557722004064 putative laminin-1 binding site; other site 557722004065 elongation factor Ts; Provisional; Region: tsf; PRK09377 557722004066 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 557722004067 Elongation factor TS; Region: EF_TS; pfam00889 557722004068 Elongation factor TS; Region: EF_TS; pfam00889 557722004069 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 557722004070 putative nucleotide binding site [chemical binding]; other site 557722004071 uridine monophosphate binding site [chemical binding]; other site 557722004072 homohexameric interface [polypeptide binding]; other site 557722004073 ribosome recycling factor; Reviewed; Region: frr; PRK00083 557722004074 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 557722004075 hinge region; other site 557722004076 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 557722004077 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 557722004078 catalytic residue [active] 557722004079 putative FPP diphosphate binding site; other site 557722004080 putative FPP binding hydrophobic cleft; other site 557722004081 dimer interface [polypeptide binding]; other site 557722004082 putative IPP diphosphate binding site; other site 557722004083 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 557722004084 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 557722004085 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 557722004086 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 557722004087 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 557722004088 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 557722004089 zinc metallopeptidase RseP; Provisional; Region: PRK10779 557722004090 active site 557722004091 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 557722004092 protein binding site [polypeptide binding]; other site 557722004093 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 557722004094 protein binding site [polypeptide binding]; other site 557722004095 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 557722004096 putative substrate binding region [chemical binding]; other site 557722004097 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 557722004098 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722004099 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722004100 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722004101 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722004102 Surface antigen; Region: Bac_surface_Ag; cl03097 557722004103 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 557722004104 periplasmic chaperone; Provisional; Region: PRK10780 557722004105 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 557722004106 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 557722004107 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 557722004108 trimer interface [polypeptide binding]; other site 557722004109 active site 557722004110 UDP-GlcNAc binding site [chemical binding]; other site 557722004111 lipid binding site [chemical binding]; lipid-binding site 557722004112 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 557722004113 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 557722004114 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 557722004115 active site 557722004116 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 557722004117 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 557722004118 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 557722004119 RNA/DNA hybrid binding site [nucleotide binding]; other site 557722004120 active site 557722004121 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 557722004122 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 557722004123 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 557722004124 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 557722004125 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 557722004126 generic binding surface II; other site 557722004127 generic binding surface I; other site 557722004128 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722004129 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 557722004130 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 557722004131 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 557722004132 Ligand Binding Site [chemical binding]; other site 557722004133 TilS substrate binding domain; Region: TilS; pfam09179 557722004134 B3/4 domain; Region: B3_4; cl11458 557722004135 CTP synthetase; Validated; Region: pyrG; PRK05380 557722004136 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 557722004137 Catalytic site [active] 557722004138 active site 557722004139 UTP binding site [chemical binding]; other site 557722004140 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 557722004141 active site 557722004142 putative oxyanion hole; other site 557722004143 catalytic triad [active] 557722004144 NeuB family; Region: NeuB; cl00496 557722004145 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557722004146 enolase; Provisional; Region: eno; PRK00077 557722004147 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 557722004148 dimer interface [polypeptide binding]; other site 557722004149 metal binding site [ion binding]; metal-binding site 557722004150 substrate binding pocket [chemical binding]; other site 557722004151 Septum formation initiator; Region: DivIC; cl11433 557722004152 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 557722004153 substrate binding site [chemical binding]; other site 557722004154 dimer interface [polypeptide binding]; other site 557722004155 YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system...; Region: YedF; cd03422 557722004156 CPxP motif; other site 557722004157 putative inner membrane protein; Provisional; Region: PRK11099 557722004158 Sulphur transport; Region: Sulf_transp; cl01018 557722004159 transcriptional regulator; Provisional; Region: PRK10632 557722004160 Helix-turn-helix domains; Region: HTH; cl00088 557722004161 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like_1; cd08470 557722004162 putative effector binding pocket; other site 557722004163 putative dimerization interface [polypeptide binding]; other site 557722004164 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 557722004165 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 557722004166 substrate binding site [chemical binding]; other site 557722004167 catalytic Zn binding site [ion binding]; other site 557722004168 NAD binding site [chemical binding]; other site 557722004169 structural Zn binding site [ion binding]; other site 557722004170 dimer interface [polypeptide binding]; other site 557722004171 Predicted esterase [General function prediction only]; Region: COG0627 557722004172 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722004173 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 557722004174 homotrimer interaction site [polypeptide binding]; other site 557722004175 zinc binding site [ion binding]; other site 557722004176 CDP-binding sites; other site 557722004177 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 557722004178 PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_EcTruD; cd02575 557722004179 Permutation of conserved domain; other site 557722004180 active site 557722004181 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 557722004182 Survival protein SurE; Region: SurE; cl00448 557722004183 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 557722004184 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722004185 S-adenosylmethionine binding site [chemical binding]; other site 557722004186 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 557722004187 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722004188 putative peptidoglycan binding site; other site 557722004189 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 557722004190 RNA polymerase sigma factor RpoS; Validated; Region: PRK05657 557722004191 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557722004192 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722004193 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557722004194 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722004195 DNA binding residues [nucleotide binding] 557722004196 Ferredoxin [Energy production and conversion]; Region: COG1146 557722004197 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 557722004198 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 557722004199 MutS domain I; Region: MutS_I; pfam01624 557722004200 MutS domain II; Region: MutS_II; pfam05188 557722004201 MutS family domain IV; Region: MutS_IV; pfam05190 557722004202 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 557722004203 Walker A/P-loop; other site 557722004204 ATP binding site [chemical binding]; other site 557722004205 Q-loop/lid; other site 557722004206 ABC transporter signature motif; other site 557722004207 Walker B; other site 557722004208 D-loop; other site 557722004209 H-loop/switch region; other site 557722004210 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 557722004211 Competence-damaged protein; Region: CinA; cl00666 557722004212 recombinase A; Provisional; Region: recA; PRK09354 557722004213 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 557722004214 hexamer interface [polypeptide binding]; other site 557722004215 Walker A motif; other site 557722004216 ATP binding site [chemical binding]; other site 557722004217 Walker B motif; other site 557722004218 RecX family; Region: RecX; cl00936 557722004219 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 557722004220 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 557722004221 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722004222 Beta-Casp domain; Region: Beta-Casp; cl12567 557722004223 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 557722004224 Phosphoketolase [Carbohydrate transport and metabolism]; Region: COG3957 557722004225 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 557722004226 TPP-binding site [chemical binding]; other site 557722004227 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; Region: XFP; pfam03894 557722004228 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 557722004229 Domain of unknown function (DUF4146); Region: DUF4146; pfam13652 557722004230 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557722004231 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722004232 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 557722004233 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722004234 dimer interface [polypeptide binding]; other site 557722004235 conserved gate region; other site 557722004236 putative PBP binding loops; other site 557722004237 ABC-ATPase subunit interface; other site 557722004238 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 557722004239 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722004240 dimer interface [polypeptide binding]; other site 557722004241 conserved gate region; other site 557722004242 putative PBP binding loops; other site 557722004243 ABC-ATPase subunit interface; other site 557722004244 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557722004245 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722004246 Walker A/P-loop; other site 557722004247 ATP binding site [chemical binding]; other site 557722004248 Q-loop/lid; other site 557722004249 ABC transporter signature motif; other site 557722004250 Walker B; other site 557722004251 D-loop; other site 557722004252 H-loop/switch region; other site 557722004253 TOBE domain; Region: TOBE_2; cl01440 557722004254 DTW domain; Region: DTW; cl01221 557722004255 EamA-like transporter family; Region: EamA; cl01037 557722004256 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722004257 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722004258 active site 557722004259 phosphorylation site [posttranslational modification] 557722004260 intermolecular recognition site; other site 557722004261 dimerization interface [polypeptide binding]; other site 557722004262 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722004263 DNA binding residues [nucleotide binding] 557722004264 dimerization interface [polypeptide binding]; other site 557722004265 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 557722004266 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 557722004267 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 557722004268 active site 557722004269 FMN binding site [chemical binding]; other site 557722004270 substrate binding site [chemical binding]; other site 557722004271 3Fe-4S cluster binding site [ion binding]; other site 557722004272 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 557722004273 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 557722004274 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 557722004275 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722004276 DNA binding residues [nucleotide binding] 557722004277 dimerization interface [polypeptide binding]; other site 557722004278 Pseudomonas sp. MCI3434 R-amidase and related proteins (putative class 13 nitrilases); Region: R-amidase_like; cd07576 557722004279 putative active site [active] 557722004280 catalytic triad [active] 557722004281 putative dimer interface [polypeptide binding]; other site 557722004282 amino acid transporter; Region: 2A0306; TIGR00909 557722004283 Spore germination protein; Region: Spore_permease; cl15802 557722004284 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722004285 Helix-turn-helix domains; Region: HTH; cl00088 557722004286 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like_2; cd08448 557722004287 putative dimerization interface [polypeptide binding]; other site 557722004288 putative substrate binding pocket [chemical binding]; other site 557722004289 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722004290 isovaleryl CoA dehydrogenase; Provisional; Region: PRK11561 557722004291 active site 557722004292 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 557722004293 CoA-transferase family III; Region: CoA_transf_3; pfam02515 557722004294 enoyl-CoA hydratase; Provisional; Region: PRK08138 557722004295 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722004296 substrate binding site [chemical binding]; other site 557722004297 oxyanion hole (OAH) forming residues; other site 557722004298 trimer interface [polypeptide binding]; other site 557722004299 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 557722004300 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004301 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722004302 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722004303 acetyl-CoA acetyltransferase; Provisional; Region: PRK08131 557722004304 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722004305 dimer interface [polypeptide binding]; other site 557722004306 active site 557722004307 outer membrane porin, OprD family; Region: OprD; pfam03573 557722004308 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 557722004309 Helix-turn-helix domains; Region: HTH; cl00088 557722004310 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 557722004311 putative dimerization interface [polypeptide binding]; other site 557722004312 short chain dehydrogenase; Validated; Region: PRK05855 557722004313 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 557722004314 GlpM protein; Region: GlpM; cl01212 557722004315 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 557722004316 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 557722004317 Helix-turn-helix domains; Region: HTH; cl00088 557722004318 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722004319 glycerol kinase; Provisional; Region: glpK; PRK00047 557722004320 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 557722004321 N- and C-terminal domain interface [polypeptide binding]; other site 557722004322 active site 557722004323 MgATP binding site [chemical binding]; other site 557722004324 catalytic site [active] 557722004325 metal binding site [ion binding]; metal-binding site 557722004326 glycerol binding site [chemical binding]; other site 557722004327 homotetramer interface [polypeptide binding]; other site 557722004328 homodimer interface [polypeptide binding]; other site 557722004329 FBP binding site [chemical binding]; other site 557722004330 protein IIAGlc interface [polypeptide binding]; other site 557722004331 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 557722004332 amphipathic channel; other site 557722004333 Asn-Pro-Ala signature motifs; other site 557722004334 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 557722004335 putative deacylase active site [active] 557722004336 glycerol kinase; Region: glycerol_kin; TIGR01311 557722004337 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 557722004338 N- and C-terminal domain interface [polypeptide binding]; other site 557722004339 active site 557722004340 MgATP binding site [chemical binding]; other site 557722004341 catalytic site [active] 557722004342 metal binding site [ion binding]; metal-binding site 557722004343 glycerol binding site [chemical binding]; other site 557722004344 homotetramer interface [polypeptide binding]; other site 557722004345 homodimer interface [polypeptide binding]; other site 557722004346 FBP binding site [chemical binding]; other site 557722004347 protein IIAGlc interface [polypeptide binding]; other site 557722004348 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 557722004349 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722004350 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557722004351 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 557722004352 Helix-turn-helix domains; Region: HTH; cl00088 557722004353 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 557722004354 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722004355 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 557722004356 putative substrate translocation pore; other site 557722004357 Cupin domain; Region: Cupin_2; cl09118 557722004358 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722004359 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722004360 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 557722004361 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722004362 tetrameric interface [polypeptide binding]; other site 557722004363 NAD binding site [chemical binding]; other site 557722004364 catalytic residues [active] 557722004365 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004366 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 557722004367 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 557722004368 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 557722004369 AMP-binding enzyme; Region: AMP-binding; cl15778 557722004370 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722004371 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 557722004372 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 557722004373 putative NAD(P) binding site [chemical binding]; other site 557722004374 dimer interface [polypeptide binding]; other site 557722004375 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722004376 Helix-turn-helix domains; Region: HTH; cl00088 557722004377 transcriptional activator TtdR; Provisional; Region: PRK09801 557722004378 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722004379 putative effector binding pocket; other site 557722004380 dimerization interface [polypeptide binding]; other site 557722004381 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557722004382 active site 557722004383 DNA-binding transcriptional regulator FruR; Provisional; Region: PRK11303 557722004384 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557722004385 DNA binding site [nucleotide binding] 557722004386 domain linker motif; other site 557722004387 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 557722004388 dimerization interface [polypeptide binding]; other site 557722004389 ligand binding site [chemical binding]; other site 557722004390 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional; Region: PRK11109 557722004391 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 557722004392 active site 557722004393 phosphorylation site [posttranslational modification] 557722004394 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cl00163 557722004395 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 557722004396 dimerization domain swap beta strand [polypeptide binding]; other site 557722004397 regulatory protein interface [polypeptide binding]; other site 557722004398 active site 557722004399 regulatory phosphorylation site [posttranslational modification]; other site 557722004400 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 557722004401 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 557722004402 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 557722004403 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722004404 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 557722004405 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 557722004406 putative substrate binding site [chemical binding]; other site 557722004407 putative ATP binding site [chemical binding]; other site 557722004408 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 557722004409 P-loop; other site 557722004410 active site 557722004411 phosphorylation site [posttranslational modification] 557722004412 PTS system fructose-specific transporter subunits IIBC; Provisional; Region: PRK10712 557722004413 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 557722004414 P-loop; other site 557722004415 active site 557722004416 phosphorylation site [posttranslational modification] 557722004417 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 557722004418 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 557722004419 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004420 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 557722004421 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004422 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722004423 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722004424 4-amino-4-deoxy-L-arabinose transferase; Provisional; Region: arnT; PRK13279 557722004425 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 557722004426 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 557722004427 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 557722004428 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 557722004429 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated; Region: PRK08125 557722004430 active site 557722004431 substrate binding site [chemical binding]; other site 557722004432 cosubstrate binding site; other site 557722004433 catalytic site [active] 557722004434 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 557722004435 active site 557722004436 hexamer interface [polypeptide binding]; other site 557722004437 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 557722004438 NAD binding site [chemical binding]; other site 557722004439 substrate binding site [chemical binding]; other site 557722004440 active site 557722004441 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 557722004442 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 557722004443 Ligand binding site; other site 557722004444 Putative Catalytic site; other site 557722004445 DXD motif; other site 557722004446 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 557722004447 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 557722004448 inhibitor-cofactor binding pocket; inhibition site 557722004449 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722004450 catalytic residue [active] 557722004451 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 557722004452 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 557722004453 Substrate binding site; other site 557722004454 Cupin domain; Region: Cupin_2; cl09118 557722004455 Alginate O-acetyl transferase AlgF; Region: AlgF; pfam11182 557722004456 MBOAT, membrane-bound O-acyltransferase family; Region: MBOAT; cl00738 557722004457 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cd00244 557722004458 active site 557722004459 Right handed beta helix region; Region: Beta_helix; pfam13229 557722004460 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 557722004461 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 557722004462 cellulose synthase subunit BcsC; Provisional; Region: PRK11447 557722004463 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722004464 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722004465 Sel1 repeat; Region: Sel1; cl02723 557722004466 Sel1 repeat; Region: Sel1; cl02723 557722004467 PilZ domain; Region: PilZ; cl01260 557722004468 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004469 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557722004470 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722004471 active site 557722004472 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 557722004473 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004474 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 557722004475 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004476 Protein of unknown function (DUF328); Region: DUF328; cl01143 557722004477 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557722004478 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 557722004479 Walker A/P-loop; other site 557722004480 ATP binding site [chemical binding]; other site 557722004481 Q-loop/lid; other site 557722004482 ABC transporter signature motif; other site 557722004483 Walker B; other site 557722004484 D-loop; other site 557722004485 H-loop/switch region; other site 557722004486 TOBE domain; Region: TOBE_2; cl01440 557722004487 ornithine carbamoyltransferase; Provisional; Region: PRK00779 557722004488 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557722004489 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004490 Peptidase S8 family domain in Autotransporter serine proteases; Region: Peptidases_S8_Autotransporter_serine_protease_like; cd04848 557722004491 putative active site [active] 557722004492 catalytic triad [active] 557722004493 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; cl15373 557722004494 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 557722004495 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722004496 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 557722004497 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to...; Region: MopB_1; cd02762 557722004498 putative [Fe4-S4] binding site [ion binding]; other site 557722004499 putative molybdopterin cofactor binding site [chemical binding]; other site 557722004500 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_1; cd02782 557722004501 putative molybdopterin cofactor binding site; other site 557722004502 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 557722004503 putative GSH binding site [chemical binding]; other site 557722004504 catalytic residues [active] 557722004505 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722004506 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 557722004507 Ferritin-like domain; Region: Ferritin; pfam00210 557722004508 heme binding site [chemical binding]; other site 557722004509 ferroxidase pore; other site 557722004510 ferroxidase diiron center [ion binding]; other site 557722004511 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557722004512 peroxidase; Provisional; Region: PRK15000 557722004513 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 557722004514 dimer interface [polypeptide binding]; other site 557722004515 decamer (pentamer of dimers) interface [polypeptide binding]; other site 557722004516 catalytic triad [active] 557722004517 peroxidatic and resolving cysteines [active] 557722004518 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 557722004519 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 557722004520 dimer interface [polypeptide binding]; other site 557722004521 putative active site [active] 557722004522 putative substrate binding site [chemical binding]; other site 557722004523 catalytic site [active] 557722004524 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 557722004525 active site 557722004526 substrate binding pocket [chemical binding]; other site 557722004527 dimer interface [polypeptide binding]; other site 557722004528 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 557722004529 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722004530 ligand binding site [chemical binding]; other site 557722004531 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 557722004532 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 557722004533 ANP binding site [chemical binding]; other site 557722004534 Substrate Binding Site II [chemical binding]; other site 557722004535 Substrate Binding Site I [chemical binding]; other site 557722004536 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722004537 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 557722004538 dimer interface [polypeptide binding]; other site 557722004539 active site 557722004540 metal binding site [ion binding]; metal-binding site 557722004541 glutathione binding site [chemical binding]; other site 557722004542 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722004543 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004544 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004545 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 557722004546 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722004547 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722004548 metal-binding site [ion binding] 557722004549 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 557722004550 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 557722004551 tetramer interface [polypeptide binding]; other site 557722004552 active site 557722004553 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 557722004554 Adenylosuccinate lyase [Nucleotide transport and metabolism]; Region: PurB; COG0015 557722004555 tetramer interface [polypeptide binding]; other site 557722004556 active site 557722004557 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722004558 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722004559 S-adenosylmethionine binding site [chemical binding]; other site 557722004560 endonuclease III; Provisional; Region: PRK10702 557722004561 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557722004562 minor groove reading motif; other site 557722004563 helix-hairpin-helix signature motif; other site 557722004564 substrate binding pocket [chemical binding]; other site 557722004565 active site 557722004566 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 557722004567 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557722004568 FMN-binding domain; Region: FMN_bind; cl01081 557722004569 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 557722004570 electron transport complex protein RnfC; Provisional; Region: PRK05035 557722004571 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 557722004572 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 557722004573 SLBB domain; Region: SLBB; pfam10531 557722004574 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 557722004575 electron transport complex protein RnfB; Provisional; Region: PRK05113 557722004576 Putative Fe-S cluster; Region: FeS; pfam04060 557722004577 4Fe-4S binding domain; Region: Fer4; cl02805 557722004578 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557722004579 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 557722004580 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 557722004581 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 557722004582 active site 557722004583 HIGH motif; other site 557722004584 KMSKS motif; other site 557722004585 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 557722004586 tRNA binding surface [nucleotide binding]; other site 557722004587 anticodon binding site; other site 557722004588 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 557722004589 putative tRNA-binding site [nucleotide binding]; other site 557722004590 dimer interface [polypeptide binding]; other site 557722004591 antiporter inner membrane protein; Provisional; Region: PRK11670 557722004592 Domain of unknown function DUF59; Region: DUF59; cl00941 557722004593 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 557722004594 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 557722004595 trimer interface [polypeptide binding]; other site 557722004596 active site 557722004597 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722004598 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 557722004599 This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the...; Region: GT1_Gtf_like; cd03784 557722004600 homodimer interface [polypeptide binding]; other site 557722004601 active site 557722004602 TDP-binding site; other site 557722004603 acceptor substrate-binding pocket; other site 557722004604 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 557722004605 Autoinducer binding domain; Region: Autoind_bind; pfam03472 557722004606 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722004607 DNA binding residues [nucleotide binding] 557722004608 dimerization interface [polypeptide binding]; other site 557722004609 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722004610 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 557722004611 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722004612 substrate binding pocket [chemical binding]; other site 557722004613 membrane-bound complex binding site; other site 557722004614 hinge residues; other site 557722004615 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557722004616 Predicted permeases [General function prediction only]; Region: RarD; COG2962 557722004617 EamA-like transporter family; Region: EamA; cl01037 557722004618 NlpC/P60 family; Region: NLPC_P60; cl11438 557722004619 malate dehydrogenase; Provisional; Region: PRK13529 557722004620 Malic enzyme, N-terminal domain; Region: malic; pfam00390 557722004621 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 557722004622 NAD(P) binding site [chemical binding]; other site 557722004623 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_31; cd04690 557722004624 nudix motif; other site 557722004625 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 557722004626 folate binding site [chemical binding]; other site 557722004627 NADP+ binding site [chemical binding]; other site 557722004628 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722004629 benzoate transport; Region: 2A0115; TIGR00895 557722004630 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722004631 putative substrate translocation pore; other site 557722004632 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722004633 helicase 45; Provisional; Region: PTZ00424 557722004634 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 557722004635 ATP binding site [chemical binding]; other site 557722004636 Mg++ binding site [ion binding]; other site 557722004637 motif III; other site 557722004638 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722004639 nucleotide binding region [chemical binding]; other site 557722004640 ATP-binding site [chemical binding]; other site 557722004641 Transmembrane secretion effector; Region: MFS_3; pfam05977 557722004642 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722004643 putative substrate translocation pore; other site 557722004644 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; cl03005 557722004645 LES prophage 4 557722004646 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 557722004647 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722004648 non-specific DNA binding site [nucleotide binding]; other site 557722004649 salt bridge; other site 557722004650 sequence-specific DNA binding site [nucleotide binding]; other site 557722004651 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722004652 Catalytic site [active] 557722004653 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722004654 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 557722004655 Integrase core domain; Region: rve; cl01316 557722004656 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 557722004657 AAA domain; Region: AAA_22; pfam13401 557722004658 Bacteriophage Mu Gam like protein; Region: Phage_Mu_Gam; cl01825 557722004659 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 557722004660 Mor transcription activator family; Region: Mor; cl02360 557722004661 virion protein; Provisional; Region: V; PHA02564 557722004662 Protein of unknown function (DUF1804); Region: DUF1804; pfam08822 557722004663 Helix-turn-helix domains; Region: HTH; cl00088 557722004664 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 557722004665 Protein of unknown function (DUF935); Region: DUF935; pfam06074 557722004666 Mu-like prophage protein gp29 [Function unknown]; Region: COG4383 557722004667 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 557722004668 Mu-like prophage I protein [General function prediction only]; Region: COG4388 557722004669 Mu-like prophage I protein; Region: Mu-like_Pro; pfam10123 557722004670 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 557722004671 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 557722004672 Mu-like prophage major head subunit gpT; Region: Mu-like_gpT; cl01826 557722004673 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 557722004674 Phage-related minor tail protein [Function unknown]; Region: COG5281 557722004675 phage tail tape measure protein, lambda family; Region: tape_meas_lam_C; TIGR01541 557722004676 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 557722004677 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 557722004678 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 557722004679 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 557722004680 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 557722004681 Putative phage tail protein; Region: Phage-tail_3; pfam13550 557722004682 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 557722004683 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 557722004684 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 557722004685 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 557722004686 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722004687 dimer interface [polypeptide binding]; other site 557722004688 phosphorylation site [posttranslational modification] 557722004689 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722004690 ATP binding site [chemical binding]; other site 557722004691 Mg2+ binding site [ion binding]; other site 557722004692 G-X-G motif; other site 557722004693 Response regulator receiver domain; Region: Response_reg; pfam00072 557722004694 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722004695 active site 557722004696 phosphorylation site [posttranslational modification] 557722004697 intermolecular recognition site; other site 557722004698 dimerization interface [polypeptide binding]; other site 557722004699 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 557722004700 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 557722004701 putative oligomer interface [polypeptide binding]; other site 557722004702 putative active site [active] 557722004703 metal binding site [ion binding]; metal-binding site 557722004704 GNAT-family acetyltransferase TIGR03103; Region: trio_acet_GNAT 557722004705 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722004706 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722004707 asparagine synthase family amidotransferase; Region: trio_amidotrans; TIGR03104 557722004708 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557722004709 active site 557722004710 dimer interface [polypeptide binding]; other site 557722004711 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557722004712 Ligand Binding Site [chemical binding]; other site 557722004713 Molecular Tunnel; other site 557722004714 Helix-turn-helix domains; Region: HTH; cl00088 557722004715 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557722004716 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557722004717 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 557722004718 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722004719 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 557722004720 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 557722004721 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 557722004722 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 557722004723 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722004724 dimer interface [polypeptide binding]; other site 557722004725 active site 557722004726 Protein of unknown function, DUF480; Region: DUF480; cl01209 557722004727 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004728 Predicted dehydrogenase [General function prediction only]; Region: COG0579 557722004729 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 557722004730 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 557722004731 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 557722004732 dimer interface [polypeptide binding]; other site 557722004733 decamer (pentamer of dimers) interface [polypeptide binding]; other site 557722004734 catalytic triad [active] 557722004735 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722004736 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722004737 substrate binding pocket [chemical binding]; other site 557722004738 membrane-bound complex binding site; other site 557722004739 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722004740 dimer interface [polypeptide binding]; other site 557722004741 conserved gate region; other site 557722004742 putative PBP binding loops; other site 557722004743 ABC-ATPase subunit interface; other site 557722004744 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 557722004745 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557722004746 Walker A/P-loop; other site 557722004747 ATP binding site [chemical binding]; other site 557722004748 Q-loop/lid; other site 557722004749 ABC transporter signature motif; other site 557722004750 Walker B; other site 557722004751 D-loop; other site 557722004752 H-loop/switch region; other site 557722004753 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722004754 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722004755 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722004756 substrate binding pocket [chemical binding]; other site 557722004757 membrane-bound complex binding site; other site 557722004758 hinge residues; other site 557722004759 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 557722004760 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 557722004761 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 557722004762 active site 557722004763 dimer interface [polypeptide binding]; other site 557722004764 non-prolyl cis peptide bond; other site 557722004765 insertion regions; other site 557722004766 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722004767 dimer interface [polypeptide binding]; other site 557722004768 conserved gate region; other site 557722004769 putative PBP binding loops; other site 557722004770 ABC-ATPase subunit interface; other site 557722004771 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 557722004772 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722004773 Walker A/P-loop; other site 557722004774 ATP binding site [chemical binding]; other site 557722004775 Q-loop/lid; other site 557722004776 ABC transporter signature motif; other site 557722004777 Walker B; other site 557722004778 D-loop; other site 557722004779 H-loop/switch region; other site 557722004780 TOBE domain; Region: TOBE_2; cl01440 557722004781 HopJ type III effector protein; Region: HopJ; pfam08888 557722004782 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 557722004783 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 557722004784 homooctamer interface [polypeptide binding]; other site 557722004785 active site 557722004786 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 557722004787 homodecamer interface [polypeptide binding]; other site 557722004788 GTP cyclohydrolase I; Provisional; Region: PLN03044 557722004789 active site 557722004790 putative catalytic site residues [active] 557722004791 zinc binding site [ion binding]; other site 557722004792 GTP-CH-I/GFRP interaction surface; other site 557722004793 dihydromonapterin reductase; Provisional; Region: PRK06483 557722004794 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004795 NAD(P) binding site [chemical binding]; other site 557722004796 active site 557722004797 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722004798 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722004799 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 557722004800 Helix-turn-helix domains; Region: HTH; cl00088 557722004801 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 557722004802 putative dimerization interface [polypeptide binding]; other site 557722004803 LrgA family; Region: LrgA; cl00608 557722004804 LrgB-like family; Region: LrgB; cl00596 557722004805 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 557722004806 intersubunit interface [polypeptide binding]; other site 557722004807 active site 557722004808 Zn2+ binding site [ion binding]; other site 557722004809 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722004810 (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Region: hydroxyacyl-CoA-like_DH_SDR_c-like; cd05353 557722004811 homodimer interface [polypeptide binding]; other site 557722004812 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 557722004813 NAD binding site [chemical binding]; other site 557722004814 active site 557722004815 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 557722004816 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722004817 substrate binding site [chemical binding]; other site 557722004818 oxyanion hole (OAH) forming residues; other site 557722004819 trimer interface [polypeptide binding]; other site 557722004820 Cupin domain; Region: Cupin_2; cl09118 557722004821 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722004822 FAD dependent oxidoreductase; Region: DAO; pfam01266 557722004823 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722004824 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722004825 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722004826 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 557722004827 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 557722004828 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722004829 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722004830 DNA binding residues [nucleotide binding] 557722004831 dimerization interface [polypeptide binding]; other site 557722004832 Uncharacterized conserved protein [Function unknown]; Region: COG2912 557722004833 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 557722004834 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 557722004835 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 557722004836 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 557722004837 NAD binding site [chemical binding]; other site 557722004838 Phe binding site; other site 557722004839 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 557722004840 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 557722004841 TPP-binding site [chemical binding]; other site 557722004842 tetramer interface [polypeptide binding]; other site 557722004843 heterodimer interface [polypeptide binding]; other site 557722004844 phosphorylation loop region [posttranslational modification] 557722004845 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 557722004846 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 557722004847 alpha subunit interface [polypeptide binding]; other site 557722004848 TPP binding site [chemical binding]; other site 557722004849 heterodimer interface [polypeptide binding]; other site 557722004850 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557722004851 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 557722004852 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722004853 E3 interaction surface; other site 557722004854 lipoyl attachment site [posttranslational modification]; other site 557722004855 e3 binding domain; Region: E3_binding; pfam02817 557722004856 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 557722004857 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 557722004858 YebG protein; Region: YebG; cl01217 557722004859 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 557722004860 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; Region: Sig70_bacteroi1; TIGR02985 557722004861 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722004862 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722004863 DNA binding residues [nucleotide binding] 557722004864 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722004865 FecR protein; Region: FecR; pfam04773 557722004866 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722004867 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 557722004868 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722004869 N-terminal plug; other site 557722004870 ligand-binding site [chemical binding]; other site 557722004871 Heme-binding protein A (HasA); Region: HasA; pfam06438 557722004872 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 557722004873 This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export...; Region: ABCC_Protease_Secretion; cd03246 557722004874 Walker A/P-loop; other site 557722004875 ATP binding site [chemical binding]; other site 557722004876 Q-loop/lid; other site 557722004877 ABC transporter signature motif; other site 557722004878 Walker B; other site 557722004879 D-loop; other site 557722004880 H-loop/switch region; other site 557722004881 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 557722004882 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004883 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004884 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 557722004885 Phosphate-starvation-inducible E; Region: PsiE; cl01264 557722004886 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004887 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 557722004888 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722004889 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 557722004890 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722004891 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 557722004892 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722004893 Protein of unknown function (DUF1375); Region: DUF1375; cl11456 557722004894 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 557722004895 Helix-turn-helix domains; Region: HTH; cl00088 557722004896 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 557722004897 putative dimerization interface [polypeptide binding]; other site 557722004898 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 557722004899 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 557722004900 FAD binding pocket [chemical binding]; other site 557722004901 FAD binding motif [chemical binding]; other site 557722004902 phosphate binding motif [ion binding]; other site 557722004903 beta-alpha-beta structure motif; other site 557722004904 NAD binding pocket [chemical binding]; other site 557722004905 NosL; Region: NosL; cl01769 557722004906 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722004907 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 557722004908 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 557722004909 nitrous-oxide reductase; Validated; Region: PRK02888 557722004910 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722004911 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 557722004912 FMN-binding domain; Region: FMN_bind; cl01081 557722004913 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 557722004914 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557722004915 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 557722004916 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722004917 active site 557722004918 metal binding site [ion binding]; metal-binding site 557722004919 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722004920 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 557722004921 homodimer interaction site [polypeptide binding]; other site 557722004922 cofactor binding site; other site 557722004923 RhlG and related beta-ketoacyl reductases, classical (c) SDRs; Region: RhlG_SDR_c; cd08942 557722004924 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 557722004925 NADP binding site [chemical binding]; other site 557722004926 active site 557722004927 Protein of Unknown function (DUF2784); Region: DUF2784; pfam10861 557722004928 Arc-like DNA binding domain; Region: Arc; pfam03869 557722004929 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 557722004930 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 557722004931 Walker A/P-loop; other site 557722004932 ATP binding site [chemical binding]; other site 557722004933 Q-loop/lid; other site 557722004934 ABC transporter signature motif; other site 557722004935 Walker B; other site 557722004936 D-loop; other site 557722004937 H-loop/switch region; other site 557722004938 NMT1-like family; Region: NMT1_2; cl15260 557722004939 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 557722004940 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 557722004941 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722004942 dimer interface [polypeptide binding]; other site 557722004943 conserved gate region; other site 557722004944 ABC-ATPase subunit interface; other site 557722004945 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722004946 DNA-binding site [nucleotide binding]; DNA binding site 557722004947 UTRA domain; Region: UTRA; cl01230 557722004948 Phosphonate metabolism protein PhnG; Region: PhnG; cl01454 557722004949 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; cl01455 557722004950 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; cl01456 557722004951 Phosphonate metabolism protein PhnJ; Region: PhnJ; cl01457 557722004952 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 557722004953 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722004954 Walker A/P-loop; other site 557722004955 ATP binding site [chemical binding]; other site 557722004956 Q-loop/lid; other site 557722004957 ABC transporter signature motif; other site 557722004958 Walker B; other site 557722004959 D-loop; other site 557722004960 H-loop/switch region; other site 557722004961 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722004962 ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PhnL; COG4778 557722004963 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722004964 Walker A/P-loop; other site 557722004965 ATP binding site [chemical binding]; other site 557722004966 Q-loop/lid; other site 557722004967 ABC transporter signature motif; other site 557722004968 Walker B; other site 557722004969 D-loop; other site 557722004970 H-loop/switch region; other site 557722004971 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 557722004972 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 557722004973 active site 557722004974 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722004975 AAA domain; Region: AAA_18; pfam13238 557722004976 active site 557722004977 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722004978 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 557722004979 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722004980 Coenzyme A binding pocket [chemical binding]; other site 557722004981 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722004982 RHS Repeat; Region: RHS_repeat; cl11982 557722004983 RHS Repeat; Region: RHS_repeat; cl11982 557722004984 RHS Repeat; Region: RHS_repeat; cl11982 557722004985 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722004986 RHS Repeat; Region: RHS_repeat; cl11982 557722004987 RHS Repeat; Region: RHS_repeat; cl11982 557722004988 RHS Repeat; Region: RHS_repeat; cl11982 557722004989 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 557722004990 HTH-like domain; Region: HTH_21; pfam13276 557722004991 Integrase core domain; Region: rve; cl01316 557722004992 DDE domain; Region: DDE_Tnp_IS240; pfam13610 557722004993 Integrase core domain; Region: rve_3; cl15866 557722004994 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 557722004995 Predicted amidohydrolase [General function prediction only]; Region: COG0388 557722004996 multimer interface [polypeptide binding]; other site 557722004997 active site 557722004998 catalytic triad [active] 557722004999 dimer interface [polypeptide binding]; other site 557722005000 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722005001 Walker A motif; other site 557722005002 ATP binding site [chemical binding]; other site 557722005003 Walker B motif; other site 557722005004 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722005005 Periplasmic binding domain of amidase (AmiC) that belongs to the type I periplasmic binding fold protein family; Region: PBP1_AmiC; cd06357 557722005006 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 557722005007 ligand binding site [chemical binding]; other site 557722005008 regulator interaction site; other site 557722005009 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 557722005010 ANTAR domain; Region: ANTAR; cl04297 557722005011 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 557722005012 Fucose-binding lectin II (PA-IIL); Region: PA-IIL; pfam07472 557722005013 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 557722005014 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722005015 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722005016 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 557722005017 Predicted membrane protein [Function unknown]; Region: COG4129 557722005018 EamA-like transporter family; Region: EamA; cl01037 557722005019 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 557722005020 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 557722005021 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722005022 catalytic residue [active] 557722005023 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722005024 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722005025 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722005026 putative substrate translocation pore; other site 557722005027 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722005028 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 557722005029 Flagellar regulator YcgR; Region: YcgR; pfam07317 557722005030 PilZ domain; Region: PilZ; cl01260 557722005031 FlgN protein; Region: FlgN; cl09176 557722005032 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 557722005033 SAF domain; Region: SAF; cl00555 557722005034 SAF-like; Region: SAF_2; pfam13144 557722005035 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 557722005036 Response regulator receiver domain; Region: Response_reg; pfam00072 557722005037 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005038 active site 557722005039 phosphorylation site [posttranslational modification] 557722005040 intermolecular recognition site; other site 557722005041 dimerization interface [polypeptide binding]; other site 557722005042 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 557722005043 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 557722005044 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005045 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 557722005046 anti sigma factor interaction site; other site 557722005047 regulatory phosphorylation site [posttranslational modification]; other site 557722005048 Response regulator receiver domain; Region: Response_reg; pfam00072 557722005049 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005050 active site 557722005051 phosphorylation site [posttranslational modification] 557722005052 intermolecular recognition site; other site 557722005053 dimerization interface [polypeptide binding]; other site 557722005054 Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]; Region: RsbU; COG2208 557722005055 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 557722005056 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722005057 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 557722005058 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722005059 ATP binding site [chemical binding]; other site 557722005060 putative Mg++ binding site [ion binding]; other site 557722005061 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722005062 nucleotide binding region [chemical binding]; other site 557722005063 ATP-binding site [chemical binding]; other site 557722005064 RQC domain; Region: RQC; cl09632 557722005065 HRDC domain; Region: HRDC; cl02578 557722005066 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 557722005067 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722005068 metal binding site [ion binding]; metal-binding site 557722005069 active site 557722005070 I-site; other site 557722005071 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 557722005072 transcriptional regulator SlyA; Provisional; Region: PRK03573 557722005073 Helix-turn-helix domains; Region: HTH; cl00088 557722005074 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 557722005075 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 557722005076 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 557722005077 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 557722005078 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 557722005079 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 557722005080 active site 557722005081 nucleophile elbow; other site 557722005082 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 557722005083 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722005084 Surface antigen; Region: Bac_surface_Ag; cl03097 557722005085 Rdx family; Region: Rdx; cl01407 557722005086 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 557722005087 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 557722005088 NADP binding site [chemical binding]; other site 557722005089 homopentamer interface [polypeptide binding]; other site 557722005090 substrate binding site [chemical binding]; other site 557722005091 active site 557722005092 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722005093 putative substrate translocation pore; other site 557722005094 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722005095 S-adenosylmethionine binding site [chemical binding]; other site 557722005096 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 557722005097 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 557722005098 dimer interface [polypeptide binding]; other site 557722005099 active site 557722005100 CoA binding pocket [chemical binding]; other site 557722005101 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722005102 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 557722005103 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005104 short chain dehydrogenase; Provisional; Region: PRK06914 557722005105 NAD(P) binding site [chemical binding]; other site 557722005106 active site 557722005107 Condensation domain; Region: Condensation; pfam00668 557722005108 Wax ester synthase-like Acyl-CoA acyltransferase domain; Region: WES_acyltransf; pfam03007 557722005109 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 557722005110 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005111 peptide synthase; Provisional; Region: PRK12316 557722005112 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722005113 AMP-binding enzyme; Region: AMP-binding; cl15778 557722005114 AMP-binding enzyme; Region: AMP-binding; cl15778 557722005115 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722005116 peptide synthase; Provisional; Region: PRK12467 557722005117 AMP-binding enzyme; Region: AMP-binding; cl15778 557722005118 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722005119 ATP-dependent Clp protease proteolytic subunit; Reviewed; Region: PRK12553 557722005120 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 557722005121 oligomer interface [polypeptide binding]; other site 557722005122 active site residues [active] 557722005123 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 557722005124 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 557722005125 short chain dehydrogenase; Validated; Region: PRK05855 557722005126 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005127 classical (c) SDRs; Region: SDR_c; cd05233 557722005128 NAD(P) binding site [chemical binding]; other site 557722005129 active site 557722005130 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 557722005131 active site 557722005132 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg2; cd04778 557722005133 DNA binding residues [nucleotide binding] 557722005134 putative dimer interface [polypeptide binding]; other site 557722005135 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722005136 Helix-turn-helix domains; Region: HTH; cl00088 557722005137 The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; Region: PBP2_ToxR; cd08465 557722005138 putative substrate binding pocket [chemical binding]; other site 557722005139 putative dimerization interface [polypeptide binding]; other site 557722005140 Protein of unknown function, DUF606; Region: DUF606; cl01273 557722005141 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 557722005142 Phosphoesterase family; Region: Phosphoesterase; cl15450 557722005143 Domain of unknown function (DUF756); Region: DUF756; pfam05506 557722005144 Domain of unknown function (DUF756); Region: DUF756; pfam05506 557722005145 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 557722005146 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722005147 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 557722005148 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722005149 Walker A/P-loop; other site 557722005150 ATP binding site [chemical binding]; other site 557722005151 Q-loop/lid; other site 557722005152 ABC transporter signature motif; other site 557722005153 Walker B; other site 557722005154 D-loop; other site 557722005155 H-loop/switch region; other site 557722005156 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 557722005157 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl15306 557722005158 substrate binding pocket [chemical binding]; other site 557722005159 membrane-bound complex binding site; other site 557722005160 hinge residues; other site 557722005161 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557722005162 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005163 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 557722005164 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 557722005165 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 557722005166 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722005167 metal binding site [ion binding]; metal-binding site 557722005168 active site 557722005169 I-site; other site 557722005170 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722005171 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 557722005172 Sulfatase; Region: Sulfatase; cl10460 557722005173 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722005174 Ligand Binding Site [chemical binding]; other site 557722005175 ATP-dependent helicase HepA; Validated; Region: PRK04914 557722005176 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722005177 ATP binding site [chemical binding]; other site 557722005178 putative Mg++ binding site [ion binding]; other site 557722005179 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722005180 nucleotide binding region [chemical binding]; other site 557722005181 ATP-binding site [chemical binding]; other site 557722005182 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722005183 Fusaric acid resistance protein family; Region: FUSC; pfam04632 557722005184 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 557722005185 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 557722005186 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722005187 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722005188 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557722005189 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 557722005190 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 557722005191 dimer interaction site [polypeptide binding]; other site 557722005192 substrate-binding tunnel; other site 557722005193 active site 557722005194 catalytic site [active] 557722005195 substrate binding site [chemical binding]; other site 557722005196 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 557722005197 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005198 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005199 long-chain-fatty-acid--CoA ligase; Provisional; Region: PRK12492 557722005200 AMP-binding enzyme; Region: AMP-binding; cl15778 557722005201 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722005202 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 557722005203 AMP-binding enzyme; Region: AMP-binding; cl15778 557722005204 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722005205 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 557722005206 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722005207 ATP binding site [chemical binding]; other site 557722005208 putative Mg++ binding site [ion binding]; other site 557722005209 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722005210 nucleotide binding region [chemical binding]; other site 557722005211 ATP-binding site [chemical binding]; other site 557722005212 Helicase associated domain (HA2); Region: HA2; cl04503 557722005213 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 557722005214 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 557722005215 alkaline phosphatase; Provisional; Region: PRK10518 557722005216 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 557722005217 active site 557722005218 dimer interface [polypeptide binding]; other site 557722005219 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 557722005220 HIT family signature motif; other site 557722005221 catalytic residue [active] 557722005222 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722005223 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722005224 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722005225 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 557722005226 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 557722005227 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 557722005228 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 557722005229 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 557722005230 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 557722005231 Isochorismatase family; Region: Isochorismatase; pfam00857 557722005232 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 557722005233 catalytic triad [active] 557722005234 conserved cis-peptide bond; other site 557722005235 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 557722005236 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 557722005237 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 557722005238 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 557722005239 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 557722005240 active site 557722005241 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 557722005242 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722005243 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722005244 Protein of unknown function (DUF692); Region: DUF692; cl01263 557722005245 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 557722005246 DoxX; Region: DoxX; cl00976 557722005247 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 557722005248 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 557722005249 short chain dehydrogenase; Provisional; Region: PRK05650 557722005250 classical (c) SDRs; Region: SDR_c; cd05233 557722005251 NAD(P) binding site [chemical binding]; other site 557722005252 active site 557722005253 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 557722005254 Lhr-like helicases [General function prediction only]; Region: Lhr; COG1201 557722005255 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722005256 ATP binding site [chemical binding]; other site 557722005257 putative Mg++ binding site [ion binding]; other site 557722005258 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722005259 nucleotide binding region [chemical binding]; other site 557722005260 ATP-binding site [chemical binding]; other site 557722005261 DEAD/H associated; Region: DEAD_assoc; pfam08494 557722005262 Sodium:solute symporter family; Region: SSF; cl00456 557722005263 PAS fold; Region: PAS_7; pfam12860 557722005264 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 557722005265 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722005266 dimer interface [polypeptide binding]; other site 557722005267 phosphorylation site [posttranslational modification] 557722005268 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722005269 ATP binding site [chemical binding]; other site 557722005270 Mg2+ binding site [ion binding]; other site 557722005271 G-X-G motif; other site 557722005272 Response regulator receiver domain; Region: Response_reg; pfam00072 557722005273 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005274 active site 557722005275 phosphorylation site [posttranslational modification] 557722005276 intermolecular recognition site; other site 557722005277 dimerization interface [polypeptide binding]; other site 557722005278 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557722005279 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722005280 Cupin domain; Region: Cupin_2; cl09118 557722005281 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722005282 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005283 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005284 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 557722005285 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722005286 N-terminal plug; other site 557722005287 ligand-binding site [chemical binding]; other site 557722005288 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722005289 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722005290 putative substrate translocation pore; other site 557722005291 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 557722005292 putative acyl-acceptor binding pocket; other site 557722005293 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557722005294 DNA-binding site [nucleotide binding]; DNA binding site 557722005295 RNA-binding motif; other site 557722005296 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722005297 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 557722005298 Membrane transport protein; Region: Mem_trans; cl09117 557722005299 Putative exonuclease, RdgC; Region: RdgC; cl01122 557722005300 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 557722005301 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 557722005302 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722005303 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 557722005304 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722005305 substrate binding pocket [chemical binding]; other site 557722005306 membrane-bound complex binding site; other site 557722005307 hinge residues; other site 557722005308 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722005309 non-specific DNA binding site [nucleotide binding]; other site 557722005310 salt bridge; other site 557722005311 sequence-specific DNA binding site [nucleotide binding]; other site 557722005312 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722005313 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 557722005314 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722005315 metal binding site [ion binding]; metal-binding site 557722005316 active site 557722005317 I-site; other site 557722005318 carboxy-terminal protease; Provisional; Region: PRK11186 557722005319 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 557722005320 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 557722005321 protein binding site [polypeptide binding]; other site 557722005322 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 557722005323 Catalytic dyad [active] 557722005324 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 557722005325 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 557722005326 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 557722005327 NAD(P) binding site [chemical binding]; other site 557722005328 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722005329 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557722005330 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722005331 Walker A/P-loop; other site 557722005332 ATP binding site [chemical binding]; other site 557722005333 Q-loop/lid; other site 557722005334 ABC transporter signature motif; other site 557722005335 Walker B; other site 557722005336 D-loop; other site 557722005337 H-loop/switch region; other site 557722005338 TOBE domain; Region: TOBE_2; cl01440 557722005339 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722005340 dimer interface [polypeptide binding]; other site 557722005341 conserved gate region; other site 557722005342 putative PBP binding loops; other site 557722005343 ABC-ATPase subunit interface; other site 557722005344 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 557722005345 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722005346 dimer interface [polypeptide binding]; other site 557722005347 conserved gate region; other site 557722005348 putative PBP binding loops; other site 557722005349 ABC-ATPase subunit interface; other site 557722005350 Uncharacterized proteins of the AP superfamily [General function prediction only]; Region: COG1524 557722005351 Sulfatase; Region: Sulfatase; cl10460 557722005352 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722005353 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 557722005354 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722005355 DNA-binding site [nucleotide binding]; DNA binding site 557722005356 transcriptional regulator protein; Region: phnR; TIGR03337 557722005357 UTRA domain; Region: UTRA; cl01230 557722005358 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722005359 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557722005360 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 557722005361 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 557722005362 active site 557722005363 metal binding site [ion binding]; metal-binding site 557722005364 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 557722005365 active site 557722005366 Septum formation topological specificity factor MinE; Region: MinE; cl00538 557722005367 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 557722005368 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 557722005369 Switch I; other site 557722005370 Switch II; other site 557722005371 septum formation inhibitor; Reviewed; Region: minC; PRK00339 557722005372 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 557722005373 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 557722005374 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 557722005375 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 557722005376 putative acyl-acceptor binding pocket; other site 557722005377 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 557722005378 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 557722005379 active site 557722005380 nucleophile elbow; other site 557722005381 Pirin-related protein [General function prediction only]; Region: COG1741 557722005382 Cupin domain; Region: Cupin_2; cl09118 557722005383 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 557722005384 VacJ like lipoprotein; Region: VacJ; cl01073 557722005385 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 557722005386 NMT1-like family; Region: NMT1_2; cl15260 557722005387 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 557722005388 Protein of unknown function, DUF485; Region: DUF485; cl01231 557722005389 Sodium:solute symporter family; Region: SSF; cl00456 557722005390 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557722005391 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 557722005392 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722005393 ligand binding site [chemical binding]; other site 557722005394 flexible hinge region; other site 557722005395 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP...; Region: CBS_pair_CAP-ED_DUF294_assoc_bac; cd04589 557722005396 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557722005397 metal binding triad; other site 557722005398 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 557722005399 active site 557722005400 substrate binding site [chemical binding]; other site 557722005401 catalytic site [active] 557722005402 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 557722005403 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722005404 Protein of unknown function, DUF482; Region: DUF482; pfam04339 557722005405 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 557722005406 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 557722005407 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722005408 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 557722005409 Walker A/P-loop; other site 557722005410 ATP binding site [chemical binding]; other site 557722005411 Q-loop/lid; other site 557722005412 ABC transporter signature motif; other site 557722005413 Walker B; other site 557722005414 D-loop; other site 557722005415 H-loop/switch region; other site 557722005416 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 557722005417 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 557722005418 substrate binding site [chemical binding]; other site 557722005419 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005420 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722005421 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005422 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722005423 Helix-turn-helix domains; Region: HTH; cl00088 557722005424 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722005425 dimerization interface [polypeptide binding]; other site 557722005426 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722005427 EamA-like transporter family; Region: EamA; cl01037 557722005428 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 557722005429 dimer interface [polypeptide binding]; other site 557722005430 putative tRNA-binding site [nucleotide binding]; other site 557722005431 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005432 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722005433 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005434 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557722005435 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 557722005436 putative active site [active] 557722005437 putative metal binding site [ion binding]; other site 557722005438 MASE2 domain; Region: MASE2; pfam05230 557722005439 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 557722005440 cyclase homology domain; Region: CHD; cd07302 557722005441 nucleotidyl binding site; other site 557722005442 metal binding site [ion binding]; metal-binding site 557722005443 dimer interface [polypeptide binding]; other site 557722005444 Protein of unknown function (DUF962); Region: DUF962; cl01879 557722005445 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722005446 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722005447 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005448 Protein of unknown function (DUF330); Region: DUF330; cl01135 557722005449 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 557722005450 mce related protein; Region: MCE; pfam02470 557722005451 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 557722005452 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722005453 Walker A/P-loop; other site 557722005454 ATP binding site [chemical binding]; other site 557722005455 Q-loop/lid; other site 557722005456 ABC transporter signature motif; other site 557722005457 Walker B; other site 557722005458 D-loop; other site 557722005459 H-loop/switch region; other site 557722005460 Permease; Region: Permease; cl00510 557722005461 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 557722005462 Cation transport protein; Region: TrkH; cl10514 557722005463 Flagellin N-methylase; Region: FliB; cl00497 557722005464 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 557722005465 putative FMN binding site [chemical binding]; other site 557722005466 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722005467 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722005468 ATP binding site [chemical binding]; other site 557722005469 Mg2+ binding site [ion binding]; other site 557722005470 G-X-G motif; other site 557722005471 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 557722005472 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722005473 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005474 active site 557722005475 phosphorylation site [posttranslational modification] 557722005476 intermolecular recognition site; other site 557722005477 dimerization interface [polypeptide binding]; other site 557722005478 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722005479 DNA binding site [nucleotide binding] 557722005480 YCII-related domain; Region: YCII; cl00999 557722005481 Intracellular septation protein A; Region: IspA; cl01098 557722005482 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 557722005483 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 557722005484 ScpA/B protein; Region: ScpA_ScpB; cl00598 557722005485 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 557722005486 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 557722005487 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005488 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 557722005489 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 557722005490 Dehydratase family; Region: ILVD_EDD; cl00340 557722005491 6-phosphogluconate dehydratase; Region: edd; TIGR01196 557722005492 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 557722005493 glucokinase, proteobacterial type; Region: glk; TIGR00749 557722005494 osmolarity response regulator; Provisional; Region: ompR; PRK09468 557722005495 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005496 active site 557722005497 phosphorylation site [posttranslational modification] 557722005498 intermolecular recognition site; other site 557722005499 dimerization interface [polypeptide binding]; other site 557722005500 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722005501 DNA binding site [nucleotide binding] 557722005502 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 557722005503 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722005504 ATP binding site [chemical binding]; other site 557722005505 Mg2+ binding site [ion binding]; other site 557722005506 G-X-G motif; other site 557722005507 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722005508 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722005509 dimer interface [polypeptide binding]; other site 557722005510 conserved gate region; other site 557722005511 putative PBP binding loops; other site 557722005512 ABC-ATPase subunit interface; other site 557722005513 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 557722005514 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722005515 dimer interface [polypeptide binding]; other site 557722005516 conserved gate region; other site 557722005517 putative PBP binding loops; other site 557722005518 ABC-ATPase subunit interface; other site 557722005519 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 557722005520 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 557722005521 Walker A/P-loop; other site 557722005522 ATP binding site [chemical binding]; other site 557722005523 Q-loop/lid; other site 557722005524 ABC transporter signature motif; other site 557722005525 Walker B; other site 557722005526 D-loop; other site 557722005527 H-loop/switch region; other site 557722005528 TOBE domain; Region: TOBE_2; cl01440 557722005529 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 557722005530 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 557722005531 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 557722005532 active site 557722005533 phosphate binding residues; other site 557722005534 catalytic residues [active] 557722005535 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 557722005536 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 557722005537 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 557722005538 putative active site [active] 557722005539 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 557722005540 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 557722005541 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 557722005542 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 557722005543 putative active site [active] 557722005544 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 557722005545 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 557722005546 active site 557722005547 intersubunit interface [polypeptide binding]; other site 557722005548 catalytic residue [active] 557722005549 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_23; cd04682 557722005550 nudix motif; other site 557722005551 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 557722005552 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722005553 RNA binding surface [nucleotide binding]; other site 557722005554 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 557722005555 probable active site [active] 557722005556 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722005557 metal binding site [ion binding]; metal-binding site 557722005558 active site 557722005559 I-site; other site 557722005560 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 557722005561 Arginase family; Region: Arginase; cl00306 557722005562 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722005563 Helix-turn-helix domains; Region: HTH; cl00088 557722005564 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722005565 short chain dehydrogenase; Provisional; Region: PRK08703 557722005566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005567 NAD(P) binding site [chemical binding]; other site 557722005568 active site 557722005569 phosphoglycolate phosphatase; Provisional; Region: PRK13222 557722005570 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722005571 motif II; other site 557722005572 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 557722005573 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722005574 S-adenosylmethionine binding site [chemical binding]; other site 557722005575 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 557722005576 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 557722005577 active site 557722005578 putative substrate binding pocket [chemical binding]; other site 557722005579 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 557722005580 Initiation factor 2 subunit family; Region: IF-2B; pfam01008 557722005581 DNA gyrase subunit A; Validated; Region: PRK05560 557722005582 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 557722005583 CAP-like domain; other site 557722005584 active site 557722005585 primary dimer interface [polypeptide binding]; other site 557722005586 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557722005587 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557722005588 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557722005589 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557722005590 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557722005591 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557722005592 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 557722005593 homodimer interface [polypeptide binding]; other site 557722005594 substrate-cofactor binding pocket; other site 557722005595 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722005596 catalytic residue [active] 557722005597 Chorismate mutase type II; Region: CM_2; cl00693 557722005598 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 557722005599 Prephenate dehydratase; Region: PDT; pfam00800 557722005600 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 557722005601 putative L-Phe binding site [chemical binding]; other site 557722005602 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 557722005603 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722005604 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722005605 homodimer interface [polypeptide binding]; other site 557722005606 catalytic residue [active] 557722005607 bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK14806 557722005608 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005609 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 557722005610 hinge; other site 557722005611 active site 557722005612 cytidylate kinase; Provisional; Region: cmk; PRK00023 557722005613 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 557722005614 CMP-binding site; other site 557722005615 The sites determining sugar specificity; other site 557722005616 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 557722005617 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 557722005618 RNA binding site [nucleotide binding]; other site 557722005619 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 557722005620 RNA binding site [nucleotide binding]; other site 557722005621 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 557722005622 RNA binding site [nucleotide binding]; other site 557722005623 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557722005624 RNA binding site [nucleotide binding]; other site 557722005625 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557722005626 RNA binding site [nucleotide binding]; other site 557722005627 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 557722005628 RNA binding site [nucleotide binding]; other site 557722005629 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 557722005630 IHF dimer interface [polypeptide binding]; other site 557722005631 IHF - DNA interface [nucleotide binding]; other site 557722005632 Chain length determinant protein [Cell envelope biogenesis, outer membrane]; Region: WzzB; COG3765 557722005633 Chain length determinant protein; Region: Wzz; cl15801 557722005634 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 557722005635 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 557722005636 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005637 Vi polysaccharide biosynthesis protein TviC; Provisional; Region: PRK15181 557722005638 UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs; Region: UDP_AE_SDR_e; cd05256 557722005639 NAD binding site [chemical binding]; other site 557722005640 substrate binding site [chemical binding]; other site 557722005641 homodimer interface [polypeptide binding]; other site 557722005642 active site 557722005643 MatE; Region: MatE; cl10513 557722005644 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722005645 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 557722005646 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557722005647 active site 557722005648 dimer interface [polypeptide binding]; other site 557722005649 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557722005650 Ligand Binding Site [chemical binding]; other site 557722005651 Molecular Tunnel; other site 557722005652 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 557722005653 This family is most closely related to the GT1 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis; Region: GT1_WbnK_like; cd03807 557722005654 putative ADP-binding pocket [chemical binding]; other site 557722005655 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 557722005656 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722005657 putative ADP-binding pocket [chemical binding]; other site 557722005658 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005659 active site 557722005660 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 557722005661 Mg++ binding site [ion binding]; other site 557722005662 putative catalytic motif [active] 557722005663 putative substrate binding site [chemical binding]; other site 557722005664 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 557722005665 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005666 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 557722005667 NAD(P) binding site [chemical binding]; other site 557722005668 homodimer interface [polypeptide binding]; other site 557722005669 substrate binding site [chemical binding]; other site 557722005670 active site 557722005671 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 557722005672 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 557722005673 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722005674 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722005675 homodimer interface [polypeptide binding]; other site 557722005676 catalytic residue [active] 557722005677 excinuclease ABC subunit B; Provisional; Region: PRK05298 557722005678 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722005679 ATP binding site [chemical binding]; other site 557722005680 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722005681 nucleotide binding region [chemical binding]; other site 557722005682 ATP-binding site [chemical binding]; other site 557722005683 Ultra-violet resistance protein B; Region: UvrB; pfam12344 557722005684 UvrB/uvrC motif; Region: UVR; pfam02151 557722005685 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722005686 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557722005687 putative substrate translocation pore; other site 557722005688 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 557722005689 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722005690 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722005691 LysR family transcriptional regulator; Provisional; Region: PRK14997 557722005692 Helix-turn-helix domains; Region: HTH; cl00088 557722005693 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722005694 putative effector binding pocket; other site 557722005695 dimerization interface [polypeptide binding]; other site 557722005696 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 557722005697 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 557722005698 HIGH motif; other site 557722005699 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 557722005700 active site 557722005701 KMSKS motif; other site 557722005702 Helix-turn-helix domains; Region: HTH; cl00088 557722005703 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 557722005704 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005705 Entner-Doudoroff aldolase; Region: eda; TIGR01182 557722005706 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 557722005707 active site 557722005708 intersubunit interface [polypeptide binding]; other site 557722005709 catalytic residue [active] 557722005710 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722005711 active site 557722005712 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 557722005713 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 557722005714 FMN binding site [chemical binding]; other site 557722005715 active site 557722005716 catalytic residues [active] 557722005717 substrate binding site [chemical binding]; other site 557722005718 short chain dehydrogenase; Provisional; Region: PRK06123 557722005719 classical (c) SDRs; Region: SDR_c; cd05233 557722005720 NAD(P) binding site [chemical binding]; other site 557722005721 active site 557722005722 BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins; Region: BLMT_like; cd08350 557722005723 dimer interface [polypeptide binding]; other site 557722005724 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722005725 ligand binding site [chemical binding]; other site 557722005726 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722005727 Coenzyme A binding pocket [chemical binding]; other site 557722005728 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 557722005729 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 557722005730 putative dimer interface [polypeptide binding]; other site 557722005731 SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases; Region: XynE_like; cd01830 557722005732 active site 557722005733 catalytic triad [active] 557722005734 oxyanion hole [active] 557722005735 transcriptional regulator; Provisional; Region: PRK10632 557722005736 Helix-turn-helix domains; Region: HTH; cl00088 557722005737 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_10; cd08480 557722005738 putative effector binding pocket; other site 557722005739 putative dimerization interface [polypeptide binding]; other site 557722005740 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 557722005741 homotrimer interaction site [polypeptide binding]; other site 557722005742 putative active site [active] 557722005743 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722005744 Helix-turn-helix domains; Region: HTH; cl00088 557722005745 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722005746 dimerization interface [polypeptide binding]; other site 557722005747 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 557722005748 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 557722005749 substrate binding site [chemical binding]; other site 557722005750 ligand binding site [chemical binding]; other site 557722005751 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 557722005752 substrate binding site [chemical binding]; other site 557722005753 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 557722005754 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722005755 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 557722005756 tartrate dehydrogenase; Provisional; Region: PRK08194 557722005757 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 557722005758 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005759 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 557722005760 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK05671 557722005761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005762 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 557722005763 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 557722005764 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 557722005765 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 557722005766 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 557722005767 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 557722005768 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 557722005769 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 557722005770 dimerization interface 3.5A [polypeptide binding]; other site 557722005771 active site 557722005772 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 557722005773 active site 557722005774 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 557722005775 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722005776 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 557722005777 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557722005778 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 557722005779 Sporulation related domain; Region: SPOR; cl10051 557722005780 Colicin V production protein; Region: Colicin_V; cl00567 557722005781 amidophosphoribosyltransferase; Provisional; Region: PRK09246 557722005782 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 557722005783 active site 557722005784 tetramer interface [polypeptide binding]; other site 557722005785 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722005786 active site 557722005787 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 557722005788 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 557722005789 homodimer interface [polypeptide binding]; other site 557722005790 substrate-cofactor binding pocket; other site 557722005791 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722005792 catalytic residue [active] 557722005793 oxidoreductase; Validated; Region: PRK05717 557722005794 Clostridium thermocellum A3DFK9-like, a putative carbohydrate or polyalcohol metabolizing SDR, classical (c) SDRs; Region: A3DFK9-like_SDR_c; cd09761 557722005795 NAD binding site [chemical binding]; other site 557722005796 active site 557722005797 homodimer interface [polypeptide binding]; other site 557722005798 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 557722005799 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722005800 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722005801 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722005802 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722005803 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 557722005804 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 557722005805 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 557722005806 Walker A motif; other site 557722005807 ATP binding site [chemical binding]; other site 557722005808 Walker B motif; other site 557722005809 general secretion pathway protein F; Region: GspF; TIGR02120 557722005810 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722005811 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722005812 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 557722005813 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 557722005814 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722005815 general secretion pathway protein I; Region: gspI; TIGR01707 557722005816 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 557722005817 general secretion pathway protein J; Region: gspJ; TIGR01711 557722005818 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 557722005819 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 557722005820 Type II secretory pathway, component PulL [Intracellular trafficking and secretion]; Region: PulL; COG3297 557722005821 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 557722005822 GspL periplasmic domain; Region: GspL_C; cl14909 557722005823 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 557722005824 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722005825 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722005826 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005827 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 557722005828 active site 557722005829 catalytic triad [active] 557722005830 dimer interface [polypeptide binding]; other site 557722005831 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 557722005832 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 557722005833 active site 557722005834 FMN binding site [chemical binding]; other site 557722005835 2,4-decadienoyl-CoA binding site; other site 557722005836 catalytic residue [active] 557722005837 4Fe-4S cluster binding site [ion binding]; other site 557722005838 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 557722005839 Domain of unknown function (DUF1853); Region: DUF1853; cl01545 557722005840 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 557722005841 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 557722005842 Pseudomonas aeruginosa PA3087 and related proteins, metallophosphatase domain; Region: MPP_PA3087; cd07413 557722005843 active site 557722005844 metal binding site [ion binding]; metal-binding site 557722005845 Rhomboid family; Region: Rhomboid; cl11446 557722005846 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 557722005847 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 557722005848 aminopeptidase N; Provisional; Region: pepN; PRK14015 557722005849 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 557722005850 active site 557722005851 Zn binding site [ion binding]; other site 557722005852 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 557722005853 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 557722005854 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 557722005855 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 557722005856 sensor protein BasS/PmrB; Provisional; Region: PRK10755 557722005857 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722005858 dimer interface [polypeptide binding]; other site 557722005859 phosphorylation site [posttranslational modification] 557722005860 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 557722005861 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722005862 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005863 active site 557722005864 phosphorylation site [posttranslational modification] 557722005865 intermolecular recognition site; other site 557722005866 dimerization interface [polypeptide binding]; other site 557722005867 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722005868 DNA binding site [nucleotide binding] 557722005869 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005870 Oxygen tolerance; Region: BatD; pfam13584 557722005871 cysteinyl-tRNA synthetase; Provisional; Region: PRK12418 557722005872 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722005873 metal ion-dependent adhesion site (MIDAS); other site 557722005874 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 557722005875 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722005876 metal ion-dependent adhesion site (MIDAS); other site 557722005877 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 557722005878 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722005879 MoxR-like ATPases [General function prediction only]; Region: COG0714 557722005880 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722005881 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 557722005882 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005883 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557722005884 Helix-turn-helix domains; Region: HTH; cl00088 557722005885 Isochorismatase family; Region: Isochorismatase; pfam00857 557722005886 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 557722005887 catalytic triad [active] 557722005888 conserved cis-peptide bond; other site 557722005889 TM1410 hypothetical-related protein; Region: DUF297; cl00997 557722005890 C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria; Region: CE4_PelA_like_C; cd10922 557722005891 putative active site [active] 557722005892 Tetratricopeptide repeat; Region: TPR_15; pfam13429 557722005893 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 557722005894 GAF domain; Region: GAF_2; pfam13185 557722005895 GAF domain; Region: GAF; cl15785 557722005896 HEAT repeats; Region: HEAT_2; pfam13646 557722005897 tetratricopeptide repeat protein; Provisional; Region: PRK11788 557722005898 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_3; cd03813 557722005899 Predicted membrane protein [Function unknown]; Region: COG4267 557722005900 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722005901 non-specific DNA binding site [nucleotide binding]; other site 557722005902 salt bridge; other site 557722005903 sequence-specific DNA binding site [nucleotide binding]; other site 557722005904 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722005905 non-specific DNA binding site [nucleotide binding]; other site 557722005906 salt bridge; other site 557722005907 sequence-specific DNA binding site [nucleotide binding]; other site 557722005908 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 557722005909 putative active site [active] 557722005910 Zn binding site [ion binding]; other site 557722005911 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005912 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722005913 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722005914 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 557722005915 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 557722005916 quinone interaction residues [chemical binding]; other site 557722005917 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 557722005918 active site 557722005919 catalytic residues [active] 557722005920 FMN binding site [chemical binding]; other site 557722005921 substrate binding site [chemical binding]; other site 557722005922 Ribosome modulation factor; Region: RMF; cl01207 557722005923 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 557722005924 THUMP domain; Region: THUMP; cl12076 557722005925 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722005926 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722005927 S-adenosylmethionine binding site [chemical binding]; other site 557722005928 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 557722005929 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722005930 Protein with unknown function (DUF469); Region: DUF469; cl01237 557722005931 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722005932 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005933 active site 557722005934 phosphorylation site [posttranslational modification] 557722005935 intermolecular recognition site; other site 557722005936 dimerization interface [polypeptide binding]; other site 557722005937 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722005938 DNA binding residues [nucleotide binding] 557722005939 dimerization interface [polypeptide binding]; other site 557722005940 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 557722005941 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722005942 dimer interface [polypeptide binding]; other site 557722005943 phosphorylation site [posttranslational modification] 557722005944 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722005945 ATP binding site [chemical binding]; other site 557722005946 Mg2+ binding site [ion binding]; other site 557722005947 G-X-G motif; other site 557722005948 Response regulator receiver domain; Region: Response_reg; pfam00072 557722005949 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722005950 active site 557722005951 phosphorylation site [posttranslational modification] 557722005952 intermolecular recognition site; other site 557722005953 dimerization interface [polypeptide binding]; other site 557722005954 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722005955 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 557722005956 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722005957 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 557722005958 Protein of unknown function (DUF1469); Region: DUF1469; cl12095 557722005959 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 557722005960 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 557722005961 outer membrane porin, OprD family; Region: OprD; pfam03573 557722005962 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722005963 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557722005964 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722005965 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 557722005966 putative C-terminal domain interface [polypeptide binding]; other site 557722005967 putative GSH binding site (G-site) [chemical binding]; other site 557722005968 putative dimer interface [polypeptide binding]; other site 557722005969 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 557722005970 putative N-terminal domain interface [polypeptide binding]; other site 557722005971 putative dimer interface [polypeptide binding]; other site 557722005972 putative substrate binding pocket (H-site) [chemical binding]; other site 557722005973 putative transcriptional regulator; Provisional; Region: PRK11640 557722005974 Helix-turn-helix domains; Region: HTH; cl00088 557722005975 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722005976 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 557722005977 Cytochrome c; Region: Cytochrom_C; cl11414 557722005978 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 557722005979 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 557722005980 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 557722005981 GTP binding site; other site 557722005982 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 557722005983 MPT binding site; other site 557722005984 trimer interface [polypeptide binding]; other site 557722005985 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 557722005986 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 557722005987 dimer interface [polypeptide binding]; other site 557722005988 putative functional site; other site 557722005989 putative MPT binding site; other site 557722005990 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722005991 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722005992 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722005993 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557722005994 FAD binding domain; Region: FAD_binding_4; pfam01565 557722005995 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 557722005996 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 557722005997 uncharacterized ygcE-like proteins, N-terminal domain; Region: FGGY_ygcE_like; cd07779 557722005998 putative N- and C-terminal domain interface [polypeptide binding]; other site 557722005999 putative active site [active] 557722006000 putative MgATP binding site [chemical binding]; other site 557722006001 catalytic site [active] 557722006002 metal binding site [ion binding]; metal-binding site 557722006003 putative carbohydrate binding site [chemical binding]; other site 557722006004 lipid kinase; Reviewed; Region: PRK13054 557722006005 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 557722006006 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 557722006007 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 557722006008 MOSC domain; Region: MOSC; pfam03473 557722006009 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 557722006010 lytic murein transglycosylase; Provisional; Region: PRK11619 557722006011 lytic murein transglycosylase; Provisional; Region: PRK11619 557722006012 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722006013 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722006014 catalytic residue [active] 557722006015 ABC transporter ATPase component; Reviewed; Region: PRK11147 557722006016 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006017 Walker A/P-loop; other site 557722006018 ATP binding site [chemical binding]; other site 557722006019 Q-loop/lid; other site 557722006020 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722006021 ABC transporter signature motif; other site 557722006022 Walker B; other site 557722006023 ABC transporter; Region: ABC_tran_2; pfam12848 557722006024 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722006025 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722006026 Ligand Binding Site [chemical binding]; other site 557722006027 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 557722006028 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 557722006029 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722006030 substrate binding site [chemical binding]; other site 557722006031 oxyanion hole (OAH) forming residues; other site 557722006032 trimer interface [polypeptide binding]; other site 557722006033 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006034 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722006035 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 557722006036 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722006037 dimer interface [polypeptide binding]; other site 557722006038 active site 557722006039 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 557722006040 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 557722006041 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 557722006042 active site 557722006043 interdomain interaction site; other site 557722006044 putative metal-binding site [ion binding]; other site 557722006045 nucleotide binding site [chemical binding]; other site 557722006046 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 557722006047 domain I; other site 557722006048 DNA binding groove [nucleotide binding] 557722006049 phosphate binding site [ion binding]; other site 557722006050 domain II; other site 557722006051 domain III; other site 557722006052 nucleotide binding site [chemical binding]; other site 557722006053 catalytic site [active] 557722006054 domain IV; other site 557722006055 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557722006056 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557722006057 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 557722006058 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 557722006059 Cell division inhibitor SulA; Region: SulA; cl01880 557722006060 LexA repressor; Validated; Region: PRK00215 557722006061 Helix-turn-helix domains; Region: HTH; cl00088 557722006062 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722006063 Catalytic site [active] 557722006064 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722006065 Helix-turn-helix domains; Region: HTH; cl00088 557722006066 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 557722006067 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 557722006068 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 557722006069 transcription-repair coupling factor; Provisional; Region: PRK10689 557722006070 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 557722006071 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722006072 ATP binding site [chemical binding]; other site 557722006073 putative Mg++ binding site [ion binding]; other site 557722006074 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722006075 nucleotide binding region [chemical binding]; other site 557722006076 ATP-binding site [chemical binding]; other site 557722006077 TRCF domain; Region: TRCF; cl04088 557722006078 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 557722006079 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006080 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 557722006081 aromatic amino acid transporter; Provisional; Region: PRK10238 557722006082 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 557722006083 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722006084 E3 interaction surface; other site 557722006085 lipoyl attachment site [posttranslational modification]; other site 557722006086 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 557722006087 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 557722006088 FMN-binding domain; Region: FMN_bind; cl01081 557722006089 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 557722006090 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557722006091 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557722006092 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 557722006093 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722006094 catalytic loop [active] 557722006095 iron binding site [ion binding]; other site 557722006096 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 557722006097 FAD binding pocket [chemical binding]; other site 557722006098 FAD binding motif [chemical binding]; other site 557722006099 phosphate binding motif [ion binding]; other site 557722006100 beta-alpha-beta structure motif; other site 557722006101 NAD binding pocket [chemical binding]; other site 557722006102 ApbE family; Region: ApbE; cl00643 557722006103 Protein of unknown function (DUF539); Region: DUF539; cl01129 557722006104 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 557722006105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006106 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722006107 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722006108 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 557722006109 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 557722006110 active site 557722006111 catalytic site [active] 557722006112 metal binding site [ion binding]; metal-binding site 557722006113 PilZ domain; Region: PilZ; cl01260 557722006114 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 557722006115 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557722006116 FtsX-like permease family; Region: FtsX; cl15850 557722006117 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 557722006118 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 557722006119 Walker A/P-loop; other site 557722006120 ATP binding site [chemical binding]; other site 557722006121 Q-loop/lid; other site 557722006122 ABC transporter signature motif; other site 557722006123 Walker B; other site 557722006124 D-loop; other site 557722006125 H-loop/switch region; other site 557722006126 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 557722006127 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557722006128 FtsX-like permease family; Region: FtsX; cl15850 557722006129 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 557722006130 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 557722006131 Competence protein; Region: Competence; cl00471 557722006132 Competence protein; Region: Competence; cl00471 557722006133 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722006134 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722006135 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557722006136 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 557722006137 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 557722006138 Trm112p-like protein; Region: Trm112p; cl01066 557722006139 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 557722006140 Ligand binding site; other site 557722006141 oligomer interface; other site 557722006142 Low molecular weight phosphatase family; Region: LMWPc; cd00115 557722006143 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 557722006144 active site 557722006145 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 557722006146 FAD binding domain; Region: FAD_binding_4; pfam01565 557722006147 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 557722006148 ribonuclease E; Reviewed; Region: rne; PRK10811 557722006149 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 557722006150 homodimer interface [polypeptide binding]; other site 557722006151 oligonucleotide binding site [chemical binding]; other site 557722006152 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 557722006153 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722006154 RNA binding surface [nucleotide binding]; other site 557722006155 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 557722006156 active site 557722006157 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 557722006158 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722006159 motif II; other site 557722006160 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 557722006161 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 557722006162 tandem repeat interface [polypeptide binding]; other site 557722006163 oligomer interface [polypeptide binding]; other site 557722006164 active site residues [active] 557722006165 Maf-like protein; Region: Maf; pfam02545 557722006166 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 557722006167 active site 557722006168 dimer interface [polypeptide binding]; other site 557722006169 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 557722006170 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 557722006171 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 557722006172 Acyl transferase domain; Region: Acyl_transf_1; cl08282 557722006173 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 557722006174 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 557722006175 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 557722006176 NAD(P) binding site [chemical binding]; other site 557722006177 homotetramer interface [polypeptide binding]; other site 557722006178 homodimer interface [polypeptide binding]; other site 557722006179 active site 557722006180 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722006181 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 557722006182 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 557722006183 dimer interface [polypeptide binding]; other site 557722006184 active site 557722006185 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 557722006186 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722006187 catalytic residue [active] 557722006188 YceG-like family; Region: YceG; pfam02618 557722006189 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 557722006190 dimerization interface [polypeptide binding]; other site 557722006191 thymidylate kinase; Validated; Region: tmk; PRK00698 557722006192 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 557722006193 TMP-binding site; other site 557722006194 ATP-binding site [chemical binding]; other site 557722006195 DNA polymerase III subunit delta'; Validated; Region: PRK05707 557722006196 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006197 PilZ domain; Region: PilZ; cl01260 557722006198 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557722006199 active site 557722006200 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 557722006201 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722006202 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722006203 catalytic residue [active] 557722006204 Helix-turn-helix domains; Region: HTH; cl00088 557722006205 WHG domain; Region: WHG; pfam13305 557722006206 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722006207 Radical SAM superfamily; Region: Radical_SAM; pfam04055 557722006208 FeS/SAM binding site; other site 557722006209 Protein of unknown function (DUF1285); Region: DUF1285; cl01571 557722006210 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006211 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 557722006212 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 557722006213 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 557722006214 Ligand binding site [chemical binding]; other site 557722006215 Electron transfer flavoprotein domain; Region: ETF; pfam01012 557722006216 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 557722006217 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 557722006218 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 557722006219 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 557722006220 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006221 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 557722006222 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is 'interfacial activation', the process of becoming...; Region: Lipase; cl14883 557722006223 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722006224 nucleophilic elbow; other site 557722006225 catalytic triad; other site 557722006226 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722006227 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 557722006228 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 557722006229 Probable cobalt transporter subunit (CbtA); Region: CbtA; cl02266 557722006230 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 557722006231 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006232 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 557722006233 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 557722006234 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 557722006235 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 557722006236 NeuB family; Region: NeuB; cl00496 557722006237 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557722006238 Mg-chelatase subunit ChlI [Coenzyme metabolism]; Region: ChlI; COG1239 557722006239 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722006240 Walker A motif; other site 557722006241 ATP binding site [chemical binding]; other site 557722006242 Walker B motif; other site 557722006243 arginine finger; other site 557722006244 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722006245 metal ion-dependent adhesion site (MIDAS); other site 557722006246 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722006247 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 557722006248 dimer interface [polypeptide binding]; other site 557722006249 active site 557722006250 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 557722006251 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 557722006252 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cd00538 557722006253 PA/protease or protease-like domain interface [polypeptide binding]; other site 557722006254 M28 Zn-peptidase Streptomyces griseus Aminopeptidase and similar proteins; Region: M28_SGAP_like; cd03876 557722006255 active site 557722006256 metal binding site [ion binding]; metal-binding site 557722006257 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 557722006258 xanthine permease; Region: pbuX; TIGR03173 557722006259 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557722006260 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722006261 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722006262 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557722006263 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722006264 putative substrate translocation pore; other site 557722006265 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 557722006266 FMN binding site [chemical binding]; other site 557722006267 active site 557722006268 substrate binding site [chemical binding]; other site 557722006269 catalytic residue [active] 557722006270 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722006271 Helix-turn-helix domains; Region: HTH; cl00088 557722006272 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722006273 Helix-turn-helix domains; Region: HTH; cl00088 557722006274 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722006275 dimerization interface [polypeptide binding]; other site 557722006276 LysE type translocator; Region: LysE; cl00565 557722006277 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 557722006278 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 557722006279 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 557722006280 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722006281 Walker A/P-loop; other site 557722006282 ATP binding site [chemical binding]; other site 557722006283 Q-loop/lid; other site 557722006284 ABC transporter signature motif; other site 557722006285 Walker B; other site 557722006286 D-loop; other site 557722006287 H-loop/switch region; other site 557722006288 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722006289 dimer interface [polypeptide binding]; other site 557722006290 conserved gate region; other site 557722006291 putative PBP binding loops; other site 557722006292 ABC-ATPase subunit interface; other site 557722006293 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722006294 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722006295 dimer interface [polypeptide binding]; other site 557722006296 conserved gate region; other site 557722006297 putative PBP binding loops; other site 557722006298 ABC-ATPase subunit interface; other site 557722006299 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 557722006300 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722006301 substrate binding pocket [chemical binding]; other site 557722006302 membrane-bound complex binding site; other site 557722006303 hinge residues; other site 557722006304 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 557722006305 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 557722006306 metal binding site [ion binding]; metal-binding site 557722006307 putative dimer interface [polypeptide binding]; other site 557722006308 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 557722006309 Helix-turn-helix domains; Region: HTH; cl00088 557722006310 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722006311 dimerization interface [polypeptide binding]; other site 557722006312 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722006313 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722006314 dimer interface [polypeptide binding]; other site 557722006315 putative CheW interface [polypeptide binding]; other site 557722006316 short chain dehydrogenase; Provisional; Region: PRK12744 557722006317 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006318 NAD(P) binding site [chemical binding]; other site 557722006319 active site 557722006320 Cupin domain; Region: Cupin_2; cl09118 557722006321 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722006322 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722006323 LysE type translocator; Region: LysE; cl00565 557722006324 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722006325 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 557722006326 ABC-ATPase subunit interface; other site 557722006327 dimer interface [polypeptide binding]; other site 557722006328 putative PBP binding regions; other site 557722006329 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 557722006330 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 557722006331 putative ligand binding residues [chemical binding]; other site 557722006332 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 557722006333 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006334 Walker A/P-loop; other site 557722006335 ATP binding site [chemical binding]; other site 557722006336 Q-loop/lid; other site 557722006337 ABC transporter signature motif; other site 557722006338 Walker B; other site 557722006339 H-loop/switch region; other site 557722006340 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722006341 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722006342 N-terminal plug; other site 557722006343 ligand-binding site [chemical binding]; other site 557722006344 Predicted membrane protein [Function unknown]; Region: COG1971 557722006345 Domain of unknown function DUF; Region: DUF204; pfam02659 557722006346 Domain of unknown function DUF; Region: DUF204; pfam02659 557722006347 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 557722006348 CbiD; Region: CbiD; cl00828 557722006349 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722006350 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 557722006351 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722006352 S-adenosylmethionine binding site [chemical binding]; other site 557722006353 precorrin-3B synthase; Region: CobG; TIGR02435 557722006354 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557722006355 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 557722006356 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722006357 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 557722006358 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 557722006359 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 557722006360 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722006361 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 557722006362 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722006363 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722006364 substrate binding pocket [chemical binding]; other site 557722006365 membrane-bound complex binding site; other site 557722006366 hinge residues; other site 557722006367 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 557722006368 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722006369 ligand binding site [chemical binding]; other site 557722006370 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722006371 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722006372 active site 557722006373 phosphorylation site [posttranslational modification] 557722006374 intermolecular recognition site; other site 557722006375 dimerization interface [polypeptide binding]; other site 557722006376 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722006377 DNA binding residues [nucleotide binding] 557722006378 dimerization interface [polypeptide binding]; other site 557722006379 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722006380 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722006381 DNA-binding site [nucleotide binding]; DNA binding site 557722006382 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722006383 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722006384 homodimer interface [polypeptide binding]; other site 557722006385 catalytic residue [active] 557722006386 RNA polymerase sigma factor; Provisional; Region: PRK12513 557722006387 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722006388 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722006389 DNA binding residues [nucleotide binding] 557722006390 long-chain-acyl-CoA synthetase; Validated; Region: PRK08279 557722006391 AMP-binding enzyme; Region: AMP-binding; cl15778 557722006392 short chain dehydrogenase; Provisional; Region: PRK08278 557722006393 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006394 NAD(P) binding site [chemical binding]; other site 557722006395 active site 557722006396 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 557722006397 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722006398 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722006399 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557722006400 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 557722006401 carboxyltransferase (CT) interaction site; other site 557722006402 biotinylation site [posttranslational modification]; other site 557722006403 enoyl-CoA hydratase; Provisional; Region: PRK05995 557722006404 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722006405 substrate binding site [chemical binding]; other site 557722006406 oxyanion hole (OAH) forming residues; other site 557722006407 trimer interface [polypeptide binding]; other site 557722006408 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722006409 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722006410 active site 557722006411 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 557722006412 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722006413 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722006414 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006415 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722006416 NAD(P) binding site [chemical binding]; other site 557722006417 active site 557722006418 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 557722006419 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722006420 Helix-turn-helix domains; Region: HTH; cl00088 557722006421 CAAX protease self-immunity; Region: Abi; cl00558 557722006422 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 557722006423 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 557722006424 two-component VirA-like sensor kinase; Provisional; Region: PRK13837 557722006425 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 557722006426 phosphorylation site [posttranslational modification] 557722006427 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722006428 ATP binding site [chemical binding]; other site 557722006429 Mg2+ binding site [ion binding]; other site 557722006430 G-X-G motif; other site 557722006431 Response regulator receiver domain; Region: Response_reg; pfam00072 557722006432 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722006433 active site 557722006434 phosphorylation site [posttranslational modification] 557722006435 intermolecular recognition site; other site 557722006436 dimerization interface [polypeptide binding]; other site 557722006437 nitrogen regulation protein NR(I); Provisional; Region: glnG; PRK10923 557722006438 Predicted membrane protein [Function unknown]; Region: COG4125 557722006439 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 557722006440 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 557722006441 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722006442 Helix-turn-helix domains; Region: HTH; cl00088 557722006443 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722006444 dimerization interface [polypeptide binding]; other site 557722006445 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 557722006446 transcriptional regulator; Provisional; Region: PRK10632 557722006447 Helix-turn-helix domains; Region: HTH; cl00088 557722006448 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 557722006449 putative effector binding pocket; other site 557722006450 putative dimerization interface [polypeptide binding]; other site 557722006451 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 557722006452 active site 557722006453 dimer interface [polypeptide binding]; other site 557722006454 MoxR-like ATPases [General function prediction only]; Region: COG0714 557722006455 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722006456 Walker A motif; other site 557722006457 ATP binding site [chemical binding]; other site 557722006458 Walker B motif; other site 557722006459 arginine finger; other site 557722006460 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 557722006461 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722006462 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 557722006463 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 557722006464 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 557722006465 CHAD domain; Region: CHAD; cl10506 557722006466 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 557722006467 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 557722006468 active site 557722006469 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557722006470 active site 2 [active] 557722006471 active site 1 [active] 557722006472 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722006473 metal binding site [ion binding]; metal-binding site 557722006474 active site 557722006475 I-site; other site 557722006476 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 557722006477 Terminase small subunit; Region: Terminase_2; cl01513 557722006478 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722006479 dimerization interface [polypeptide binding]; other site 557722006480 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722006481 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722006482 dimer interface [polypeptide binding]; other site 557722006483 putative CheW interface [polypeptide binding]; other site 557722006484 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557722006485 active site 557722006486 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]; Region: COG4623 557722006487 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722006488 substrate binding pocket [chemical binding]; other site 557722006489 membrane-bound complex binding site; other site 557722006490 hinge residues; other site 557722006491 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722006492 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722006493 catalytic residue [active] 557722006494 DoxX; Region: DoxX; cl00976 557722006495 Proteobacterial lipase chaperone protein; Region: Lipase_chap; cl02224 557722006496 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 557722006497 2'-5' RNA ligase; Provisional; Region: PRK15124 557722006498 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 557722006499 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 557722006500 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557722006501 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 557722006502 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 557722006503 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 557722006504 Walker A/P-loop; other site 557722006505 ATP binding site [chemical binding]; other site 557722006506 Q-loop/lid; other site 557722006507 ABC transporter signature motif; other site 557722006508 Walker B; other site 557722006509 D-loop; other site 557722006510 H-loop/switch region; other site 557722006511 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 557722006512 active site 557722006513 catalytic triad [active] 557722006514 oxyanion hole [active] 557722006515 switch loop; other site 557722006516 L,D-transpeptidase; Provisional; Region: PRK10260 557722006517 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 557722006518 Protein of unknown function (DUF3359); Region: DUF3359; pfam11839 557722006519 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 557722006520 elongation factor P; Validated; Region: PRK00529 557722006521 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 557722006522 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 557722006523 RNA binding site [nucleotide binding]; other site 557722006524 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 557722006525 RNA binding site [nucleotide binding]; other site 557722006526 OsmC-like protein; Region: OsmC; cl00767 557722006527 Transcriptional regulators [Transcription]; Region: MarR; COG1846 557722006528 Helix-turn-helix domains; Region: HTH; cl00088 557722006529 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722006530 Helix-turn-helix domains; Region: HTH; cl00088 557722006531 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722006532 putative effector binding pocket; other site 557722006533 dimerization interface [polypeptide binding]; other site 557722006534 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557722006535 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722006536 Helix-turn-helix domains; Region: HTH; cl00088 557722006537 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722006538 dimerization interface [polypeptide binding]; other site 557722006539 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 557722006540 Protein of unknown function (DUF1006); Region: DUF1006; cl15826 557722006541 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 557722006542 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722006543 enoyl-CoA hydratase; Provisional; Region: PRK06563 557722006544 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722006545 substrate binding site [chemical binding]; other site 557722006546 oxyanion hole (OAH) forming residues; other site 557722006547 trimer interface [polypeptide binding]; other site 557722006548 helicase 45; Provisional; Region: PTZ00424 557722006549 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 557722006550 ATP binding site [chemical binding]; other site 557722006551 Mg++ binding site [ion binding]; other site 557722006552 motif III; other site 557722006553 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722006554 nucleotide binding region [chemical binding]; other site 557722006555 ATP-binding site [chemical binding]; other site 557722006556 DbpA RNA binding domain; Region: DbpA; pfam03880 557722006557 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 557722006558 putative active site [active] 557722006559 metal binding site [ion binding]; metal-binding site 557722006560 transcriptional regulator; Provisional; Region: PRK10632 557722006561 Helix-turn-helix domains; Region: HTH; cl00088 557722006562 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722006563 putative effector binding pocket; other site 557722006564 dimerization interface [polypeptide binding]; other site 557722006565 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722006566 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 557722006567 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722006568 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722006569 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557722006570 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722006571 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722006572 Helix-turn-helix domains; Region: HTH; cl00088 557722006573 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_1; cd08460 557722006574 putative substrate binding pocket [chemical binding]; other site 557722006575 putative dimerization interface [polypeptide binding]; other site 557722006576 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722006577 Ligand Binding Site [chemical binding]; other site 557722006578 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722006579 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 557722006580 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 557722006581 putative active site [active] 557722006582 Zn binding site [ion binding]; other site 557722006583 Peptidase family M48; Region: Peptidase_M48; cl12018 557722006584 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 557722006585 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722006586 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722006587 homodimer interface [polypeptide binding]; other site 557722006588 catalytic residue [active] 557722006589 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 557722006590 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 557722006591 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 557722006592 catalytic residues [active] 557722006593 dimer interface [polypeptide binding]; other site 557722006594 Helix-turn-helix domains; Region: HTH; cl00088 557722006595 Transcriptional regulators [Transcription]; Region: MarR; COG1846 557722006596 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 557722006597 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 557722006598 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722006599 ATP binding site [chemical binding]; other site 557722006600 Mg2+ binding site [ion binding]; other site 557722006601 G-X-G motif; other site 557722006602 Response regulator receiver domain; Region: Response_reg; pfam00072 557722006603 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722006604 active site 557722006605 phosphorylation site [posttranslational modification] 557722006606 intermolecular recognition site; other site 557722006607 dimerization interface [polypeptide binding]; other site 557722006608 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 557722006609 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006610 GAF domain; Region: GAF; cl15785 557722006611 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722006612 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 557722006613 C-terminal domain interface [polypeptide binding]; other site 557722006614 GSH binding site (G-site) [chemical binding]; other site 557722006615 dimer interface [polypeptide binding]; other site 557722006616 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 557722006617 N-terminal domain interface [polypeptide binding]; other site 557722006618 dimer interface [polypeptide binding]; other site 557722006619 substrate binding pocket (H-site) [chemical binding]; other site 557722006620 Killing trait; Region: RebB; pfam11747 557722006621 Killing trait; Region: RebB; pfam11747 557722006622 Killing trait; Region: RebB; pfam11747 557722006623 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 557722006624 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722006625 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 557722006626 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722006627 ligand binding site [chemical binding]; other site 557722006628 flexible hinge region; other site 557722006629 Helix-turn-helix domains; Region: HTH; cl00088 557722006630 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 557722006631 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 557722006632 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 557722006633 active site 557722006634 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 557722006635 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 557722006636 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722006637 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 557722006638 putative C-terminal domain interface [polypeptide binding]; other site 557722006639 putative GSH binding site (G-site) [chemical binding]; other site 557722006640 putative dimer interface [polypeptide binding]; other site 557722006641 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 557722006642 putative N-terminal domain interface [polypeptide binding]; other site 557722006643 putative dimer interface [polypeptide binding]; other site 557722006644 putative substrate binding pocket (H-site) [chemical binding]; other site 557722006645 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 557722006646 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006647 Walker A/P-loop; other site 557722006648 ATP binding site [chemical binding]; other site 557722006649 Q-loop/lid; other site 557722006650 ABC transporter signature motif; other site 557722006651 Walker B; other site 557722006652 D-loop; other site 557722006653 H-loop/switch region; other site 557722006654 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722006655 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 557722006656 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722006657 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722006658 dimer interface [polypeptide binding]; other site 557722006659 phosphorylation site [posttranslational modification] 557722006660 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722006661 ATP binding site [chemical binding]; other site 557722006662 Mg2+ binding site [ion binding]; other site 557722006663 G-X-G motif; other site 557722006664 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 557722006665 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722006666 active site 557722006667 phosphorylation site [posttranslational modification] 557722006668 intermolecular recognition site; other site 557722006669 dimerization interface [polypeptide binding]; other site 557722006670 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722006671 DNA binding site [nucleotide binding] 557722006672 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722006673 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 557722006674 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 557722006675 Domain of unknown function (DUF4404); Region: DUF4404; pfam14357 557722006676 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722006677 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 557722006678 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 557722006679 transcriptional regulator protein; Region: phnR; TIGR03337 557722006680 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722006681 DNA-binding site [nucleotide binding]; DNA binding site 557722006682 UTRA domain; Region: UTRA; cl01230 557722006683 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722006684 active site 557722006685 VacJ like lipoprotein; Region: VacJ; cl01073 557722006686 PilZ domain; Region: PilZ; cl01260 557722006687 Response regulator receiver domain; Region: Response_reg; pfam00072 557722006688 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722006689 active site 557722006690 phosphorylation site [posttranslational modification] 557722006691 intermolecular recognition site; other site 557722006692 dimerization interface [polypeptide binding]; other site 557722006693 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 557722006694 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 557722006695 anti sigma factor interaction site; other site 557722006696 regulatory phosphorylation site [posttranslational modification]; other site 557722006697 transaldolase-like protein; Provisional; Region: PTZ00411 557722006698 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 557722006699 active site 557722006700 dimer interface [polypeptide binding]; other site 557722006701 catalytic residue [active] 557722006702 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 557722006703 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 557722006704 FMN binding site [chemical binding]; other site 557722006705 active site 557722006706 catalytic residues [active] 557722006707 substrate binding site [chemical binding]; other site 557722006708 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 557722006709 catalytic triad [active] 557722006710 conserved cis-peptide bond; other site 557722006711 drug efflux system protein MdtG; Provisional; Region: PRK09874 557722006712 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722006713 putative substrate translocation pore; other site 557722006714 Right handed beta helix region; Region: Beta_helix; pfam13229 557722006715 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 557722006716 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 557722006717 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722006718 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722006719 dimer interface [polypeptide binding]; other site 557722006720 putative CheW interface [polypeptide binding]; other site 557722006721 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 557722006722 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 557722006723 metal binding site [ion binding]; metal-binding site 557722006724 dimer interface [polypeptide binding]; other site 557722006725 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722006726 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 557722006727 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 557722006728 active site 557722006729 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 557722006730 Carbohydrate binding domain; Region: CBM_4_9; pfam02018 557722006731 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722006732 non-specific DNA binding site [nucleotide binding]; other site 557722006733 salt bridge; other site 557722006734 sequence-specific DNA binding site [nucleotide binding]; other site 557722006735 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 557722006736 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39A; cd02549 557722006737 putative active site [active] 557722006738 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 557722006739 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006740 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722006741 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 557722006742 GAF domain; Region: GAF; cl15785 557722006743 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722006744 metal binding site [ion binding]; metal-binding site 557722006745 active site 557722006746 I-site; other site 557722006747 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 557722006748 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722006749 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_19; cd04678 557722006750 nudix motif; other site 557722006751 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 557722006752 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722006753 substrate binding site [chemical binding]; other site 557722006754 oxyanion hole (OAH) forming residues; other site 557722006755 trimer interface [polypeptide binding]; other site 557722006756 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 557722006757 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722006758 Helix-turn-helix domains; Region: HTH; cl00088 557722006759 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 557722006760 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722006761 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722006762 Cupin domain; Region: Cupin_2; cl09118 557722006763 outer membrane porin, OprD family; Region: OprD; pfam03573 557722006764 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722006765 Helix-turn-helix domains; Region: HTH; cl00088 557722006766 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722006767 dimerization interface [polypeptide binding]; other site 557722006768 Predicted membrane protein [Function unknown]; Region: COG4125 557722006769 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 557722006770 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 557722006771 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 557722006772 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 557722006773 secondary substrate binding site; other site 557722006774 primary substrate binding site; other site 557722006775 inhibition loop; other site 557722006776 dimerization interface [polypeptide binding]; other site 557722006777 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 557722006778 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 557722006779 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557722006780 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 557722006781 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 557722006782 Endonuclease I; Region: Endonuclease_1; cl01003 557722006783 DNA-specific endonuclease I; Provisional; Region: PRK15137 557722006784 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 557722006785 active site 557722006786 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 557722006787 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722006788 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 557722006789 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 557722006790 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 557722006791 Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ThrRS_core; cd00771 557722006792 active site 557722006793 dimer interface [polypeptide binding]; other site 557722006794 motif 1; other site 557722006795 motif 2; other site 557722006796 motif 3; other site 557722006797 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 557722006798 anticodon binding site; other site 557722006799 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 557722006800 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 557722006801 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 557722006802 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 557722006803 ribosomal protein L20; Region: rpl20; CHL00068 557722006804 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 557722006805 23S rRNA binding site [nucleotide binding]; other site 557722006806 L21 binding site [polypeptide binding]; other site 557722006807 L13 binding site [polypeptide binding]; other site 557722006808 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 557722006809 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 557722006810 Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible...; Region: PheRS_alpha_core; cd00496 557722006811 dimer interface [polypeptide binding]; other site 557722006812 motif 1; other site 557722006813 active site 557722006814 motif 2; other site 557722006815 motif 3; other site 557722006816 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 557722006817 tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate...; Region: tRNA_bind_bactPheRS; cd02796 557722006818 putative tRNA-binding site [nucleotide binding]; other site 557722006819 B3/4 domain; Region: B3_4; cl11458 557722006820 tRNA synthetase B5 domain; Region: B5; cl08394 557722006821 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 557722006822 dimer interface [polypeptide binding]; other site 557722006823 motif 1; other site 557722006824 motif 3; other site 557722006825 motif 2; other site 557722006826 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 557722006827 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 557722006828 IHF dimer interface [polypeptide binding]; other site 557722006829 IHF - DNA interface [nucleotide binding]; other site 557722006830 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557722006831 DNA binding residues [nucleotide binding] 557722006832 LESGI-1 557722006833 Helix-turn-helix domains; Region: HTH; cl00088 557722006834 putative transposase OrfB; Reviewed; Region: PHA02517 557722006835 HTH-like domain; Region: HTH_21; pfam13276 557722006836 Integrase core domain; Region: rve; cl01316 557722006837 Integrase core domain; Region: rve_3; cl15866 557722006838 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 557722006839 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 557722006840 Protein of unknown function (DUF524); Region: DUF524; pfam04411 557722006841 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 557722006842 Domain of unknown function (DUF932); Region: DUF932; cl12129 557722006843 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006844 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3972 557722006845 Family description; Region: UvrD_C_2; cl15862 557722006846 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 557722006847 WYL domain; Region: WYL; cl14852 557722006848 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722006849 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 557722006850 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 557722006851 HerA helicase [Replication, recombination, and repair]; Region: COG0433 557722006852 Domain of unknown function DUF87; Region: DUF87; pfam01935 557722006853 Catalytic domain of Protein Kinases; Region: PKc; cd00180 557722006854 active site 557722006855 ATP binding site [chemical binding]; other site 557722006856 substrate binding site [chemical binding]; other site 557722006857 activation loop (A-loop); other site 557722006858 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 557722006859 active site 557722006860 Int/Topo IB signature motif; other site 557722006861 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722006862 Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They belong to the superfamily...; Region: INT_Lambda_C; cd00800 557722006863 dimer interface [polypeptide binding]; other site 557722006864 Int/Topo IB signature motif; other site 557722006865 active site 557722006866 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; Region: MPN_NLPC_P60; cd08073 557722006867 MPN+ (JAMM) motif; other site 557722006868 Zinc-binding site [ion binding]; other site 557722006869 NlpC/P60 family; Region: NLPC_P60; cl11438 557722006870 putative transposase OrfB; Reviewed; Region: PHA02517 557722006871 HTH-like domain; Region: HTH_21; pfam13276 557722006872 Integrase core domain; Region: rve; cl01316 557722006873 Integrase core domain; Region: rve_3; cl15866 557722006874 Helix-turn-helix domains; Region: HTH; cl00088 557722006875 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 557722006876 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 557722006877 HTH-like domain; Region: HTH_21; pfam13276 557722006878 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722006879 active site 557722006880 ATP binding site [chemical binding]; other site 557722006881 substrate binding site [chemical binding]; other site 557722006882 activation loop (A-loop); other site 557722006883 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 557722006884 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006885 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 557722006886 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722006887 Family description; Region: UvrD_C_2; cl15862 557722006888 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 557722006889 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 557722006890 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 557722006891 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722006892 Walker A motif; other site 557722006893 ATP binding site [chemical binding]; other site 557722006894 Walker B motif; other site 557722006895 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722006896 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 557722006897 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 557722006898 dimer interface [polypeptide binding]; other site 557722006899 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 557722006900 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 557722006901 potential catalytic triad [active] 557722006902 conserved cys residue [active] 557722006903 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557722006904 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 557722006905 DNA binding residues [nucleotide binding] 557722006906 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 557722006907 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722006908 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722006909 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 557722006910 putative active site [active] 557722006911 putative FMN binding site [chemical binding]; other site 557722006912 putative substrate binding site [chemical binding]; other site 557722006913 putative catalytic residue [active] 557722006914 Ferredoxin [Energy production and conversion]; Region: COG1146 557722006915 4Fe-4S binding domain; Region: Fer4; cl02805 557722006916 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 557722006917 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 557722006918 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to...; Region: MopB_1; cd02762 557722006919 putative [Fe4-S4] binding site [ion binding]; other site 557722006920 putative molybdopterin cofactor binding site [chemical binding]; other site 557722006921 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722006922 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_1; cd02782 557722006923 putative molybdopterin cofactor binding site; other site 557722006924 Helix-turn-helix domains; Region: HTH; cl00088 557722006925 Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen...; Region: KU; cl02666 557722006926 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 557722006927 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722006928 LysE type translocator; Region: LysE; cl00565 557722006929 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557722006930 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 557722006931 dimer interface [polypeptide binding]; other site 557722006932 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722006933 catalytic residue [active] 557722006934 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557722006935 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 557722006936 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722006937 Walker A motif; other site 557722006938 ATP binding site [chemical binding]; other site 557722006939 Walker B motif; other site 557722006940 arginine finger; other site 557722006941 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 557722006942 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722006943 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722006944 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722006945 Transmembrane secretion effector; Region: MFS_3; pfam05977 557722006946 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722006947 putative substrate translocation pore; other site 557722006948 outer membrane porin, OprD family; Region: OprD; pfam03573 557722006949 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 557722006950 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 557722006951 active site 557722006952 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 557722006953 Isochorismatase family; Region: Isochorismatase; pfam00857 557722006954 catalytic triad [active] 557722006955 dimer interface [polypeptide binding]; other site 557722006956 conserved cis-peptide bond; other site 557722006957 Protein of unknown function (DUF1427); Region: DUF1427; cl01771 557722006958 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722006959 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722006960 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722006961 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 557722006962 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 557722006963 catalytic residues [active] 557722006964 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 557722006965 Predicted transcriptional regulator [Transcription]; Region: COG1959 557722006966 Helix-turn-helix domains; Region: HTH; cl00088 557722006967 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 557722006968 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722006969 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722006970 outer membrane receptor FepA; Provisional; Region: PRK13524 557722006971 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722006972 N-terminal plug; other site 557722006973 ligand-binding site [chemical binding]; other site 557722006974 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 557722006975 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722006976 ATP binding site [chemical binding]; other site 557722006977 Mg2+ binding site [ion binding]; other site 557722006978 G-X-G motif; other site 557722006979 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722006980 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722006981 active site 557722006982 phosphorylation site [posttranslational modification] 557722006983 intermolecular recognition site; other site 557722006984 dimerization interface [polypeptide binding]; other site 557722006985 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722006986 DNA binding site [nucleotide binding] 557722006987 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722006988 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722006989 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722006990 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 557722006991 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 557722006992 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 557722006993 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722006994 RHS Repeat; Region: RHS_repeat; cl11982 557722006995 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722006996 RHS Repeat; Region: RHS_repeat; cl11982 557722006997 RHS Repeat; Region: RHS_repeat; cl11982 557722006998 RHS Repeat; Region: RHS_repeat; cl11982 557722006999 RHS Repeat; Region: RHS_repeat; cl11982 557722007000 RHS Repeat; Region: RHS_repeat; cl11982 557722007001 RHS protein; Region: RHS; pfam03527 557722007002 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 557722007003 serine racemase; Region: PLN02970 557722007004 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 557722007005 tetramer interface [polypeptide binding]; other site 557722007006 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722007007 catalytic residue [active] 557722007008 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 557722007009 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722007010 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722007011 Helix-turn-helix domains; Region: HTH; cl00088 557722007012 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722007013 putative effector binding pocket; other site 557722007014 dimerization interface [polypeptide binding]; other site 557722007015 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 557722007016 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 557722007017 NADP binding site [chemical binding]; other site 557722007018 dimer interface [polypeptide binding]; other site 557722007019 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 557722007020 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722007021 S-adenosylmethionine binding site [chemical binding]; other site 557722007022 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722007023 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 557722007024 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 557722007025 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 557722007026 Walker A motif; other site 557722007027 ATP binding site [chemical binding]; other site 557722007028 Walker B motif; other site 557722007029 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 557722007030 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722007031 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722007032 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722007033 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 557722007034 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 557722007035 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 557722007036 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 557722007037 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722007038 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 557722007039 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 557722007040 active site 557722007041 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 557722007042 GAF domain; Region: GAF; cl15785 557722007043 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722007044 Walker A motif; other site 557722007045 ATP binding site [chemical binding]; other site 557722007046 Walker B motif; other site 557722007047 arginine finger; other site 557722007048 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 557722007049 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 557722007050 heme-binding site [chemical binding]; other site 557722007051 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 557722007052 FAD binding pocket [chemical binding]; other site 557722007053 FAD binding motif [chemical binding]; other site 557722007054 phosphate binding motif [ion binding]; other site 557722007055 beta-alpha-beta structure motif; other site 557722007056 NAD binding pocket [chemical binding]; other site 557722007057 Heme binding pocket [chemical binding]; other site 557722007058 NnrS protein; Region: NnrS; cl01258 557722007059 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 557722007060 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 557722007061 Predicted membrane protein [Function unknown]; Region: COG3212 557722007062 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722007063 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722007064 active site 557722007065 phosphorylation site [posttranslational modification] 557722007066 intermolecular recognition site; other site 557722007067 dimerization interface [polypeptide binding]; other site 557722007068 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722007069 DNA binding site [nucleotide binding] 557722007070 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722007071 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722007072 ATP binding site [chemical binding]; other site 557722007073 Mg2+ binding site [ion binding]; other site 557722007074 G-X-G motif; other site 557722007075 Cache domain; Region: Cache_1; pfam02743 557722007076 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722007077 dimerization interface [polypeptide binding]; other site 557722007078 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722007079 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722007080 dimer interface [polypeptide binding]; other site 557722007081 putative CheW interface [polypeptide binding]; other site 557722007082 Predicted permease [General function prediction only]; Region: COG2056 557722007083 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 557722007084 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 557722007085 Cache domain; Region: Cache_2; cl07034 557722007086 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722007087 dimerization interface [polypeptide binding]; other site 557722007088 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722007089 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722007090 dimer interface [polypeptide binding]; other site 557722007091 putative CheW interface [polypeptide binding]; other site 557722007092 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 557722007093 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl15780 557722007094 hypothetical protein; Reviewed; Region: PRK09588 557722007095 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722007096 S-adenosylmethionine binding site [chemical binding]; other site 557722007097 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 557722007098 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 557722007099 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 557722007100 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 557722007101 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 557722007102 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 557722007103 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 557722007104 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 557722007105 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 557722007106 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 557722007107 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 557722007108 4Fe-4S binding domain; Region: Fer4; cl02805 557722007109 4Fe-4S binding domain; Region: Fer4; cl02805 557722007110 NADH dehydrogenase; Region: NADHdh; cl00469 557722007111 NADH dehydrogenase subunit G; Validated; Region: PRK08166 557722007112 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722007113 catalytic loop [active] 557722007114 iron binding site [ion binding]; other site 557722007115 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 557722007116 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory...; Region: MopB_NDH-1_NuoG2-N7; cd02771 557722007117 [4Fe-4S] binding site [ion binding]; other site 557722007118 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex...; Region: MopB_CT_NDH-1_NuoG2-N7; cd02788 557722007119 NADH dehydrogenase I subunit F; Provisional; Region: PRK11278 557722007120 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 557722007121 SLBB domain; Region: SLBB; pfam10531 557722007122 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 557722007123 NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]; Region: NuoE; COG1905 557722007124 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 557722007125 putative dimer interface [polypeptide binding]; other site 557722007126 [2Fe-2S] cluster binding site [ion binding]; other site 557722007127 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 557722007128 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 557722007129 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 557722007130 NADH dehydrogenase subunit B; Validated; Region: PRK06411 557722007131 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 557722007132 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 557722007133 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722007134 CoenzymeA binding site [chemical binding]; other site 557722007135 subunit interaction site [polypeptide binding]; other site 557722007136 PHB binding site; other site 557722007137 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 557722007138 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 557722007139 tetramer interface [polypeptide binding]; other site 557722007140 active site 557722007141 Mg2+/Mn2+ binding site [ion binding]; other site 557722007142 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 557722007143 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722007144 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722007145 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722007146 Coenzyme A binding pocket [chemical binding]; other site 557722007147 Uncharacterized conserved protein [Function unknown]; Region: COG2850 557722007148 Cupin domain; Region: Cupin_2; cl09118 557722007149 adenylosuccinate lyase; Provisional; Region: PRK09285 557722007150 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 557722007151 tetramer interface [polypeptide binding]; other site 557722007152 active site 557722007153 EamA-like transporter family; Region: EamA; cl01037 557722007154 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557722007155 Protein of unknown function (DUF489); Region: DUF489; cl01097 557722007156 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 557722007157 tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs; Region: tRNA_Me_trans; cd01998 557722007158 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 557722007159 nudix motif; other site 557722007160 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 557722007161 isocitrate dehydrogenase; Validated; Region: PRK07362 557722007162 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 557722007163 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557722007164 DNA-binding site [nucleotide binding]; DNA binding site 557722007165 RNA-binding motif; other site 557722007166 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 557722007167 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 557722007168 Clp amino terminal domain; Region: Clp_N; pfam02861 557722007169 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722007170 Walker A motif; other site 557722007171 ATP binding site [chemical binding]; other site 557722007172 Walker B motif; other site 557722007173 arginine finger; other site 557722007174 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722007175 Walker A motif; other site 557722007176 ATP binding site [chemical binding]; other site 557722007177 Walker B motif; other site 557722007178 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722007179 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 557722007180 rRNA binding site [nucleotide binding]; other site 557722007181 predicted 30S ribosome binding site; other site 557722007182 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 557722007183 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 557722007184 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722007185 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722007186 thioredoxin reductase; Provisional; Region: PRK10262 557722007187 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722007188 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 557722007189 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722007190 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 557722007191 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 557722007192 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 557722007193 recombination factor protein RarA; Reviewed; Region: PRK13342 557722007194 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722007195 Walker A motif; other site 557722007196 ATP binding site [chemical binding]; other site 557722007197 Walker B motif; other site 557722007198 arginine finger; other site 557722007199 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 557722007200 seryl-tRNA synthetase; Provisional; Region: PRK05431 557722007201 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 557722007202 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 557722007203 dimer interface [polypeptide binding]; other site 557722007204 active site 557722007205 motif 1; other site 557722007206 motif 2; other site 557722007207 motif 3; other site 557722007208 siroheme synthase; Provisional; Region: cysG; PRK10637 557722007209 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007210 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 557722007211 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722007212 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 557722007213 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722007214 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 557722007215 putative dimer interface [polypeptide binding]; other site 557722007216 N-terminal domain interface [polypeptide binding]; other site 557722007217 putative substrate binding pocket (H-site) [chemical binding]; other site 557722007218 hypothetical protein; Validated; Region: PRK09071 557722007219 DsrC like protein; Region: DsrC; cl01101 557722007220 DsrE/DsrF-like family; Region: DrsE; cl00672 557722007221 DsrE/DsrF-like family; Region: DrsE; cl00672 557722007222 DsrE/DsrF-like family; Region: DrsE; cl00672 557722007223 YccA-like proteins; Region: YccA_like; cd10433 557722007224 LES prophage 5 557722007225 integrase; Provisional; Region: int; PHA02601 557722007226 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722007227 DNA binding site [nucleotide binding] 557722007228 Int/Topo IB signature motif; other site 557722007229 active site 557722007230 Domain of unknown function (DUF4224); Region: DUF4224; pfam13986 557722007231 Duplication 2b 557722007232 PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a...; Region: PLA2_like; cl05417 557722007233 primary metal binding site; other site 557722007234 TIR domain; Region: TIR_2; cl15770 557722007235 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007236 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722007237 DNA binding residues [nucleotide binding] 557722007238 dimerization interface [polypeptide binding]; other site 557722007239 ParB-like nuclease domain; Region: ParBc; cl02129 557722007240 KorB domain; Region: KorB; pfam08535 557722007241 Domain of unknown function DUF1828; Region: DUF1828; pfam08861 557722007242 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722007243 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722007244 Catalytic site [active] 557722007245 Cro; Region: Cro; pfam09048 557722007246 YfbU domain; Region: YfbU; cl01137 557722007247 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 557722007248 Helix-turn-helix domains; Region: HTH; cl00088 557722007249 hypothetical protein; Validated; Region: PRK07078 557722007250 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 557722007251 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 557722007252 active site 557722007253 metal binding site [ion binding]; metal-binding site 557722007254 interdomain interaction site; other site 557722007255 AAA domain; Region: AAA_25; pfam13481 557722007256 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722007257 Walker A motif; other site 557722007258 ATP binding site [chemical binding]; other site 557722007259 Walker B motif; other site 557722007260 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 557722007261 Bacteriophage Lambda NinG protein; Region: NinG; pfam05766 557722007262 potential protein location (hypothetical protein PLES_25301 [Pseudomonas aeruginosa LESB58]) that overlaps RNA (tRNA-T) 557722007263 Protein of unknown function (DUF754); Region: DUF754; pfam05449 557722007264 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 557722007265 active site 557722007266 Phage terminase, small subunit; Region: Terminase_4; cl01525 557722007267 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 557722007268 Phage Terminase; Region: Terminase_1; pfam03354 557722007269 Phage-related protein [Function unknown]; Region: COG4695; cl01923 557722007270 phage portal protein, HK97 family; Region: portal_HK97; TIGR01537 557722007271 Clp protease; Region: CLP_protease; pfam00574 557722007272 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 557722007273 oligomer interface [polypeptide binding]; other site 557722007274 active site residues [active] 557722007275 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 557722007276 Phage capsid family; Region: Phage_capsid; pfam05065 557722007277 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 557722007278 Phage head-tail joining protein; Region: Phage_H_T_join; cl11461 557722007279 Phage protein (N4 Gp49/phage Sf6 gene 66) family; Region: Phage_gp49_66; cl10351 557722007280 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722007281 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007282 Bacteriophage protein of unknown function (DUF646); Region: DUF646; cl12124 557722007283 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 557722007284 HNH endonuclease; Region: HNH_3; pfam13392 557722007285 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 557722007286 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 557722007287 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 557722007288 OpgC protein; Region: OpgC_C; cl00792 557722007289 Acyltransferase family; Region: Acyl_transf_3; pfam01757 557722007290 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722007291 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 557722007292 active site residue [active] 557722007293 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic...; Region: 4RHOD_Repeat_2; cd01533 557722007294 active site residue [active] 557722007295 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative...; Region: 4RHOD_Repeat_3; cd01534 557722007296 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 557722007297 active site residue [active] 557722007298 Member of the Rhodanese Homology Domain superfamily, repeat 4. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative...; Region: 4RHOD_Repeat_4; cd01535 557722007299 active site residue [active] 557722007300 Cysteine dioxygenase type I; Region: CDO_I; cl15835 557722007301 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722007302 Helix-turn-helix domains; Region: HTH; cl00088 557722007303 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722007304 dimerization interface [polypeptide binding]; other site 557722007305 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 557722007306 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 557722007307 dimer interface [polypeptide binding]; other site 557722007308 active site 557722007309 non-prolyl cis peptide bond; other site 557722007310 insertion regions; other site 557722007311 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722007312 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722007313 substrate binding pocket [chemical binding]; other site 557722007314 membrane-bound complex binding site; other site 557722007315 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 557722007316 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 557722007317 dimer interface [polypeptide binding]; other site 557722007318 active site 557722007319 non-prolyl cis peptide bond; other site 557722007320 insertion regions; other site 557722007321 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 557722007322 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722007323 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722007324 substrate binding pocket [chemical binding]; other site 557722007325 membrane-bound complex binding site; other site 557722007326 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722007327 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722007328 membrane-bound complex binding site; other site 557722007329 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722007330 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722007331 substrate binding pocket [chemical binding]; other site 557722007332 membrane-bound complex binding site; other site 557722007333 hinge residues; other site 557722007334 LESGI-2 557722007335 Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy; Region: CHS_like; cd00831 557722007336 Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BcsA; COG3424 557722007337 malonyl-CoA binding site [chemical binding]; other site 557722007338 dimer interface [polypeptide binding]; other site 557722007339 active site 557722007340 product binding site; other site 557722007341 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 557722007342 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007343 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722007344 Helix-turn-helix domains; Region: HTH; cl00088 557722007345 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722007346 putative effector binding pocket; other site 557722007347 dimerization interface [polypeptide binding]; other site 557722007348 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722007349 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 557722007350 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007351 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 557722007352 Beta-ketoacyl synthase; Region: PKS_KS; smart00825 557722007353 active site 557722007354 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 557722007355 Acyl transferase domain; Region: Acyl_transf_1; cl08282 557722007356 beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x); Region: KR_2_FAS_SDR_x; cd08955 557722007357 putative NADP binding site [chemical binding]; other site 557722007358 active site 557722007359 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722007360 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 557722007361 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722007362 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722007363 active site 557722007364 D-alanine--poly(phosphoribitol) ligase subunit 1; Provisional; Region: PRK04813 557722007365 AMP-binding enzyme; Region: AMP-binding; cl15778 557722007366 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 557722007367 Protein of unknown function (DUF3089); Region: DUF3089; pfam11288 557722007368 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722007369 Helix-turn-helix domains; Region: HTH; cl00088 557722007370 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 557722007371 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 557722007372 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007373 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007374 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 557722007375 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722007376 Walker A/P-loop; other site 557722007377 ATP binding site [chemical binding]; other site 557722007378 Q-loop/lid; other site 557722007379 ABC transporter signature motif; other site 557722007380 Walker B; other site 557722007381 D-loop; other site 557722007382 H-loop/switch region; other site 557722007383 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 557722007384 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722007385 Walker A/P-loop; other site 557722007386 ATP binding site [chemical binding]; other site 557722007387 Q-loop/lid; other site 557722007388 ABC transporter signature motif; other site 557722007389 Walker B; other site 557722007390 D-loop; other site 557722007391 H-loop/switch region; other site 557722007392 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 557722007393 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722007394 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722007395 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722007396 LysE type translocator; Region: LysE; cl00565 557722007397 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 557722007398 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722007399 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722007400 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722007401 DNA binding residues [nucleotide binding] 557722007402 dimerization interface [polypeptide binding]; other site 557722007403 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 557722007404 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722007405 N-terminal plug; other site 557722007406 ligand-binding site [chemical binding]; other site 557722007407 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722007408 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 557722007409 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722007410 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722007411 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722007412 hypothetical protein; Provisional; Region: PRK06753 557722007413 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007414 response regulator; Provisional; Region: PRK09483 557722007415 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722007416 active site 557722007417 phosphorylation site [posttranslational modification] 557722007418 intermolecular recognition site; other site 557722007419 dimerization interface [polypeptide binding]; other site 557722007420 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722007421 DNA binding residues [nucleotide binding] 557722007422 dimerization interface [polypeptide binding]; other site 557722007423 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 557722007424 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 557722007425 GIY-YIG motif/motif A; other site 557722007426 active site 557722007427 catalytic site [active] 557722007428 putative DNA binding site [nucleotide binding]; other site 557722007429 metal binding site [ion binding]; metal-binding site 557722007430 UvrB/uvrC motif; Region: UVR; pfam02151 557722007431 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 557722007432 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 557722007433 DNA binding site [nucleotide binding] 557722007434 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 557722007435 LESGI-3 557722007436 integrase; Provisional; Region: PRK09692 557722007437 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 557722007438 active site 557722007439 Int/Topo IB signature motif; other site 557722007440 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722007441 dimerization interface [polypeptide binding]; other site 557722007442 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 557722007443 Helix-turn-helix domains; Region: HTH; cl00088 557722007444 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 557722007445 dimerization interface [polypeptide binding]; other site 557722007446 substrate binding pocket [chemical binding]; other site 557722007447 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007448 metal-binding site [ion binding] 557722007449 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722007450 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722007451 catalytic loop [active] 557722007452 iron binding site [ion binding]; other site 557722007453 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 557722007454 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 557722007455 DNA binding residues [nucleotide binding] 557722007456 dimer interface [polypeptide binding]; other site 557722007457 copper binding site [ion binding]; other site 557722007458 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007459 metal-binding site [ion binding] 557722007460 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557722007461 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007462 metal-binding site [ion binding] 557722007463 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722007464 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722007465 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722007466 putative DNA binding site [nucleotide binding]; other site 557722007467 putative Zn2+ binding site [ion binding]; other site 557722007468 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 557722007469 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722007470 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722007471 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 557722007472 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722007473 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007474 Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156; Region: NreA-like_DUF156; cd10154 557722007475 putative homotetramer interface [polypeptide binding]; other site 557722007476 putative homodimer interface [polypeptide binding]; other site 557722007477 putative metal binding site [ion binding]; other site 557722007478 putative homodimer-homodimer interface [polypeptide binding]; other site 557722007479 putative allosteric switch controlling residues; other site 557722007480 H+ Antiporter protein; Region: 2A0121; TIGR00900 557722007481 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722007482 putative substrate translocation pore; other site 557722007483 Cation efflux family; Region: Cation_efflux; cl00316 557722007484 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722007485 dimerization interface [polypeptide binding]; other site 557722007486 putative DNA binding site [nucleotide binding]; other site 557722007487 putative Zn2+ binding site [ion binding]; other site 557722007488 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007489 metal-binding site [ion binding] 557722007490 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 557722007491 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007492 metal-binding site [ion binding] 557722007493 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722007494 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722007495 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722007496 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007497 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 557722007498 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722007499 Sugar (and other) transporter; Region: Sugar_tr; pfam00083 557722007500 mercuric reductase; Region: MerA; TIGR02053 557722007501 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722007502 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722007503 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 557722007504 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722007505 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722007506 DNA-binding site [nucleotide binding]; DNA binding site 557722007507 FCD domain; Region: FCD; cl11656 557722007508 Domain of unknown function (DUF305); Region: DUF305; cl15795 557722007509 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 557722007510 catalytic residues [active] 557722007511 NeuB family; Region: NeuB; cl00496 557722007512 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557722007513 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 557722007514 Putative helicase; Region: TraI_2; pfam07514 557722007515 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 557722007516 RES domain; Region: RES; cl02411 557722007517 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 557722007518 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 557722007519 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 557722007520 TraU protein; Region: TraU; cl06067 557722007521 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 557722007522 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 557722007523 MPN+ (JAMM) motif; other site 557722007524 Zinc-binding site [ion binding]; other site 557722007525 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722007526 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 557722007527 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 557722007528 Protein of unknown function (DUF2895); Region: DUF2895; cl12968 557722007529 Protein of unknown function (DUF3487); Region: DUF3487; cl13432 557722007530 Protein of unknown function (DUF2976); Region: DUF2976; cl12739 557722007531 Protein of unknown function (DUF3262); Region: DUF3262; cl13160 557722007532 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 557722007533 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 557722007534 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557722007535 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 557722007536 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 557722007537 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 557722007538 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722007539 Walker A motif; other site 557722007540 ATP binding site [chemical binding]; other site 557722007541 Walker B motif; other site 557722007542 arginine finger; other site 557722007543 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 557722007544 active site 557722007545 NTP binding site [chemical binding]; other site 557722007546 metal binding triad [ion binding]; metal-binding site 557722007547 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722007548 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 557722007549 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722007550 ABC transporter signature motif; other site 557722007551 Walker B; other site 557722007552 D-loop; other site 557722007553 H-loop/switch region; other site 557722007554 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 557722007555 Domain of unknown function DUF87; Region: DUF87; pfam01935 557722007556 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 557722007557 Protein of unknown function (DUF2859); Region: DUF2859; cl12633 557722007558 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722007559 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 557722007560 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 557722007561 DEAD-like helicases superfamily; Region: DEXDc; smart00487 557722007562 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722007563 nucleotide binding region [chemical binding]; other site 557722007564 ATP-binding site [chemical binding]; other site 557722007565 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007566 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 557722007567 Domain of unknown function (DUF932); Region: DUF932; cl12129 557722007568 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 557722007569 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 557722007570 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 557722007571 putative mercuric reductase; Provisional; Region: PRK13748 557722007572 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007573 metal-binding site [ion binding] 557722007574 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722007575 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722007576 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007577 metal-binding site [ion binding] 557722007578 MerT mercuric transport protein; Region: MerT; cl03578 557722007579 putative transcriptional regulator MerR; Provisional; Region: PRK13752 557722007580 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 557722007581 DNA binding residues [nucleotide binding] 557722007582 dimer interface [polypeptide binding]; other site 557722007583 mercury binding site [ion binding]; other site 557722007584 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional; Region: PRK09841 557722007585 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 557722007586 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007587 metal-binding site [ion binding] 557722007588 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 557722007589 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007590 metal-binding site [ion binding] 557722007591 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557722007592 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722007593 metal-binding site [ion binding] 557722007594 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722007595 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722007596 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 557722007597 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 557722007598 DNA binding residues [nucleotide binding] 557722007599 dimer interface [polypeptide binding]; other site 557722007600 putative metal binding site [ion binding]; other site 557722007601 Cation efflux family; Region: Cation_efflux; cl00316 557722007602 DNA topoisomerase III; Provisional; Region: PRK07726 557722007603 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 557722007604 active site 557722007605 putative interdomain interaction site [polypeptide binding]; other site 557722007606 putative metal-binding site [ion binding]; other site 557722007607 putative nucleotide binding site [chemical binding]; other site 557722007608 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 557722007609 domain I; other site 557722007610 DNA binding groove [nucleotide binding] 557722007611 phosphate binding site [ion binding]; other site 557722007612 domain II; other site 557722007613 domain III; other site 557722007614 nucleotide binding site [chemical binding]; other site 557722007615 catalytic site [active] 557722007616 domain IV; other site 557722007617 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557722007618 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 557722007619 dimer interface [polypeptide binding]; other site 557722007620 ssDNA binding site [nucleotide binding]; other site 557722007621 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557722007622 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 557722007623 Domain of unknown function (DUF1845); Region: DUF1845; cl07481 557722007624 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 557722007625 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 557722007626 ParB-like nuclease domain; Region: ParBc; cl02129 557722007627 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 557722007628 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722007629 Magnesium ion binding site [ion binding]; other site 557722007630 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557722007631 Domain of unknown function (DUF305); Region: DUF305; cl15795 557722007632 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 557722007633 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722007634 substrate binding pocket [chemical binding]; other site 557722007635 membrane-bound complex binding site; other site 557722007636 hinge residues; other site 557722007637 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722007638 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722007639 substrate binding pocket [chemical binding]; other site 557722007640 membrane-bound complex binding site; other site 557722007641 hinge residues; other site 557722007642 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722007643 dimer interface [polypeptide binding]; other site 557722007644 phosphorylation site [posttranslational modification] 557722007645 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722007646 ATP binding site [chemical binding]; other site 557722007647 Mg2+ binding site [ion binding]; other site 557722007648 G-X-G motif; other site 557722007649 Response regulator receiver domain; Region: Response_reg; pfam00072 557722007650 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722007651 active site 557722007652 phosphorylation site [posttranslational modification] 557722007653 intermolecular recognition site; other site 557722007654 dimerization interface [polypeptide binding]; other site 557722007655 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 557722007656 putative RNA binding sites [nucleotide binding]; other site 557722007657 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722007658 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 557722007659 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557722007660 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722007661 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722007662 Helix-turn-helix domains; Region: HTH; cl00088 557722007663 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557722007664 EamA-like transporter family; Region: EamA; cl01037 557722007665 EamA-like transporter family; Region: EamA; cl01037 557722007666 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 557722007667 dimer interface [polypeptide binding]; other site 557722007668 FMN binding site [chemical binding]; other site 557722007669 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 557722007670 Fatty acid desaturase; Region: FA_desaturase; pfam00487 557722007671 Di-iron ligands [ion binding]; other site 557722007672 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 557722007673 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722007674 dimerization interface [polypeptide binding]; other site 557722007675 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722007676 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722007677 dimer interface [polypeptide binding]; other site 557722007678 putative CheW interface [polypeptide binding]; other site 557722007679 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 557722007680 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722007681 active site 557722007682 phosphorylation site [posttranslational modification] 557722007683 intermolecular recognition site; other site 557722007684 dimerization interface [polypeptide binding]; other site 557722007685 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722007686 sensory histidine kinase AtoS; Provisional; Region: PRK11360 557722007687 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722007688 ATP binding site [chemical binding]; other site 557722007689 Mg2+ binding site [ion binding]; other site 557722007690 G-X-G motif; other site 557722007691 PA-IL-like protein; Region: PA-IL; pfam07828 557722007692 GAF domain; Region: GAF; cl15785 557722007693 GAF domain; Region: GAF_2; pfam13185 557722007694 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722007695 metal binding site [ion binding]; metal-binding site 557722007696 active site 557722007697 I-site; other site 557722007698 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722007699 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722007700 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 557722007701 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722007702 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 557722007703 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 557722007704 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722007705 dimerization interface [polypeptide binding]; other site 557722007706 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722007707 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722007708 dimer interface [polypeptide binding]; other site 557722007709 putative CheW interface [polypeptide binding]; other site 557722007710 Catalase-like heme-binding proteins and protein domains; Region: catalase_like; cl09506 557722007711 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 557722007712 MgtC family; Region: MgtC; pfam02308 557722007713 AMP-binding domain protein; Validated; Region: PRK08315 557722007714 AMP-binding enzyme; Region: AMP-binding; cl15778 557722007715 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722007716 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722007717 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722007718 SurA N-terminal domain; Region: SurA_N_3; cl07813 557722007719 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722007720 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 557722007721 AMP-binding enzyme; Region: AMP-binding; cl15778 557722007722 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722007723 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 557722007724 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 557722007725 NAD binding site [chemical binding]; other site 557722007726 homotetramer interface [polypeptide binding]; other site 557722007727 homodimer interface [polypeptide binding]; other site 557722007728 active site 557722007729 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 557722007730 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722007731 dimer interface [polypeptide binding]; other site 557722007732 active site 557722007733 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722007734 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722007735 active site 557722007736 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 557722007737 Helix-turn-helix domains; Region: HTH; cl00088 557722007738 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 557722007739 substrate binding pocket [chemical binding]; other site 557722007740 dimerization interface [polypeptide binding]; other site 557722007741 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722007742 Acyl-CoA dehydrogenases similar to fadE2; Region: ACAD_FadE2; cd01155 557722007743 FAD binding site [chemical binding]; other site 557722007744 substrate binding site [chemical binding]; other site 557722007745 catalytic base [active] 557722007746 Integral membrane protein TerC family; Region: TerC; cl10468 557722007747 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722007748 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722007749 ligand binding site [chemical binding]; other site 557722007750 Helix-turn-helix domains; Region: HTH; cl00088 557722007751 LysR family transcriptional regulator; Provisional; Region: PRK14997 557722007752 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722007753 putative effector binding pocket; other site 557722007754 dimerization interface [polypeptide binding]; other site 557722007755 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 557722007756 dimer interface [polypeptide binding]; other site 557722007757 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722007758 metal binding site [ion binding]; metal-binding site 557722007759 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 557722007760 putative phosphate binding site [ion binding]; other site 557722007761 putative catalytic site [active] 557722007762 active site 557722007763 metal binding site A [ion binding]; metal-binding site 557722007764 DNA binding site [nucleotide binding] 557722007765 putative AP binding site [nucleotide binding]; other site 557722007766 putative metal binding site B [ion binding]; other site 557722007767 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722007768 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 557722007769 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722007770 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722007771 Surface antigen; Region: Bac_surface_Ag; cl03097 557722007772 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 557722007773 Family of unknown function (DUF490); Region: DUF490; pfam04357 557722007774 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 557722007775 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 557722007776 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722007777 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722007778 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 557722007779 active site 557722007780 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 557722007781 active site 557722007782 catalytic residues [active] 557722007783 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 557722007784 putative acyl-acceptor binding pocket; other site 557722007785 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 557722007786 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 557722007787 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722007788 active site 557722007789 catalytic tetrad [active] 557722007790 Helix-turn-helix domains; Region: HTH; cl00088 557722007791 LysR family transcriptional regulator; Provisional; Region: PRK14997 557722007792 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 557722007793 putative effector binding pocket; other site 557722007794 putative dimerization interface [polypeptide binding]; other site 557722007795 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 557722007796 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 557722007797 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 557722007798 dimer interface [polypeptide binding]; other site 557722007799 catalytic triad [active] 557722007800 peroxidatic and resolving cysteines [active] 557722007801 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 557722007802 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722007803 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722007804 homodimer interface [polypeptide binding]; other site 557722007805 catalytic residue [active] 557722007806 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557722007807 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557722007808 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 557722007809 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 557722007810 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007811 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007812 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 557722007813 Protein export membrane protein; Region: SecD_SecF; cl14618 557722007814 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; cl02090 557722007815 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 557722007816 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722007817 synaptic vesicle protein SV2; Region: synapt_SV2; TIGR01299 557722007818 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 557722007819 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722007820 dimerization interface [polypeptide binding]; other site 557722007821 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722007822 dimer interface [polypeptide binding]; other site 557722007823 phosphorylation site [posttranslational modification] 557722007824 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722007825 ATP binding site [chemical binding]; other site 557722007826 Mg2+ binding site [ion binding]; other site 557722007827 G-X-G motif; other site 557722007828 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 557722007829 Helix-turn-helix domains; Region: HTH; cl00088 557722007830 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 557722007831 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007832 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 557722007833 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007834 heavy metal efflux pump (cobalt-zinc-cadmium); Region: 2A0601; TIGR00914 557722007835 Cupin domain; Region: Cupin_2; cl09118 557722007836 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722007837 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722007838 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722007839 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 557722007840 Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to...; Region: Rieske_RO_Alpha_HBDO; cd03542 557722007841 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 557722007842 putative alpha subunit interface [polypeptide binding]; other site 557722007843 putative active site [active] 557722007844 putative substrate binding site [chemical binding]; other site 557722007845 Fe binding site [ion binding]; other site 557722007846 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 557722007847 inter-subunit interface; other site 557722007848 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 557722007849 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722007850 catalytic loop [active] 557722007851 iron binding site [ion binding]; other site 557722007852 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 557722007853 FAD binding pocket [chemical binding]; other site 557722007854 FAD binding motif [chemical binding]; other site 557722007855 phosphate binding motif [ion binding]; other site 557722007856 beta-alpha-beta structure motif; other site 557722007857 NAD binding pocket [chemical binding]; other site 557722007858 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 557722007859 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722007860 putative NAD(P) binding site [chemical binding]; other site 557722007861 active site 557722007862 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 557722007863 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722007864 catalytic loop [active] 557722007865 iron binding site [ion binding]; other site 557722007866 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 557722007867 FAD binding pocket [chemical binding]; other site 557722007868 FAD binding motif [chemical binding]; other site 557722007869 phosphate binding motif [ion binding]; other site 557722007870 beta-alpha-beta structure motif; other site 557722007871 NAD binding pocket [chemical binding]; other site 557722007872 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 557722007873 inter-subunit interface; other site 557722007874 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 557722007875 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 557722007876 iron-sulfur cluster [ion binding]; other site 557722007877 [2Fe-2S] cluster binding site [ion binding]; other site 557722007878 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 557722007879 putative alpha subunit interface [polypeptide binding]; other site 557722007880 putative active site [active] 557722007881 putative substrate binding site [chemical binding]; other site 557722007882 Fe binding site [ion binding]; other site 557722007883 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722007884 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 557722007885 Helix-turn-helix domains; Region: HTH; cl00088 557722007886 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722007887 dimerization interface [polypeptide binding]; other site 557722007888 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 557722007889 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 557722007890 octamer interface [polypeptide binding]; other site 557722007891 active site 557722007892 Muconolactone delta-isomerase; Region: MIase; cl01992 557722007893 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 557722007894 Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of...; Region: 1,2-CTD; cd03460 557722007895 dimer interface [polypeptide binding]; other site 557722007896 active site 557722007897 outer membrane porin, OprD family; Region: OprD; pfam03573 557722007898 Uncharacterized protein conserved in bacteria (DUF2314); Region: DUF2314; pfam10077 557722007899 Protein of unknown function (DUF2185); Region: DUF2185; cl02019 557722007900 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 557722007901 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722007902 active site 557722007903 ATP binding site [chemical binding]; other site 557722007904 substrate binding site [chemical binding]; other site 557722007905 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722007906 activation loop (A-loop); other site 557722007907 activation loop (A-loop); other site 557722007908 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 557722007909 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722007910 putative substrate translocation pore; other site 557722007911 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 557722007912 nucleoside/Zn binding site; other site 557722007913 dimer interface [polypeptide binding]; other site 557722007914 catalytic motif [active] 557722007915 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 557722007916 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 557722007917 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 557722007918 Helix-turn-helix domains; Region: HTH; cl00088 557722007919 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722007920 dimerization interface [polypeptide binding]; other site 557722007921 Mycothiol maleylpyruvate isomerase N-terminal domain; Region: MDMPI_N; cl00986 557722007922 DinB superfamily; Region: DinB_2; pfam12867 557722007923 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 557722007924 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722007925 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007926 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722007927 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR2; cd08268 557722007928 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 557722007929 putative NAD(P) binding site [chemical binding]; other site 557722007930 Cupin domain; Region: Cupin_2; cl09118 557722007931 Cupin domain; Region: Cupin_2; cl09118 557722007932 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722007933 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722007934 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722007935 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722007936 Helix-turn-helix domains; Region: HTH; cl00088 557722007937 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 557722007938 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 557722007939 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 557722007940 Cytochrome c; Region: Cytochrom_C; cl11414 557722007941 Cytochrome c; Region: Cytochrom_C; cl11414 557722007942 Cytochrome c [Energy production and conversion]; Region: COG3258 557722007943 Cytochrome c; Region: Cytochrom_C; cl11414 557722007944 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722007945 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722007946 dimer interface [polypeptide binding]; other site 557722007947 phosphorylation site [posttranslational modification] 557722007948 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722007949 ATP binding site [chemical binding]; other site 557722007950 G-X-G motif; other site 557722007951 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 557722007952 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722007953 active site 557722007954 phosphorylation site [posttranslational modification] 557722007955 intermolecular recognition site; other site 557722007956 dimerization interface [polypeptide binding]; other site 557722007957 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722007958 DNA binding site [nucleotide binding] 557722007959 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 557722007960 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 557722007961 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 557722007962 DsbD alpha interface [polypeptide binding]; other site 557722007963 catalytic residues [active] 557722007964 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 557722007965 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 557722007966 catalytic residues [active] 557722007967 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 557722007968 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 557722007969 dimerization domain [polypeptide binding]; other site 557722007970 dimer interface [polypeptide binding]; other site 557722007971 catalytic residues [active] 557722007972 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; cl12078 557722007973 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557722007974 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 557722007975 maleylacetoacetate isomerase; Region: maiA; TIGR01262 557722007976 C-terminal domain interface [polypeptide binding]; other site 557722007977 GSH binding site (G-site) [chemical binding]; other site 557722007978 putative dimer interface [polypeptide binding]; other site 557722007979 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 557722007980 dimer interface [polypeptide binding]; other site 557722007981 N-terminal domain interface [polypeptide binding]; other site 557722007982 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 557722007983 benzoate transport; Region: 2A0115; TIGR00895 557722007984 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722007985 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722007986 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722007987 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 557722007988 Cupin domain; Region: Cupin_2; cl09118 557722007989 Helix-turn-helix domains; Region: HTH; cl00088 557722007990 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 557722007991 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722007992 dimerization interface [polypeptide binding]; other site 557722007993 RNA polymerase sigma factor; Provisional; Region: PRK12528 557722007994 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722007995 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722007996 DNA binding residues [nucleotide binding] 557722007997 fec operon regulator FecR; Reviewed; Region: PRK09774 557722007998 FecR protein; Region: FecR; pfam04773 557722007999 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722008000 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 557722008001 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722008002 N-terminal plug; other site 557722008003 ligand-binding site [chemical binding]; other site 557722008004 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722008005 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722008006 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722008007 Surface antigen; Region: Bac_surface_Ag; cl03097 557722008008 haemagglutination activity domain; Region: Haemagg_act; cl05436 557722008009 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 557722008010 adhesin HecA family 20-residue repeat (two copies); Region: fil_hemag_20aa; TIGR01731 557722008011 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 557722008012 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 557722008013 The BURPS668_1122 family of deaminases; Region: Toxin-deaminase; pfam14424 557722008014 RHS Repeat; Region: RHS_repeat; cl11982 557722008015 RHS Repeat; Region: RHS_repeat; cl11982 557722008016 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722008017 RHS Repeat; Region: RHS_repeat; cl11982 557722008018 RHS Repeat; Region: RHS_repeat; cl11982 557722008019 RHS Repeat; Region: RHS_repeat; cl11982 557722008020 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 557722008021 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722008022 RHS Repeat; Region: RHS_repeat; cl11982 557722008023 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 557722008024 RHS Repeat; Region: RHS_repeat; cl11982 557722008025 Predicted acetyltransferase [General function prediction only]; Region: COG3153 557722008026 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722008027 Coenzyme A binding pocket [chemical binding]; other site 557722008028 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722008029 S-adenosylmethionine binding site [chemical binding]; other site 557722008030 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 557722008031 Domain of unknown function (DUF3327); Region: DUF3327; pfam11806 557722008032 Enterochelin esterase and related enzymes [Inorganic ion transport and metabolism]; Region: Fes; COG2382 557722008033 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722008034 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 557722008035 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 557722008036 putative aromatic amino acid binding site; other site 557722008037 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722008038 Walker A motif; other site 557722008039 ATP binding site [chemical binding]; other site 557722008040 Walker B motif; other site 557722008041 arginine finger; other site 557722008042 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 557722008043 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 557722008044 active site 557722008045 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008046 Helix-turn-helix domains; Region: HTH; cl00088 557722008047 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722008048 dimerization interface [polypeptide binding]; other site 557722008049 putative effector binding pocket; other site 557722008050 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 557722008051 lipoyl attachment site [posttranslational modification]; other site 557722008052 glycine dehydrogenase; Provisional; Region: PRK05367 557722008053 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 557722008054 tetramer interface [polypeptide binding]; other site 557722008055 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722008056 catalytic residue [active] 557722008057 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 557722008058 tetramer interface [polypeptide binding]; other site 557722008059 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722008060 catalytic residue [active] 557722008061 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 557722008062 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 557722008063 dimer interface [polypeptide binding]; other site 557722008064 glycine-pyridoxal phosphate binding site [chemical binding]; other site 557722008065 active site 557722008066 folate binding site [chemical binding]; other site 557722008067 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 557722008068 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 557722008069 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 557722008070 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 557722008071 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 557722008072 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is...; Region: SANT; cl15779 557722008073 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 557722008074 putative active site [active] 557722008075 putative metal binding site [ion binding]; other site 557722008076 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 557722008077 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 557722008078 HflC protein; Region: hflC; TIGR01932 557722008079 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 557722008080 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 557722008081 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 557722008082 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722008083 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008084 Helix-turn-helix domains; Region: HTH; cl00088 557722008085 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722008086 putative effector binding pocket; other site 557722008087 dimerization interface [polypeptide binding]; other site 557722008088 Fusaric acid resistance protein family; Region: FUSC; pfam04632 557722008089 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 557722008090 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 557722008091 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722008092 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722008093 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 557722008094 extracytoplasmic-function sigma-70 factor; Validated; Region: PRK07037 557722008095 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722008096 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722008097 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 557722008098 peptide synthase; Validated; Region: PRK05691 557722008099 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008100 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008101 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008102 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008103 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008104 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008105 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008106 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008107 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 557722008108 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008109 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008110 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008111 Prophage antirepressor [Transcription]; Region: COG3617 557722008112 BRO family, N-terminal domain; Region: Bro-N; cl10591 557722008113 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557722008114 outer membrane porin, OprD family; Region: OprD; pfam03573 557722008115 Isochorismatase family; Region: Isochorismatase; pfam00857 557722008116 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 557722008117 catalytic triad [active] 557722008118 dimer interface [polypeptide binding]; other site 557722008119 conserved cis-peptide bond; other site 557722008120 Pirin-related protein [General function prediction only]; Region: COG1741 557722008121 Cupin domain; Region: Cupin_2; cl09118 557722008122 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 557722008123 LysR family transcriptional regulator; Provisional; Region: PRK14997 557722008124 Helix-turn-helix domains; Region: HTH; cl00088 557722008125 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 557722008126 putative effector binding pocket; other site 557722008127 putative dimerization interface [polypeptide binding]; other site 557722008128 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 557722008129 Neutral trehalase [Carbohydrate transport and metabolism]; Region: TreA; COG1626 557722008130 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 557722008131 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 557722008132 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional; Region: PRK06938 557722008133 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722008134 inhibitor-cofactor binding pocket; inhibition site 557722008135 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722008136 catalytic residue [active] 557722008137 MbtH-like protein; Region: MbtH; cl01279 557722008138 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 557722008139 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722008140 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 557722008141 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 557722008142 ABC-ATPase subunit interface; other site 557722008143 dimer interface [polypeptide binding]; other site 557722008144 putative PBP binding regions; other site 557722008145 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 557722008146 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 557722008147 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 557722008148 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 557722008149 intersubunit interface [polypeptide binding]; other site 557722008150 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 557722008151 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 557722008152 FAD binding pocket [chemical binding]; other site 557722008153 FAD binding motif [chemical binding]; other site 557722008154 phosphate binding motif [ion binding]; other site 557722008155 NAD binding pocket [chemical binding]; other site 557722008156 peptide synthase; Provisional; Region: PRK12467 557722008157 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008158 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008159 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008160 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008161 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 557722008162 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008163 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008164 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008165 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008166 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 557722008167 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008168 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008169 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008170 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008171 Condensation domain; Region: Condensation; pfam00668 557722008172 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 557722008173 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008174 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008175 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008176 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008177 peptide synthase; Provisional; Region: PRK12316 557722008178 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008179 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008180 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008181 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008182 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 557722008183 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008184 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008185 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008186 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 557722008187 peptide synthase; Provisional; Region: PRK12467 557722008188 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008189 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008190 Thioesterase domain; Region: Thioesterase; pfam00975 557722008191 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722008192 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 557722008193 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722008194 N-terminal plug; other site 557722008195 ligand-binding site [chemical binding]; other site 557722008196 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 557722008197 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722008198 Walker A/P-loop; other site 557722008199 ATP binding site [chemical binding]; other site 557722008200 ABC transporter signature motif; other site 557722008201 Walker B; other site 557722008202 D-loop; other site 557722008203 H-loop/switch region; other site 557722008204 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722008205 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 557722008206 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722008207 N-terminal plug; other site 557722008208 ligand-binding site [chemical binding]; other site 557722008209 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 557722008210 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722008211 Walker A/P-loop; other site 557722008212 ATP binding site [chemical binding]; other site 557722008213 ABC transporter signature motif; other site 557722008214 Walker B; other site 557722008215 D-loop; other site 557722008216 H-loop/switch region; other site 557722008217 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722008218 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 557722008219 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722008220 N-terminal plug; other site 557722008221 ligand-binding site [chemical binding]; other site 557722008222 cyclic peptide transporter; Region: cyc_pep_trnsptr; TIGR01194 557722008223 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722008224 Walker A/P-loop; other site 557722008225 ATP binding site [chemical binding]; other site 557722008226 ABC transporter signature motif; other site 557722008227 Walker B; other site 557722008228 D-loop; other site 557722008229 H-loop/switch region; other site 557722008230 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 557722008231 catalytic site [active] 557722008232 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 557722008233 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 557722008234 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722008235 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722008236 catalytic residue [active] 557722008237 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 557722008238 active site 557722008239 dimer interface [polypeptide binding]; other site 557722008240 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722008241 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 557722008242 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 557722008243 Walker A/P-loop; other site 557722008244 ATP binding site [chemical binding]; other site 557722008245 Q-loop/lid; other site 557722008246 ABC transporter signature motif; other site 557722008247 Walker B; other site 557722008248 D-loop; other site 557722008249 H-loop/switch region; other site 557722008250 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557722008251 FtsX-like permease family; Region: FtsX; cl15850 557722008252 macrolide transporter subunit MacA; Provisional; Region: PRK11578 557722008253 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722008254 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722008255 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722008256 FecR protein; Region: FecR; pfam04773 557722008257 RNA polymerase sigma factor; Reviewed; Region: PRK12527 557722008258 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722008259 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 557722008260 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008261 Penicillin amidase; Region: Penicil_amidase; pfam01804 557722008262 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 557722008263 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 557722008264 active site 557722008265 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 557722008266 Helix-turn-helix domains; Region: HTH; cl00088 557722008267 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722008268 Helix-turn-helix domains; Region: HTH; cl00088 557722008269 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722008270 dimerization interface [polypeptide binding]; other site 557722008271 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 557722008272 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 557722008273 phosphate binding site [ion binding]; other site 557722008274 Protein of unknown function (DUF1654); Region: DUF1654; pfam07867 557722008275 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 557722008276 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 557722008277 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 557722008278 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 557722008279 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722008280 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 557722008281 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722008282 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722008283 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722008284 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722008285 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722008286 active site 557722008287 phosphorylation site [posttranslational modification] 557722008288 intermolecular recognition site; other site 557722008289 dimerization interface [polypeptide binding]; other site 557722008290 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722008291 DNA binding residues [nucleotide binding] 557722008292 dimerization interface [polypeptide binding]; other site 557722008293 Domain of unknown function (DUF4280); Region: DUF4280; pfam14107 557722008294 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 557722008295 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722008296 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722008297 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722008298 baseplate hub subunit and tail lysozyme; Provisional; Region: 5; PHA02596 557722008299 Gp5 C-terminal repeat (3 copies); Region: Gp5_C; pfam06715 557722008300 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 557722008301 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722008302 Walker A motif; other site 557722008303 ATP binding site [chemical binding]; other site 557722008304 Walker B motif; other site 557722008305 arginine finger; other site 557722008306 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722008307 Walker A motif; other site 557722008308 ATP binding site [chemical binding]; other site 557722008309 Walker B motif; other site 557722008310 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 557722008311 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 557722008312 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 557722008313 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557722008314 Protein of unknown function (DUF796); Region: DUF796; cl01226 557722008315 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 557722008316 Protein of unknown function (DUF877); Region: DUF877; pfam05943 557722008317 Protein of unknown function (DUF770); Region: DUF770; cl01402 557722008318 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 557722008319 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 557722008320 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 557722008321 Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]; Region: IcmF; COG3523 557722008322 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 557722008323 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 557722008324 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 557722008325 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 557722008326 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722008327 Walker A motif; other site 557722008328 ATP binding site [chemical binding]; other site 557722008329 Walker B motif; other site 557722008330 arginine finger; other site 557722008331 Helix-turn-helix domains; Region: HTH; cl00088 557722008332 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722008333 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 557722008334 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 557722008335 active site 557722008336 dimer interface [polypeptide binding]; other site 557722008337 non-prolyl cis peptide bond; other site 557722008338 insertion regions; other site 557722008339 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 557722008340 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 557722008341 Flavin binding site [chemical binding]; other site 557722008342 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722008343 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722008344 Walker A motif; other site 557722008345 ATP binding site [chemical binding]; other site 557722008346 Walker B motif; other site 557722008347 arginine finger; other site 557722008348 Predicted ATPase [General function prediction only]; Region: COG1485 557722008349 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722008350 Walker A/P-loop; other site 557722008351 ATP binding site [chemical binding]; other site 557722008352 Q-loop/lid; other site 557722008353 ABC transporter signature motif; other site 557722008354 Walker B; other site 557722008355 D-loop; other site 557722008356 H-loop/switch region; other site 557722008357 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 557722008358 Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins; Region: GDPD_SaGlpQ_like; cd08601 557722008359 active site 557722008360 catalytic site [active] 557722008361 metal binding site [ion binding]; metal-binding site 557722008362 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722008363 dimer interface [polypeptide binding]; other site 557722008364 conserved gate region; other site 557722008365 ABC-ATPase subunit interface; other site 557722008366 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 557722008367 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 557722008368 Walker A/P-loop; other site 557722008369 ATP binding site [chemical binding]; other site 557722008370 Q-loop/lid; other site 557722008371 ABC transporter signature motif; other site 557722008372 Walker B; other site 557722008373 D-loop; other site 557722008374 H-loop/switch region; other site 557722008375 NIL domain; Region: NIL; cl09633 557722008376 NMT1-like family; Region: NMT1_2; cl15260 557722008377 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 557722008378 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 557722008379 active site 557722008380 non-prolyl cis peptide bond; other site 557722008381 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 557722008382 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722008383 active site 557722008384 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 557722008385 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722008386 active site 557722008387 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 557722008388 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557722008389 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 557722008390 putative substrate binding site [chemical binding]; other site 557722008391 putative ATP binding site [chemical binding]; other site 557722008392 D-xylulose kinases, subgroup 1; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_1; cd07809 557722008393 N- and C-terminal domain interface [polypeptide binding]; other site 557722008394 D-xylulose kinase; Region: XylB; TIGR01312 557722008395 active site 557722008396 catalytic site [active] 557722008397 metal binding site [ion binding]; metal-binding site 557722008398 xylulose binding site [chemical binding]; other site 557722008399 ATP binding site [chemical binding]; other site 557722008400 putative homodimer interface [polypeptide binding]; other site 557722008401 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 557722008402 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 557722008403 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 557722008404 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 557722008405 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 557722008406 Walker A/P-loop; other site 557722008407 ATP binding site [chemical binding]; other site 557722008408 Q-loop/lid; other site 557722008409 ABC transporter signature motif; other site 557722008410 Walker B; other site 557722008411 D-loop; other site 557722008412 H-loop/switch region; other site 557722008413 TOBE domain; Region: TOBE_2; cl01440 557722008414 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 557722008415 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722008416 dimer interface [polypeptide binding]; other site 557722008417 conserved gate region; other site 557722008418 ABC-ATPase subunit interface; other site 557722008419 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722008420 dimer interface [polypeptide binding]; other site 557722008421 conserved gate region; other site 557722008422 putative PBP binding loops; other site 557722008423 ABC-ATPase subunit interface; other site 557722008424 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722008425 Cupin domain; Region: Cupin_2; cl09118 557722008426 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722008427 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722008428 Arylsulfotransferase (ASST); Region: Arylsulfotrans; pfam05935 557722008429 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722008430 substrate binding site [chemical binding]; other site 557722008431 activation loop (A-loop); other site 557722008432 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722008433 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722008434 N-terminal plug; other site 557722008435 ligand-binding site [chemical binding]; other site 557722008436 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008437 Helix-turn-helix domains; Region: HTH; cl00088 557722008438 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722008439 dimerization interface [polypeptide binding]; other site 557722008440 Sulfatase; Region: Sulfatase; cl10460 557722008441 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 557722008442 Cupin domain; Region: Cupin_2; cl09118 557722008443 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722008444 Uncharacterized conserved protein [Function unknown]; Region: COG2128 557722008445 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557722008446 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722008447 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557722008448 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557722008449 Walker A/P-loop; other site 557722008450 ATP binding site [chemical binding]; other site 557722008451 Q-loop/lid; other site 557722008452 ABC transporter signature motif; other site 557722008453 Walker B; other site 557722008454 D-loop; other site 557722008455 H-loop/switch region; other site 557722008456 NMT1-like family; Region: NMT1_2; cl15260 557722008457 NMT1/THI5 like; Region: NMT1; pfam09084 557722008458 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722008459 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 557722008460 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 557722008461 active site 557722008462 non-prolyl cis peptide bond; other site 557722008463 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 557722008464 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 557722008465 Flavin binding site [chemical binding]; other site 557722008466 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 557722008467 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 557722008468 Flavin binding site [chemical binding]; other site 557722008469 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 557722008470 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722008471 tetrameric interface [polypeptide binding]; other site 557722008472 activator binding site; other site 557722008473 NADP binding site [chemical binding]; other site 557722008474 substrate binding site [chemical binding]; other site 557722008475 catalytic residues [active] 557722008476 GntP family permease; Region: GntP_permease; pfam02447 557722008477 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 557722008478 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 557722008479 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 557722008480 ATP-binding site [chemical binding]; other site 557722008481 Gluconate-6-phosphate binding site [chemical binding]; other site 557722008482 Transcriptional regulators [Transcription]; Region: PurR; COG1609 557722008483 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557722008484 DNA binding site [nucleotide binding] 557722008485 domain linker motif; other site 557722008486 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 557722008487 putative ligand binding site [chemical binding]; other site 557722008488 putative dimerization interface [polypeptide binding]; other site 557722008489 Cupin domain; Region: Cupin_2; cl09118 557722008490 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008491 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722008492 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008493 Helix-turn-helix domains; Region: HTH; cl00088 557722008494 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_7; cd08476 557722008495 putative dimerization interface [polypeptide binding]; other site 557722008496 putative effector binding pocket; other site 557722008497 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722008498 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557722008499 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722008500 non-specific DNA binding site [nucleotide binding]; other site 557722008501 salt bridge; other site 557722008502 sequence-specific DNA binding site [nucleotide binding]; other site 557722008503 Cupin domain; Region: Cupin_2; cl09118 557722008504 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 557722008505 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 557722008506 NMT1-like family; Region: NMT1_2; cl15260 557722008507 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557722008508 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557722008509 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557722008510 Walker A/P-loop; other site 557722008511 ATP binding site [chemical binding]; other site 557722008512 Q-loop/lid; other site 557722008513 ABC transporter signature motif; other site 557722008514 Walker B; other site 557722008515 D-loop; other site 557722008516 H-loop/switch region; other site 557722008517 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722008518 LysE type translocator; Region: LysE; cl00565 557722008519 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 557722008520 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008521 peptide synthase; Validated; Region: PRK05691 557722008522 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008523 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 557722008524 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 557722008525 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 557722008526 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 557722008527 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008528 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008529 peptide synthase; Provisional; Region: PRK12467 557722008530 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008531 Condensation domain; Region: Condensation; pfam00668 557722008532 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 557722008533 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722008534 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 557722008535 PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's...; Region: PA2301; cd04939 557722008536 putative deacylase active site [active] 557722008537 GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18; Region: GH18_chitinase_D-like; cd02871 557722008538 Glycosyl hydrolases family 18; Region: Glyco_hydro_18; pfam00704 557722008539 putative active site [active] 557722008540 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 557722008541 Interdomain contacts; other site 557722008542 Cytokine receptor motif; other site 557722008543 Chitin/cellulose binding domain. Putative carbohydrate binding domain found in many different glycosyl hydrolase enzymes. May occur in tandem arrangements; Region: ChtBD3; cl00046 557722008544 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 557722008545 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722008546 DNA-binding site [nucleotide binding]; DNA binding site 557722008547 UTRA domain; Region: UTRA; cl01230 557722008548 putative oxidoreductase; Provisional; Region: PRK08275 557722008549 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008550 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 557722008551 adenosine phosphosulphate reductase, beta subunit; Region: aprB; TIGR02060 557722008552 NMT1-like family; Region: NMT1_2; cl15260 557722008553 NMT1/THI5 like; Region: NMT1; pfam09084 557722008554 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 557722008555 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557722008556 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 557722008557 Walker A/P-loop; other site 557722008558 ATP binding site [chemical binding]; other site 557722008559 Q-loop/lid; other site 557722008560 ABC transporter signature motif; other site 557722008561 Walker B; other site 557722008562 D-loop; other site 557722008563 H-loop/switch region; other site 557722008564 putative oxidoreductase/HEAT repeat-containing protein; Provisional; Region: PRK13800 557722008565 PBS lyase HEAT-like repeat; Region: HEAT_PBS; cl15388 557722008566 Protein of unknown function (DUF971); Region: DUF971; cl01414 557722008567 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 557722008568 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 557722008569 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 557722008570 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 557722008571 Trp docking motif [polypeptide binding]; other site 557722008572 putative active site [active] 557722008573 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722008574 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722008575 N-terminal plug; other site 557722008576 ligand-binding site [chemical binding]; other site 557722008577 Peptidase family M48; Region: Peptidase_M48; cl12018 557722008578 Peptidase family M48; Region: Peptidase_M48; cl12018 557722008579 Peptidase family M48; Region: Peptidase_M48; cl12018 557722008580 Helix-turn-helix domains; Region: HTH; cl00088 557722008581 DNA-binding interface [nucleotide binding]; DNA binding site 557722008582 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722008583 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722008584 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722008585 Low molecular weight phosphatase family; Region: LMWPc; cd00115 557722008586 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 557722008587 active site 557722008588 arsenical pump membrane protein; Provisional; Region: PRK15445 557722008589 Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a...; Region: ArsB_permease; cd01118 557722008590 transmembrane helices; other site 557722008591 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722008592 dimerization interface [polypeptide binding]; other site 557722008593 putative DNA binding site [nucleotide binding]; other site 557722008594 putative Zn2+ binding site [ion binding]; other site 557722008595 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 557722008596 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722008597 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722008598 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 557722008599 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 557722008600 putative NAD(P) binding site [chemical binding]; other site 557722008601 putative substrate binding site [chemical binding]; other site 557722008602 catalytic Zn binding site [ion binding]; other site 557722008603 structural Zn binding site [ion binding]; other site 557722008604 dimer interface [polypeptide binding]; other site 557722008605 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 557722008606 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 557722008607 DNA binding residues [nucleotide binding] 557722008608 dimer interface [polypeptide binding]; other site 557722008609 [2Fe-2S] cluster binding site [ion binding]; other site 557722008610 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 557722008611 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557722008612 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722008613 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557722008614 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722008615 Coenzyme A binding pocket [chemical binding]; other site 557722008616 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722008617 Helix-turn-helix domains; Region: HTH; cl00088 557722008618 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722008619 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 557722008620 conserved cys residue [active] 557722008621 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722008622 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008623 Helix-turn-helix domains; Region: HTH; cl00088 557722008624 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722008625 dimerization interface [polypeptide binding]; other site 557722008626 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557722008627 Cytochrome c; Region: Cytochrom_C; cl11414 557722008628 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 557722008629 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557722008630 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 557722008631 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional; Region: PRK15409 557722008632 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008633 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722008634 D-galactonate transporter; Region: 2A0114; TIGR00893 557722008635 putative substrate translocation pore; other site 557722008636 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 557722008637 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557722008638 substrate binding site [chemical binding]; other site 557722008639 ATP binding site [chemical binding]; other site 557722008640 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 557722008641 Transcriptional regulators [Transcription]; Region: PurR; COG1609 557722008642 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557722008643 DNA binding site [nucleotide binding] 557722008644 domain linker motif; other site 557722008645 Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Region: PBP1_RegR_EndR_KdgR_like; cd06283 557722008646 putative dimerization interface [polypeptide binding]; other site 557722008647 putative ligand binding site [chemical binding]; other site 557722008648 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008649 Helix-turn-helix domains; Region: HTH; cl00088 557722008650 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722008651 putative effector binding pocket; other site 557722008652 dimerization interface [polypeptide binding]; other site 557722008653 Cytochrome c; Region: Cytochrom_C; cl11414 557722008654 Cytochrome c; Region: Cytochrom_C; cl11414 557722008655 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2368 557722008656 4-hydroxyphenylacetate 3-hydroxylase C terminal; Region: HpaB; pfam03241 557722008657 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cd00250 557722008658 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 557722008659 substrate binding pocket [chemical binding]; other site 557722008660 active site 557722008661 iron coordination sites [ion binding]; other site 557722008662 Pyoverdine/dityrosine biosynthesis protein [Secondary metabolites biosynthesis, transport, and catabolism]; Region: DIT1; COG3207 557722008663 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 557722008664 active site 557722008665 homodimer interface [polypeptide binding]; other site 557722008666 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 557722008667 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 557722008668 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722008669 dihydrolipoamide dehydrogenase; Validated; Region: PRK05976 557722008670 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722008671 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722008672 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 557722008673 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722008674 E3 interaction surface; other site 557722008675 lipoyl attachment site [posttranslational modification]; other site 557722008676 e3 binding domain; Region: E3_binding; pfam02817 557722008677 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 557722008678 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 557722008679 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 557722008680 alpha subunit interface [polypeptide binding]; other site 557722008681 TPP binding site [chemical binding]; other site 557722008682 heterodimer interface [polypeptide binding]; other site 557722008683 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557722008684 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal; Region: OxoDH_E1alpha_N; pfam12573 557722008685 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 557722008686 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 557722008687 tetramer interface [polypeptide binding]; other site 557722008688 TPP-binding site [chemical binding]; other site 557722008689 heterodimer interface [polypeptide binding]; other site 557722008690 phosphorylation loop region [posttranslational modification] 557722008691 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722008692 Helix-turn-helix domains; Region: HTH; cl00088 557722008693 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 557722008694 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 557722008695 DNA binding site [nucleotide binding] 557722008696 active site 557722008697 Int/Topo IB signature motif; other site 557722008698 catalytic residues [active] 557722008699 putative FAD-binding dehydrogenase; Reviewed; Region: PRK06134 557722008700 OpgC protein; Region: OpgC_C; cl00792 557722008701 Acyltransferase family; Region: Acyl_transf_3; pfam01757 557722008702 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 557722008703 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722008704 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 557722008705 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 557722008706 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 557722008707 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; cl15381 557722008708 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722008709 This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides; Region: GT1_ecORF704_like; cd03822 557722008710 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 557722008711 Chain length determinant protein; Region: Wzz; cl15801 557722008712 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722008713 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 557722008714 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 557722008715 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 557722008716 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722008717 active site 557722008718 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 557722008719 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 557722008720 Substrate binding site; other site 557722008721 Cupin domain; Region: Cupin_2; cl09118 557722008722 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 557722008723 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008724 Bacterial sugar transferase; Region: Bac_transf; cl00939 557722008725 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722008726 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722008727 catalytic residue [active] 557722008728 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 557722008729 MOSC domain; Region: MOSC; pfam03473 557722008730 3-alpha domain; Region: 3-alpha; pfam03475 557722008731 LESGI-4 557722008732 sepiapterin reductase; Region: sepiapter_red; TIGR01500 557722008733 classical (c) SDRs; Region: SDR_c; cd05233 557722008734 NAD(P) binding site [chemical binding]; other site 557722008735 active site 557722008736 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722008737 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2508 557722008738 Helix-turn-helix domains; Region: HTH; cl00088 557722008739 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722008740 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 557722008741 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 557722008742 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 557722008743 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 557722008744 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008745 FAD dependent oxidoreductase; Region: DAO; pfam01266 557722008746 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722008747 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 557722008748 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008749 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008750 NAD(P) binding pocket [chemical binding]; other site 557722008751 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722008752 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722008753 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 557722008754 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 557722008755 active site 557722008756 NAD binding site [chemical binding]; other site 557722008757 metal binding site [ion binding]; metal-binding site 557722008758 amino acid transporter; Region: 2A0306; TIGR00909 557722008759 Spore germination protein; Region: Spore_permease; cl15802 557722008760 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722008761 Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like; Region: ALDH_ABALDH-YdcW; cd07092 557722008762 tetrameric interface [polypeptide binding]; other site 557722008763 NAD binding site [chemical binding]; other site 557722008764 catalytic residues [active] 557722008765 substrate binding site [chemical binding]; other site 557722008766 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 557722008767 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722008768 inhibitor-cofactor binding pocket; inhibition site 557722008769 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722008770 catalytic residue [active] 557722008771 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008772 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557722008773 Sodium:solute symporter family; Region: SSF; cl00456 557722008774 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557722008775 Protein of unknown function, DUF485; Region: DUF485; cl01231 557722008776 acyl-CoA synthetase; Validated; Region: PRK08162 557722008777 AMP-binding enzyme; Region: AMP-binding; cl15778 557722008778 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722008779 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722008780 classical (c) SDRs; Region: SDR_c; cd05233 557722008781 NAD(P) binding site [chemical binding]; other site 557722008782 active site 557722008783 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722008784 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 557722008785 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 557722008786 active site 557722008787 Phosphotransferase enzyme family; Region: APH; pfam01636 557722008788 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 557722008789 putative active site [active] 557722008790 putative substrate binding site [chemical binding]; other site 557722008791 ATP binding site [chemical binding]; other site 557722008792 Propionate catabolism activator; Region: PrpR_N; pfam06506 557722008793 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722008794 PAS domain; Region: PAS_9; pfam13426 557722008795 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 557722008796 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722008797 Walker A motif; other site 557722008798 ATP binding site [chemical binding]; other site 557722008799 Walker B motif; other site 557722008800 arginine finger; other site 557722008801 Helix-turn-helix domains; Region: HTH; cl00088 557722008802 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 557722008803 mce related protein; Region: MCE; pfam02470 557722008804 mce related protein; Region: MCE; pfam02470 557722008805 mce related protein; Region: MCE; pfam02470 557722008806 mce related protein; Region: MCE; pfam02470 557722008807 mce related protein; Region: MCE; pfam02470 557722008808 mce related protein; Region: MCE; pfam02470 557722008809 Paraquat-inducible protein A; Region: PqiA; pfam04403 557722008810 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 557722008811 dimer interface [polypeptide binding]; other site 557722008812 NADP binding site [chemical binding]; other site 557722008813 catalytic residues [active] 557722008814 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722008815 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 557722008816 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic...; Region: MR_like_2; cd03327 557722008817 putative active site pocket [active] 557722008818 putative metal binding site [ion binding]; other site 557722008819 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 557722008820 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722008821 putative substrate translocation pore; other site 557722008822 outer membrane porin, OprD family; Region: OprD; pfam03573 557722008823 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 557722008824 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 557722008825 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 557722008826 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 557722008827 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 557722008828 NMT1-like family; Region: NMT1_2; cl15260 557722008829 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 557722008830 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 557722008831 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722008832 Helix-turn-helix domains; Region: HTH; cl00088 557722008833 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722008834 dimerization interface [polypeptide binding]; other site 557722008835 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722008836 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722008837 substrate binding pocket [chemical binding]; other site 557722008838 membrane-bound complex binding site; other site 557722008839 hinge residues; other site 557722008840 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722008841 dimer interface [polypeptide binding]; other site 557722008842 conserved gate region; other site 557722008843 putative PBP binding loops; other site 557722008844 ABC-ATPase subunit interface; other site 557722008845 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722008846 dimer interface [polypeptide binding]; other site 557722008847 conserved gate region; other site 557722008848 putative PBP binding loops; other site 557722008849 ABC-ATPase subunit interface; other site 557722008850 Domain of unknown function (DUF1911); Region: DUF1911; pfam08929 557722008851 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 557722008852 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722008853 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557722008854 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722008855 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 557722008856 Prostaglandin dehydrogenases; Region: PGDH; cd05288 557722008857 NAD(P) binding site [chemical binding]; other site 557722008858 substrate binding site [chemical binding]; other site 557722008859 dimer interface [polypeptide binding]; other site 557722008860 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722008861 Helix-turn-helix domains; Region: HTH; cl00088 557722008862 Protein of unknown function (DUF2755); Region: DUF2755; pfam10954 557722008863 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 557722008864 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 557722008865 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008866 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557722008867 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 557722008868 FOG: CBS domain [General function prediction only]; Region: COG0517 557722008869 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 557722008870 Anthrax toxin LF subunit; Region: Anthrax_toxA; pfam03497 557722008871 General stress protein [General function prediction only]; Region: GsiB; COG3729 557722008872 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 557722008873 active site 557722008874 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 557722008875 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 557722008876 NAD binding site [chemical binding]; other site 557722008877 catalytic Zn binding site [ion binding]; other site 557722008878 structural Zn binding site [ion binding]; other site 557722008879 Low affinity iron permease; Region: Iron_permease; cl12096 557722008880 Manganese catalase, ferritin-like diiron-binding domain; Region: Mn_catalase; cd01051 557722008881 dimanganese center [ion binding]; other site 557722008882 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 557722008883 dinuclear metal binding motif [ion binding]; other site 557722008884 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 557722008885 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 557722008886 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 557722008887 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 557722008888 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722008889 S-adenosylmethionine binding site [chemical binding]; other site 557722008890 Yip1 domain; Region: Yip1; cl12048 557722008891 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722008892 PAS domain; Region: PAS_9; pfam13426 557722008893 putative active site [active] 557722008894 heme pocket [chemical binding]; other site 557722008895 PAS domain S-box; Region: sensory_box; TIGR00229 557722008896 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722008897 putative active site [active] 557722008898 heme pocket [chemical binding]; other site 557722008899 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722008900 dimer interface [polypeptide binding]; other site 557722008901 phosphorylation site [posttranslational modification] 557722008902 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722008903 ATP binding site [chemical binding]; other site 557722008904 Mg2+ binding site [ion binding]; other site 557722008905 G-X-G motif; other site 557722008906 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722008907 active site 557722008908 phosphorylation site [posttranslational modification] 557722008909 intermolecular recognition site; other site 557722008910 dimerization interface [polypeptide binding]; other site 557722008911 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722008912 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 557722008913 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 557722008914 metal binding site [ion binding]; metal-binding site 557722008915 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 557722008916 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 557722008917 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 557722008918 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722008919 Protein of unknown function (DUF3182); Region: DUF3182; pfam11379 557722008920 Protein of unknown function (DUF3509); Region: DUF3509; pfam12021 557722008921 glycogen synthase; Provisional; Region: glgA; PRK00654 557722008922 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 557722008923 ADP-binding pocket [chemical binding]; other site 557722008924 homodimer interface [polypeptide binding]; other site 557722008925 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 557722008926 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 557722008927 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 557722008928 catalytic site [active] 557722008929 active site 557722008930 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 557722008931 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 557722008932 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 557722008933 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 557722008934 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 557722008935 active site 557722008936 catalytic site [active] 557722008937 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 557722008938 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 557722008939 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 557722008940 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 557722008941 active site 557722008942 catalytic site [active] 557722008943 FOG: CBS domain [General function prediction only]; Region: COG0517 557722008944 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 557722008945 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1; Region: FDH_like_1; cd08283 557722008946 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 557722008947 NAD binding site [chemical binding]; other site 557722008948 catalytic Zn binding site [ion binding]; other site 557722008949 structural Zn binding site [ion binding]; other site 557722008950 Protein of unknown function DUF72; Region: DUF72; cl00777 557722008951 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 557722008952 putative catalytic site [active] 557722008953 putative metal binding site [ion binding]; other site 557722008954 putative phosphate binding site [ion binding]; other site 557722008955 cardiolipin synthase 2; Provisional; Region: PRK11263 557722008956 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 557722008957 putative active site [active] 557722008958 catalytic site [active] 557722008959 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 557722008960 putative active site [active] 557722008961 catalytic site [active] 557722008962 Predicted integral membrane protein [Function unknown]; Region: COG0392 557722008963 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 557722008964 glycogen branching enzyme; Provisional; Region: PRK05402 557722008965 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 557722008966 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 557722008967 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 557722008968 active site 557722008969 catalytic site [active] 557722008970 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 557722008971 trehalose synthase; Region: treS_nterm; TIGR02456 557722008972 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 557722008973 active site 557722008974 catalytic site [active] 557722008975 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; cl01286 557722008976 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 557722008977 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 557722008978 active site 557722008979 homodimer interface [polypeptide binding]; other site 557722008980 catalytic site [active] 557722008981 acceptor binding site [chemical binding]; other site 557722008982 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 557722008983 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 557722008984 putative DNA binding site [nucleotide binding]; other site 557722008985 putative homodimer interface [polypeptide binding]; other site 557722008986 MgtC family; Region: MgtC; pfam02308 557722008987 hydroperoxidase II; Provisional; Region: katE; PRK11249 557722008988 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 557722008989 tetramer interface [polypeptide binding]; other site 557722008990 heme binding pocket [chemical binding]; other site 557722008991 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 557722008992 domain interactions; other site 557722008993 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 557722008994 homodimer interface [polypeptide binding]; other site 557722008995 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 557722008996 active site pocket [active] 557722008997 Hypothetical protein (DUF2513); Region: DUF2513; pfam10711 557722008998 short chain dehydrogenase; Provisional; Region: PRK06701 557722008999 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 557722009000 NAD binding site [chemical binding]; other site 557722009001 metal binding site [ion binding]; metal-binding site 557722009002 active site 557722009003 Competence-damaged protein; Region: CinA; cl00666 557722009004 Prokaryotic metallothionein; Region: Metallothio_Pro; pfam02069 557722009005 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 557722009006 DNA polymerase Ligase (LigD); Region: LigD_N; cl11819 557722009007 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 557722009008 active site 557722009009 DNA binding site [nucleotide binding] 557722009010 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 557722009011 DNA binding site [nucleotide binding] 557722009012 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 557722009013 nucleotide binding site [chemical binding]; other site 557722009014 histidine kinase; Provisional; Region: PRK13557 557722009015 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 557722009016 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557722009017 Domain of unknown function (DUF305); Region: DUF305; cl15795 557722009018 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722009019 fimbrial assembly chaperone SthB; Provisional; Region: PRK15295 557722009020 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722009021 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 557722009022 Fimbrial protein; Region: Fimbrial; cl01416 557722009023 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 557722009024 PapC N-terminal domain; Region: PapC_N; pfam13954 557722009025 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 557722009026 PapC C-terminal domain; Region: PapC_C; pfam13953 557722009027 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722009028 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 557722009029 Fimbrial protein; Region: Fimbrial; cl01416 557722009030 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]; Region: COG3969 557722009031 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 557722009032 Active Sites [active] 557722009033 Domain of unknown function (DUF3440); Region: DUF3440; pfam11922 557722009034 ParB-like nuclease domain; Region: ParBc; cl02129 557722009035 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722009036 Pseudomonas putida aldehyde dehydrogenase PsfA (ACA09737)-like; Region: ALDH_PsfA-ACA09737; cd07120 557722009037 NAD(P) binding site [chemical binding]; other site 557722009038 catalytic residues [active] 557722009039 choline dehydrogenase; Validated; Region: PRK02106 557722009040 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009041 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557722009042 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722009043 Helix-turn-helix domains; Region: HTH; cl00088 557722009044 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722009045 putative effector binding pocket; other site 557722009046 dimerization interface [polypeptide binding]; other site 557722009047 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cd07812 557722009048 hydrophobic ligand binding site; other site 557722009049 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 557722009050 Helix-turn-helix domains; Region: HTH; cl00088 557722009051 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 557722009052 substrate binding pocket [chemical binding]; other site 557722009053 dimerization interface [polypeptide binding]; other site 557722009054 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722009055 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 557722009056 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 557722009057 tetramer interface [polypeptide binding]; other site 557722009058 catalytic Zn binding site [ion binding]; other site 557722009059 NADP binding site [chemical binding]; other site 557722009060 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 557722009061 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 557722009062 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 557722009063 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 557722009064 DNA binding site [nucleotide binding] 557722009065 active site 557722009066 Protein of unknown function (DUF1445); Region: DUF1445; cl01790 557722009067 Helix-turn-helix domains; Region: HTH; cl00088 557722009068 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722009069 dimerization interface [polypeptide binding]; other site 557722009070 benzoate transport; Region: 2A0115; TIGR00895 557722009071 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009072 putative substrate translocation pore; other site 557722009073 outer membrane porin, OprD family; Region: OprD; pfam03573 557722009074 LamB/YcsF family; Region: LamB_YcsF; cl00664 557722009075 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 557722009076 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 557722009077 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 557722009078 Domain of unknown function (DUF305); Region: DUF305; cl15795 557722009079 thiamine pyrophosphate protein; Provisional; Region: PRK08273 557722009080 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 557722009081 PYR/PP interface [polypeptide binding]; other site 557722009082 tetramer interface [polypeptide binding]; other site 557722009083 dimer interface [polypeptide binding]; other site 557722009084 TPP binding site [chemical binding]; other site 557722009085 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722009086 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 557722009087 TPP-binding site [chemical binding]; other site 557722009088 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009089 NAD(P) binding site [chemical binding]; other site 557722009090 active site 557722009091 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 557722009092 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 557722009093 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009094 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722009095 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722009096 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722009097 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722009098 FecR protein; Region: FecR; pfam04773 557722009099 RNA polymerase sigma factor; Provisional; Region: PRK12525 557722009100 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722009101 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722009102 DNA binding residues [nucleotide binding] 557722009103 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557722009104 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 557722009105 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722009106 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009107 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 557722009108 probable F420-dependent oxidoreductase, Rv3520c family; Region: F420_Rv3520c; TIGR03559 557722009109 dimer interface [polypeptide binding]; other site 557722009110 active site 557722009111 non-prolyl cis peptide bond; other site 557722009112 insertion regions; other site 557722009113 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722009114 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 557722009115 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722009116 N-terminal plug; other site 557722009117 ligand-binding site [chemical binding]; other site 557722009118 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009119 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722009120 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 557722009121 inter-subunit interface; other site 557722009122 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557722009123 active site 557722009124 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 557722009125 dimer interface [polypeptide binding]; other site 557722009126 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557722009127 Ligand Binding Site [chemical binding]; other site 557722009128 Molecular Tunnel; other site 557722009129 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 557722009130 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 557722009131 [2Fe-2S] cluster binding site [ion binding]; other site 557722009132 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 557722009133 putative alpha subunit interface [polypeptide binding]; other site 557722009134 putative active site [active] 557722009135 putative substrate binding site [chemical binding]; other site 557722009136 Fe binding site [ion binding]; other site 557722009137 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722009138 Helix-turn-helix domains; Region: HTH; cl00088 557722009139 Putative cyclase; Region: Cyclase; cl00814 557722009140 kynureninase; Region: kynureninase; TIGR01814 557722009141 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722009142 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722009143 catalytic residue [active] 557722009144 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 557722009145 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722009146 Helix-turn-helix domains; Region: HTH; cl00088 557722009147 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722009148 dimerization interface [polypeptide binding]; other site 557722009149 Predicted amidohydrolase [General function prediction only]; Region: COG0388 557722009150 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_2; cd07580 557722009151 putative active site [active] 557722009152 catalytic triad [active] 557722009153 putative dimer interface [polypeptide binding]; other site 557722009154 Sodium:solute symporter family; Region: SSF; cl00456 557722009155 CHASE4 domain; Region: CHASE4; cl01308 557722009156 PAS domain S-box; Region: sensory_box; TIGR00229 557722009157 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722009158 putative active site [active] 557722009159 heme pocket [chemical binding]; other site 557722009160 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722009161 metal binding site [ion binding]; metal-binding site 557722009162 active site 557722009163 I-site; other site 557722009164 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722009165 elongation factor G; Reviewed; Region: PRK00007 557722009166 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 557722009167 G1 box; other site 557722009168 putative GEF interaction site [polypeptide binding]; other site 557722009169 GTP/Mg2+ binding site [chemical binding]; other site 557722009170 Switch I region; other site 557722009171 G2 box; other site 557722009172 G3 box; other site 557722009173 Switch II region; other site 557722009174 G4 box; other site 557722009175 G5 box; other site 557722009176 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 557722009177 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 557722009178 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 557722009179 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722009180 N-terminal plug; other site 557722009181 ligand-binding site [chemical binding]; other site 557722009182 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 557722009183 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 557722009184 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 557722009185 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 557722009186 MFS_1 like family; Region: MFS_1_like; pfam12832 557722009187 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 557722009188 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722009189 motif II; other site 557722009190 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 557722009191 putative active site [active] 557722009192 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 557722009193 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722009194 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722009195 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 557722009196 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722009197 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 557722009198 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722009199 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 557722009200 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722009201 catalytic residue [active] 557722009202 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 557722009203 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722009204 Walker A/P-loop; other site 557722009205 ATP binding site [chemical binding]; other site 557722009206 Q-loop/lid; other site 557722009207 ABC transporter signature motif; other site 557722009208 Walker B; other site 557722009209 D-loop; other site 557722009210 H-loop/switch region; other site 557722009211 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722009212 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722009213 Walker A/P-loop; other site 557722009214 ATP binding site [chemical binding]; other site 557722009215 Q-loop/lid; other site 557722009216 ABC transporter signature motif; other site 557722009217 Walker B; other site 557722009218 D-loop; other site 557722009219 H-loop/switch region; other site 557722009220 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722009221 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 557722009222 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722009223 dimer interface [polypeptide binding]; other site 557722009224 conserved gate region; other site 557722009225 ABC-ATPase subunit interface; other site 557722009226 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 557722009227 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722009228 dimer interface [polypeptide binding]; other site 557722009229 conserved gate region; other site 557722009230 ABC-ATPase subunit interface; other site 557722009231 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 557722009232 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 557722009233 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722009234 N-terminal plug; other site 557722009235 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 557722009236 ligand-binding site [chemical binding]; other site 557722009237 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722009238 Helix-turn-helix domains; Region: HTH; cl00088 557722009239 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722009240 putative effector binding pocket; other site 557722009241 dimerization interface [polypeptide binding]; other site 557722009242 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557722009243 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009244 DNA-binding transcriptional regulator CynR; Provisional; Region: PRK11242 557722009245 Helix-turn-helix domains; Region: HTH; cl00088 557722009246 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold; Region: PBP2_CynR; cd08425 557722009247 dimerization interface [polypeptide binding]; other site 557722009248 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 557722009249 active site clefts [active] 557722009250 zinc binding site [ion binding]; other site 557722009251 dimer interface [polypeptide binding]; other site 557722009252 cyanate hydratase; Validated; Region: PRK02866 557722009253 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 557722009254 oligomer interface [polypeptide binding]; other site 557722009255 active site 557722009256 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722009257 FecR protein; Region: FecR; pfam04773 557722009258 RNA polymerase sigma factor; Provisional; Region: PRK12525 557722009259 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722009260 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722009261 DNA binding residues [nucleotide binding] 557722009262 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 557722009263 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 557722009264 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722009265 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 557722009266 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722009267 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722009268 Haemolytic domain; Region: Haemolytic; cl00506 557722009269 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 557722009270 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 557722009271 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSRA_1; cd02558 557722009272 probable active site [active] 557722009273 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 557722009274 Spore germination protein; Region: Spore_permease; cl15802 557722009275 amino acid transporter; Region: 2A0306; TIGR00909 557722009276 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722009277 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 557722009278 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722009279 AzlC protein; Region: AzlC; cl00570 557722009280 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 557722009281 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009282 thiamine pyrophosphate protein; Validated; Region: PRK08199 557722009283 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722009284 PYR/PP interface [polypeptide binding]; other site 557722009285 dimer interface [polypeptide binding]; other site 557722009286 TPP binding site [chemical binding]; other site 557722009287 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722009288 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 557722009289 TPP-binding site [chemical binding]; other site 557722009290 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 557722009291 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 557722009292 FAD binding pocket [chemical binding]; other site 557722009293 FAD binding motif [chemical binding]; other site 557722009294 phosphate binding motif [ion binding]; other site 557722009295 NAD binding pocket [chemical binding]; other site 557722009296 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722009297 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722009298 DNA-binding site [nucleotide binding]; DNA binding site 557722009299 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722009300 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722009301 homodimer interface [polypeptide binding]; other site 557722009302 catalytic residue [active] 557722009303 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; cl11547 557722009304 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722009305 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722009306 putative DNA binding site [nucleotide binding]; other site 557722009307 putative Zn2+ binding site [ion binding]; other site 557722009308 Helix-turn-helix domains; Region: HTH; cl00088 557722009309 Membrane transport protein; Region: Mem_trans; cl09117 557722009310 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722009311 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 557722009312 active site 557722009313 metal binding site [ion binding]; metal-binding site 557722009314 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 557722009315 active site 557722009316 tetramer interface; other site 557722009317 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 557722009318 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009319 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 557722009320 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009321 Protein of unknown function (DUF3203); Region: DUF3203; pfam11462 557722009322 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 557722009323 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722009324 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722009325 multidrug efflux protein; Reviewed; Region: PRK09577 557722009326 Protein export membrane protein; Region: SecD_SecF; cl14618 557722009327 SdiA-regulated; Region: SdiA-regulated; pfam06977 557722009328 SdiA-regulated; Region: SdiA-regulated; cd09971 557722009329 putative active site [active] 557722009330 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 557722009331 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 557722009332 DNA binding residues [nucleotide binding] 557722009333 putative dimer interface [polypeptide binding]; other site 557722009334 isovaleryl-CoA dehydrogenase; Region: PLN02519 557722009335 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 557722009336 substrate binding site [chemical binding]; other site 557722009337 FAD binding site [chemical binding]; other site 557722009338 catalytic base [active] 557722009339 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 557722009340 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722009341 gamma-carboxygeranoyl-CoA hydratase; Validated; Region: PRK05674 557722009342 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722009343 substrate binding site [chemical binding]; other site 557722009344 oxyanion hole (OAH) forming residues; other site 557722009345 trimer interface [polypeptide binding]; other site 557722009346 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 557722009347 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722009348 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722009349 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557722009350 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 557722009351 carboxyltransferase (CT) interaction site; other site 557722009352 biotinylation site [posttranslational modification]; other site 557722009353 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 557722009354 active site 557722009355 catalytic residues [active] 557722009356 metal binding site [ion binding]; metal-binding site 557722009357 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722009358 Helix-turn-helix domains; Region: HTH; cl00088 557722009359 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722009360 Cupin domain; Region: Cupin_2; cl09118 557722009361 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 557722009362 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 557722009363 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557722009364 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 557722009365 C-terminal domain interface [polypeptide binding]; other site 557722009366 GSH binding site (G-site) [chemical binding]; other site 557722009367 maleylacetoacetate isomerase; Region: maiA; TIGR01262 557722009368 putative dimer interface [polypeptide binding]; other site 557722009369 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 557722009370 dimer interface [polypeptide binding]; other site 557722009371 N-terminal domain interface [polypeptide binding]; other site 557722009372 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 557722009373 benzoate transport; Region: 2A0115; TIGR00895 557722009374 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009375 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009376 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 557722009377 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722009378 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722009379 Walker B motif; other site 557722009380 arginine finger; other site 557722009381 Helix-turn-helix domains; Region: HTH; cl00088 557722009382 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 557722009383 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 557722009384 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 557722009385 NAD binding site [chemical binding]; other site 557722009386 homotetramer interface [polypeptide binding]; other site 557722009387 homodimer interface [polypeptide binding]; other site 557722009388 substrate binding site [chemical binding]; other site 557722009389 active site 557722009390 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 557722009391 acetyl-CoA acetyltransferase; Provisional; Region: PRK05656 557722009392 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722009393 dimer interface [polypeptide binding]; other site 557722009394 active site 557722009395 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722009396 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722009397 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722009398 Helix-turn-helix domains; Region: HTH; cl00088 557722009399 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 557722009400 putative dimerization interface [polypeptide binding]; other site 557722009401 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 557722009402 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 557722009403 AMP-binding enzyme; Region: AMP-binding; cl15778 557722009404 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722009405 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722009406 Protein of unknown function (DUF419); Region: DUF419; cl15265 557722009407 Putative glycolipid-binding; Region: Glycolipid_bind; cl01425 557722009408 major facilitator superfamily transporter; Provisional; Region: PRK05122 557722009409 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009410 putative substrate translocation pore; other site 557722009411 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722009412 PAS domain S-box; Region: sensory_box; TIGR00229 557722009413 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 557722009414 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722009415 dimer interface [polypeptide binding]; other site 557722009416 phosphorylation site [posttranslational modification] 557722009417 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722009418 ATP binding site [chemical binding]; other site 557722009419 G-X-G motif; other site 557722009420 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722009421 active site 557722009422 phosphorylation site [posttranslational modification] 557722009423 intermolecular recognition site; other site 557722009424 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH4; cd08188 557722009425 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 557722009426 putative active site [active] 557722009427 metal binding site [ion binding]; metal-binding site 557722009428 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 557722009429 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722009430 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 557722009431 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722009432 FeS/SAM binding site; other site 557722009433 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 557722009434 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 557722009435 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 557722009436 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722009437 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 557722009438 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722009439 NAD(P) binding site [chemical binding]; other site 557722009440 catalytic residues [active] 557722009441 Cytochrome c; Region: Cytochrom_C; cl11414 557722009442 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 557722009443 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 557722009444 dimer interface [polypeptide binding]; other site 557722009445 Trp docking motif [polypeptide binding]; other site 557722009446 active site 557722009447 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 557722009448 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 557722009449 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 557722009450 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 557722009451 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 557722009452 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 557722009453 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722009454 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722009455 active site 557722009456 phosphorylation site [posttranslational modification] 557722009457 intermolecular recognition site; other site 557722009458 dimerization interface [polypeptide binding]; other site 557722009459 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722009460 DNA binding residues [nucleotide binding] 557722009461 dimerization interface [polypeptide binding]; other site 557722009462 Histidine kinase; Region: HisKA_3; pfam07730 557722009463 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722009464 ATP binding site [chemical binding]; other site 557722009465 Mg2+ binding site [ion binding]; other site 557722009466 G-X-G motif; other site 557722009467 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722009468 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722009469 active site 557722009470 phosphorylation site [posttranslational modification] 557722009471 intermolecular recognition site; other site 557722009472 dimerization interface [polypeptide binding]; other site 557722009473 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722009474 DNA binding residues [nucleotide binding] 557722009475 dimerization interface [polypeptide binding]; other site 557722009476 PAS fold; Region: PAS_7; pfam12860 557722009477 PAS fold; Region: PAS_7; pfam12860 557722009478 PAS fold; Region: PAS_4; pfam08448 557722009479 Intra-flagellar transport protein 57; Region: IFT57; pfam10498 557722009480 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722009481 dimer interface [polypeptide binding]; other site 557722009482 phosphorylation site [posttranslational modification] 557722009483 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722009484 ATP binding site [chemical binding]; other site 557722009485 Mg2+ binding site [ion binding]; other site 557722009486 G-X-G motif; other site 557722009487 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557722009488 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722009489 active site 557722009490 phosphorylation site [posttranslational modification] 557722009491 intermolecular recognition site; other site 557722009492 dimerization interface [polypeptide binding]; other site 557722009493 Uncharacterized conserved protein [Function unknown]; Region: COG3287 557722009494 FIST N domain; Region: FIST; cl10701 557722009495 FIST C domain; Region: FIST_C; pfam10442 557722009496 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 557722009497 coenzyme PQQ biosynthesis probable peptidase PqqF; Region: PQQ_syn_pqqF; TIGR02110 557722009498 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 557722009499 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557722009500 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 557722009501 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 557722009502 Sulfatase; Region: Sulfatase; cl10460 557722009503 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 557722009504 Potato inhibitor I family; Region: potato_inhibit; cl15459 557722009505 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 557722009506 putative substrate binding pocket [chemical binding]; other site 557722009507 trimer interface [polypeptide binding]; other site 557722009508 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 557722009509 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722009510 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722009511 ABC transporter; Region: ABC_tran_2; pfam12848 557722009512 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722009513 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722009514 LysR family transcriptional regulator; Provisional; Region: PRK14997 557722009515 Helix-turn-helix domains; Region: HTH; cl00088 557722009516 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722009517 dimerization interface [polypeptide binding]; other site 557722009518 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557722009519 DNA-binding site [nucleotide binding]; DNA binding site 557722009520 RNA-binding motif; other site 557722009521 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 557722009522 Bacitracin resistance protein BacA; Region: BacA; cl00858 557722009523 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 557722009524 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722009525 AAA domain; Region: AAA_28; pfam13521 557722009526 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39G; cd02423 557722009527 putative active site [active] 557722009528 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557722009529 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557722009530 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 557722009531 substrate binding site [chemical binding]; other site 557722009532 dimer interface [polypeptide binding]; other site 557722009533 ATP binding site [chemical binding]; other site 557722009534 Transcriptional regulators [Transcription]; Region: PurR; COG1609 557722009535 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 557722009536 DNA binding site [nucleotide binding] 557722009537 domain linker motif; other site 557722009538 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 557722009539 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 557722009540 TM-ABC transporter signature motif; other site 557722009541 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 557722009542 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_I; cd03216 557722009543 Walker A/P-loop; other site 557722009544 ATP binding site [chemical binding]; other site 557722009545 Q-loop/lid; other site 557722009546 ABC transporter signature motif; other site 557722009547 Walker B; other site 557722009548 D-loop; other site 557722009549 H-loop/switch region; other site 557722009550 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 557722009551 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 557722009552 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 557722009553 ligand binding site [chemical binding]; other site 557722009554 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722009555 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722009556 Walker A motif; other site 557722009557 ATP binding site [chemical binding]; other site 557722009558 Walker B motif; other site 557722009559 arginine finger; other site 557722009560 Helix-turn-helix domains; Region: HTH; cl00088 557722009561 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 557722009562 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 557722009563 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722009564 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 557722009565 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722009566 Coenzyme A binding pocket [chemical binding]; other site 557722009567 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage...; Region: Peptidase_C39_like; cl00296 557722009568 Catalase-like heme-binding proteins similar to the uncharacterized y4iL; Region: y4iL_like; cd08152 557722009569 putative heme binding pocket [chemical binding]; other site 557722009570 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722009571 Walker A/P-loop; other site 557722009572 ATP binding site [chemical binding]; other site 557722009573 endonuclease subunit; Provisional; Region: 46; PHA02562 557722009574 Domain of unknown function (DUF4354); Region: DUF4354; pfam14263 557722009575 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 557722009576 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 557722009577 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722009578 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 557722009579 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 557722009580 aldehyde oxidoreductase 2Fe-2S subunit; Provisional; Region: PRK11433 557722009581 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 557722009582 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722009583 PAS domain; Region: PAS_9; pfam13426 557722009584 putative active site [active] 557722009585 heme pocket [chemical binding]; other site 557722009586 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722009587 PAS domain; Region: PAS_9; pfam13426 557722009588 putative active site [active] 557722009589 heme pocket [chemical binding]; other site 557722009590 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722009591 dimer interface [polypeptide binding]; other site 557722009592 putative CheW interface [polypeptide binding]; other site 557722009593 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722009594 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557722009595 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 557722009596 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 557722009597 THF binding site; other site 557722009598 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 557722009599 substrate binding site [chemical binding]; other site 557722009600 THF binding site; other site 557722009601 zinc-binding site [ion binding]; other site 557722009602 Uncharacterized conserved protein [Function unknown]; Region: COG1944; cl09146 557722009603 YcaO-like family; Region: YcaO; pfam02624 557722009604 Uncharacterized conserved protein (DUF2149); Region: DUF2149; cl01960 557722009605 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722009606 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 557722009607 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 557722009608 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 557722009609 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 557722009610 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722009611 N-terminal plug; other site 557722009612 ligand-binding site [chemical binding]; other site 557722009613 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557722009614 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722009615 S-adenosylmethionine binding site [chemical binding]; other site 557722009616 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 557722009617 ATP cone domain; Region: ATP-cone; pfam03477 557722009618 Class III ribonucleotide reductase; Region: RNR_III; cd01675 557722009619 effector binding site; other site 557722009620 active site 557722009621 Zn binding site [ion binding]; other site 557722009622 glycine loop; other site 557722009623 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 557722009624 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722009625 FeS/SAM binding site; other site 557722009626 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009627 FAD dependent oxidoreductase; Region: DAO; pfam01266 557722009628 Cupin domain; Region: Cupin_2; cl09118 557722009629 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 557722009630 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 557722009631 Purine catabolism regulatory protein-like family; Region: PucR; pfam07905 557722009632 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2508 557722009633 Helix-turn-helix domains; Region: HTH; cl00088 557722009634 Protein of unknown function (DUF2599); Region: DUF2599; pfam10783 557722009635 RNA polymerase sigma factor; Provisional; Region: PRK12528 557722009636 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722009637 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722009638 DNA binding residues [nucleotide binding] 557722009639 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722009640 FecR protein; Region: FecR; pfam04773 557722009641 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722009642 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722009643 N-terminal plug; other site 557722009644 ligand-binding site [chemical binding]; other site 557722009645 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722009646 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722009647 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722009648 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009649 putative substrate translocation pore; other site 557722009650 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722009651 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 557722009652 Platelet-activating factor acetylhydrolase, isoform II; Region: PAF-AH_p_II; pfam03403 557722009653 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 557722009654 Pyridoxamine-phosphate oxidase [Coenzyme metabolism]; Region: PdxH; COG0259 557722009655 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557722009656 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 557722009657 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722009658 Phenazine biosynthesis-like protein; Region: PhzC-PhzF; pfam02567 557722009659 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557722009660 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557722009661 Glutamine amidotransferase class-I; Region: GATase; pfam00117 557722009662 glutamine binding [chemical binding]; other site 557722009663 catalytic triad [active] 557722009664 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological...; Region: isochorismatase; cd01013 557722009665 hydrophobic substrate binding pocket; other site 557722009666 Isochorismatase family; Region: Isochorismatase; pfam00857 557722009667 active site 557722009668 conserved cis-peptide bond; other site 557722009669 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 557722009670 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722009671 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722009672 DNA-binding transcriptional activator SdiA; Provisional; Region: PRK10188 557722009673 Autoinducer binding domain; Region: Autoind_bind; pfam03472 557722009674 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722009675 DNA binding residues [nucleotide binding] 557722009676 dimerization interface [polypeptide binding]; other site 557722009677 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 557722009678 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 557722009679 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 557722009680 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722009681 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 557722009682 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 557722009683 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 557722009684 active site 557722009685 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722009686 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 557722009687 putative C-terminal domain interface [polypeptide binding]; other site 557722009688 putative GSH binding site (G-site) [chemical binding]; other site 557722009689 putative dimer interface [polypeptide binding]; other site 557722009690 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 557722009691 putative N-terminal domain interface [polypeptide binding]; other site 557722009692 putative dimer interface [polypeptide binding]; other site 557722009693 putative substrate binding pocket (H-site) [chemical binding]; other site 557722009694 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 557722009695 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 557722009696 dimer interface [polypeptide binding]; other site 557722009697 active site 557722009698 catalytic residue [active] 557722009699 DNA polymerase II; Reviewed; Region: PRK05762 557722009700 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 557722009701 active site 557722009702 catalytic site [active] 557722009703 substrate binding site [chemical binding]; other site 557722009704 DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as...; Region: POLBc_Pol_II; cd05537 557722009705 active site 557722009706 metal-binding site 557722009707 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557722009708 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722009709 Coenzyme A binding pocket [chemical binding]; other site 557722009710 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 557722009711 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 557722009712 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722009713 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 557722009714 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 557722009715 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 557722009716 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 557722009717 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722009718 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 557722009719 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722009720 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722009721 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722009722 non-specific DNA binding site [nucleotide binding]; other site 557722009723 salt bridge; other site 557722009724 sequence-specific DNA binding site [nucleotide binding]; other site 557722009725 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722009726 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 557722009727 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722009728 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722009729 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 557722009730 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39_likeD; cd02421 557722009731 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722009732 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722009733 Walker A/P-loop; other site 557722009734 ATP binding site [chemical binding]; other site 557722009735 Q-loop/lid; other site 557722009736 ABC transporter signature motif; other site 557722009737 Walker B; other site 557722009738 D-loop; other site 557722009739 H-loop/switch region; other site 557722009740 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 557722009741 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 557722009742 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 557722009743 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 557722009744 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 557722009745 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 557722009746 EcsC protein family; Region: EcsC; pfam12787 557722009747 Peptidase family M23; Region: Peptidase_M23; pfam01551 557722009748 Phosphopantetheine attachment site; Region: PP-binding; cl09936 557722009749 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 557722009750 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722009751 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722009752 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722009753 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722009754 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 557722009755 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 557722009756 DEAD-like helicases superfamily; Region: DEXDc2; smart00488 557722009757 DEAD_2; Region: DEAD_2; pfam06733 557722009758 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 557722009759 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722009760 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 557722009761 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 557722009762 Helix-turn-helix domains; Region: HTH; cl00088 557722009763 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 557722009764 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 557722009765 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722009766 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722009767 dimer interface [polypeptide binding]; other site 557722009768 conserved gate region; other site 557722009769 putative PBP binding loops; other site 557722009770 ABC-ATPase subunit interface; other site 557722009771 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 557722009772 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722009773 Walker A/P-loop; other site 557722009774 ATP binding site [chemical binding]; other site 557722009775 Q-loop/lid; other site 557722009776 ABC transporter signature motif; other site 557722009777 Walker B; other site 557722009778 D-loop; other site 557722009779 H-loop/switch region; other site 557722009780 TOBE domain; Region: TOBE_2; cl01440 557722009781 Leucine carboxyl methyltransferase; Region: LCM; cl01306 557722009782 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722009783 Helix-turn-helix domains; Region: HTH; cl00088 557722009784 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA; cd08478 557722009785 putative effector binding pocket; other site 557722009786 dimerization interface [polypeptide binding]; other site 557722009787 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722009788 Protein of unknown function (DUF808); Region: DUF808; cl01002 557722009789 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 557722009790 Low-spin heme binding site [chemical binding]; other site 557722009791 Putative water exit pathway; other site 557722009792 Binuclear center (active site) [active] 557722009793 Putative proton exit pathway; other site 557722009794 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 557722009795 HPP family; Region: HPP; pfam04982 557722009796 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 557722009797 transcriptional regulator HdfR; Provisional; Region: PRK03601 557722009798 Helix-turn-helix domains; Region: HTH; cl00088 557722009799 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722009800 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722009801 metal binding site [ion binding]; metal-binding site 557722009802 active site 557722009803 I-site; other site 557722009804 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 557722009805 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 557722009806 conserved cys residue [active] 557722009807 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722009808 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722009809 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 557722009810 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 557722009811 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722009812 putative substrate translocation pore; other site 557722009813 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557722009814 IscR-regulated protein YhgI; Region: YhgI_GntY; TIGR03341 557722009815 NifU-like domain; Region: NifU; cl00484 557722009816 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 557722009817 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 557722009818 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 557722009819 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 557722009820 substrate binding pocket [chemical binding]; other site 557722009821 dimer interface [polypeptide binding]; other site 557722009822 inhibitor binding site; inhibition site 557722009823 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 557722009824 B12 binding site [chemical binding]; other site 557722009825 cobalt ligand [ion binding]; other site 557722009826 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 557722009827 Protein with unknown function (DUF469); Region: DUF469; cl01237 557722009828 Uncharacterized conserved protein [Function unknown]; Region: COG3760 557722009829 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 557722009830 putative deacylase active site [active] 557722009831 Domain of unknown function (DUF1883); Region: DUF1883; pfam08980 557722009832 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14464 557722009833 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 557722009834 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 557722009835 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557722009836 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557722009837 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 557722009838 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722009839 Helix-turn-helix domains; Region: HTH; cl00088 557722009840 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722009841 CoenzymeA binding site [chemical binding]; other site 557722009842 subunit interaction site [polypeptide binding]; other site 557722009843 PHB binding site; other site 557722009844 Yhdh and yhfp-like putative quinone oxidoreductases; Region: MDR_yhdh_yhfp; cd05280 557722009845 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 557722009846 NADP binding site [chemical binding]; other site 557722009847 dimer interface [polypeptide binding]; other site 557722009848 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 557722009849 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 557722009850 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 557722009851 tandem repeat interface [polypeptide binding]; other site 557722009852 oligomer interface [polypeptide binding]; other site 557722009853 active site residues [active] 557722009854 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 557722009855 catalytic core [active] 557722009856 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 557722009857 SCP-2 sterol transfer family; Region: SCP2; cl01225 557722009858 Predicted aminoglycoside phosphotransferase [General function prediction only]; Region: COG3173 557722009859 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 557722009860 putative active site [active] 557722009861 putative substrate binding site [chemical binding]; other site 557722009862 ATP binding site [chemical binding]; other site 557722009863 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722009864 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 557722009865 classical (c) SDRs; Region: SDR_c; cd05233 557722009866 NAD(P) binding site [chemical binding]; other site 557722009867 active site 557722009868 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722009869 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009870 NAD(P) binding site [chemical binding]; other site 557722009871 active site 557722009872 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 557722009873 Helix-turn-helix domains; Region: HTH; cl00088 557722009874 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 557722009875 dimerization interface [polypeptide binding]; other site 557722009876 substrate binding pocket [chemical binding]; other site 557722009877 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557722009878 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 557722009879 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 557722009880 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 557722009881 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 557722009882 putative NADH binding site [chemical binding]; other site 557722009883 putative active site [active] 557722009884 nudix motif; other site 557722009885 putative metal binding site [ion binding]; other site 557722009886 enoyl-CoA hydratase; Provisional; Region: PRK06142 557722009887 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722009888 substrate binding site [chemical binding]; other site 557722009889 oxyanion hole (OAH) forming residues; other site 557722009890 trimer interface [polypeptide binding]; other site 557722009891 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722009892 arginine:agmatin antiporter; Provisional; Region: PRK10644 557722009893 arginine decarboxylase; Provisional; Region: PRK15029 557722009894 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 557722009895 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 557722009896 homodimer interface [polypeptide binding]; other site 557722009897 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722009898 catalytic residue [active] 557722009899 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 557722009900 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722009901 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 557722009902 active site 557722009903 substrate binding site [chemical binding]; other site 557722009904 catalytic site [active] 557722009905 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 557722009906 RNA/DNA hybrid binding site [nucleotide binding]; other site 557722009907 active site 557722009908 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722009909 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 557722009910 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722009911 MltD lipid attachment motif; Region: MLTD_N; pfam06474 557722009912 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 557722009913 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722009914 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722009915 catalytic residue [active] 557722009916 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722009917 putative peptidoglycan binding site; other site 557722009918 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722009919 putative peptidoglycan binding site; other site 557722009920 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722009921 putative peptidoglycan binding site; other site 557722009922 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 557722009923 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 557722009924 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 557722009925 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 557722009926 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 557722009927 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722009928 dimer interface [polypeptide binding]; other site 557722009929 conserved gate region; other site 557722009930 putative PBP binding loops; other site 557722009931 ABC-ATPase subunit interface; other site 557722009932 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 557722009933 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 557722009934 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722009935 dimer interface [polypeptide binding]; other site 557722009936 conserved gate region; other site 557722009937 putative PBP binding loops; other site 557722009938 ABC-ATPase subunit interface; other site 557722009939 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 557722009940 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722009941 Walker A/P-loop; other site 557722009942 ATP binding site [chemical binding]; other site 557722009943 Q-loop/lid; other site 557722009944 ABC transporter signature motif; other site 557722009945 Walker B; other site 557722009946 D-loop; other site 557722009947 H-loop/switch region; other site 557722009948 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722009949 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722009950 Walker A/P-loop; other site 557722009951 ATP binding site [chemical binding]; other site 557722009952 Q-loop/lid; other site 557722009953 ABC transporter signature motif; other site 557722009954 Walker B; other site 557722009955 D-loop; other site 557722009956 H-loop/switch region; other site 557722009957 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722009958 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 557722009959 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 557722009960 NAD binding site [chemical binding]; other site 557722009961 homotetramer interface [polypeptide binding]; other site 557722009962 homodimer interface [polypeptide binding]; other site 557722009963 substrate binding site [chemical binding]; other site 557722009964 active site 557722009965 periplasmic folding chaperone; Provisional; Region: PRK10788 557722009966 SurA N-terminal domain; Region: SurA_N_3; cl07813 557722009967 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722009968 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 557722009969 IHF dimer interface [polypeptide binding]; other site 557722009970 IHF - DNA interface [nucleotide binding]; other site 557722009971 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 557722009972 Found in ATP-dependent protease La (LON); Region: LON; smart00464 557722009973 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722009974 Walker A motif; other site 557722009975 ATP binding site [chemical binding]; other site 557722009976 Walker B motif; other site 557722009977 arginine finger; other site 557722009978 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 557722009979 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 557722009980 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 557722009981 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722009982 Walker A motif; other site 557722009983 ATP binding site [chemical binding]; other site 557722009984 Walker B motif; other site 557722009985 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722009986 Clp protease; Region: CLP_protease; pfam00574 557722009987 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 557722009988 oligomer interface [polypeptide binding]; other site 557722009989 active site residues [active] 557722009990 trigger factor; Provisional; Region: tig; PRK01490 557722009991 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722009992 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 557722009993 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 557722009994 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722009995 active site 557722009996 phosphorylation site [posttranslational modification] 557722009997 intermolecular recognition site; other site 557722009998 dimerization interface [polypeptide binding]; other site 557722009999 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722010000 DNA binding site [nucleotide binding] 557722010001 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 557722010002 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722010003 dimerization interface [polypeptide binding]; other site 557722010004 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722010005 dimer interface [polypeptide binding]; other site 557722010006 phosphorylation site [posttranslational modification] 557722010007 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722010008 ATP binding site [chemical binding]; other site 557722010009 Mg2+ binding site [ion binding]; other site 557722010010 G-X-G motif; other site 557722010011 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 557722010012 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722010013 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 557722010014 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 557722010015 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 557722010016 homodimer interface [polypeptide binding]; other site 557722010017 NADP binding site [chemical binding]; other site 557722010018 substrate binding site [chemical binding]; other site 557722010019 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 557722010020 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 557722010021 active site 557722010022 HIGH motif; other site 557722010023 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 557722010024 KMSKS motif; other site 557722010025 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 557722010026 tRNA binding surface [nucleotide binding]; other site 557722010027 anticodon binding site; other site 557722010028 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 557722010029 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722010030 active site 557722010031 HIGH motif; other site 557722010032 nucleotide binding site [chemical binding]; other site 557722010033 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 557722010034 KMSKS motif; other site 557722010035 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 557722010036 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 557722010037 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 557722010038 substrate binding site [chemical binding]; other site 557722010039 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557722010040 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 557722010041 putative active site [active] 557722010042 putative metal binding site [ion binding]; other site 557722010043 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 557722010044 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 557722010045 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 557722010046 active site 557722010047 dinuclear metal binding site [ion binding]; other site 557722010048 dimerization interface [polypeptide binding]; other site 557722010049 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 557722010050 universal stress protein UspE; Provisional; Region: PRK11175 557722010051 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722010052 Ligand Binding Site [chemical binding]; other site 557722010053 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 557722010054 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 557722010055 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 557722010056 substrate binding site [chemical binding]; other site 557722010057 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 557722010058 substrate binding site [chemical binding]; other site 557722010059 ligand binding site [chemical binding]; other site 557722010060 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 557722010061 NMT1-like family; Region: NMT1_2; cl15260 557722010062 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 557722010063 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722010064 active site 557722010065 phosphorylation site [posttranslational modification] 557722010066 intermolecular recognition site; other site 557722010067 dimerization interface [polypeptide binding]; other site 557722010068 ANTAR domain; Region: ANTAR; cl04297 557722010069 Alginate lyase; Region: Alginate_lyase2; pfam08787 557722010070 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 557722010071 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010072 putative substrate translocation pore; other site 557722010073 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 557722010074 Protein kinase domain; Region: Pkinase; pfam00069 557722010075 Catalytic domain of Protein Kinases; Region: PKc; cd00180 557722010076 active site 557722010077 ATP binding site [chemical binding]; other site 557722010078 substrate binding site [chemical binding]; other site 557722010079 activation loop (A-loop); other site 557722010080 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 557722010081 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722010082 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557722010083 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557722010084 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557722010085 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 557722010086 [2Fe-2S] cluster binding site [ion binding]; other site 557722010087 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 557722010088 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 557722010089 [4Fe-4S] binding site [ion binding]; other site 557722010090 molybdopterin cofactor binding site; other site 557722010091 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 557722010092 molybdopterin cofactor binding site; other site 557722010093 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 557722010094 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557722010095 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722010096 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 557722010097 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722010098 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722010099 ligand binding site [chemical binding]; other site 557722010100 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 557722010101 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722010102 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722010103 DNA binding residues [nucleotide binding] 557722010104 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722010105 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 557722010106 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 557722010107 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 557722010108 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722010109 phosphoenolpyruvate synthase; Validated; Region: PRK06464 557722010110 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 557722010111 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 557722010112 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722010113 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 557722010114 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 557722010115 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 557722010116 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 557722010117 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722010118 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 557722010119 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722010120 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557722010121 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39G; cd02423 557722010122 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 557722010123 putative active site [active] 557722010124 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722010125 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722010126 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722010127 DNA binding residues [nucleotide binding] 557722010128 dimerization interface [polypeptide binding]; other site 557722010129 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722010130 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722010131 DNA binding residues [nucleotide binding] 557722010132 dimerization interface [polypeptide binding]; other site 557722010133 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 557722010134 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 557722010135 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557722010136 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722010137 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 557722010138 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 557722010139 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 557722010140 Active Sites [active] 557722010141 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 557722010142 Helix-turn-helix domains; Region: HTH; cl00088 557722010143 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 557722010144 substrate binding site [chemical binding]; other site 557722010145 dimerization interface [polypeptide binding]; other site 557722010146 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722010147 Ligand Binding Site [chemical binding]; other site 557722010148 2-dehydropantoate 2-reductase; Provisional; Region: PRK06249 557722010149 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010150 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 557722010151 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 557722010152 catalytic residues [active] 557722010153 NeuB family; Region: NeuB; cl00496 557722010154 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557722010155 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 557722010156 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722010157 substrate binding site [chemical binding]; other site 557722010158 oxyanion hole (OAH) forming residues; other site 557722010159 trimer interface [polypeptide binding]; other site 557722010160 Macro domain, Poa1p_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Poa1p_like; cd02901 557722010161 ADP-ribose binding site [chemical binding]; other site 557722010162 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 557722010163 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 557722010164 catalytic triad [active] 557722010165 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722010166 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 557722010167 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722010168 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 557722010169 active site 557722010170 catalytic tetrad [active] 557722010171 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722010172 Helix-turn-helix domains; Region: HTH; cl00088 557722010173 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 557722010174 putative effector binding pocket; other site 557722010175 putative dimerization interface [polypeptide binding]; other site 557722010176 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 557722010177 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722010178 substrate binding site [chemical binding]; other site 557722010179 oxyanion hole (OAH) forming residues; other site 557722010180 trimer interface [polypeptide binding]; other site 557722010181 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010182 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722010183 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 557722010184 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722010185 dimer interface [polypeptide binding]; other site 557722010186 active site 557722010187 Membrane transport protein; Region: Mem_trans; cl09117 557722010188 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557722010189 Cytochrome c; Region: Cytochrom_C; cl11414 557722010190 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 557722010191 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 557722010192 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 557722010193 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 557722010194 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; cl00980 557722010195 Uncharacterized conserved protein [Function unknown]; Region: COG2308 557722010196 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 557722010197 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 557722010198 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 557722010199 catalytic triad [active] 557722010200 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 557722010201 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 557722010202 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 557722010203 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722010204 metal binding site [ion binding]; metal-binding site 557722010205 active site 557722010206 I-site; other site 557722010207 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722010208 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 557722010209 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 557722010210 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 557722010211 Fibronectin type III-like domain; Region: Fn3-like; cl15273 557722010212 type III secretion apparatus protein, HrpE/YscL family; Region: HrpE_YscL_not; TIGR02499 557722010213 Flagellar assembly protein FliH; Region: FliH; pfam02108 557722010214 YOP proteins translocation protein K (YscK); Region: YscK; pfam06578 557722010215 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 557722010216 Type III secretion needle MxiH like; Region: MxiH; cl09641 557722010217 YopR Core; Region: YopR_core; cl07585 557722010218 Bacterial type II secretion system chaperone protein (type_III_yscG); Region: Type_III_YscG; cl09712 557722010219 Type III secretion needle MxiH like; Region: MxiH; cl09641 557722010220 Protein of unknown function (DUF1895); Region: DUF1895; cl07553 557722010221 type III secretion apparatus protein, YscD/HrpQ family; Region: type_III_yscD; TIGR02500 557722010222 type III secretion outer membrane pore, YscC/HrcC family; Region: type_III_yscC; TIGR02516 557722010223 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722010224 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722010225 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722010226 Tir chaperone protein (CesT) family; Region: CesT; cl08444 557722010227 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 557722010228 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722010229 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722010230 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722010231 type III secretion system chaperone YscW; Region: YscW; TIGR02567 557722010232 Tir chaperone protein (CesT) family; Region: CesT; cl08444 557722010233 YopD protein; Region: YopD; pfam05844 557722010234 Uncharacterized conserved protein [Function unknown]; Region: COG5613 557722010235 V antigen (LcrV) protein; Region: LcrV; pfam04792 557722010236 LcrG protein; Region: LcrG; cl06311 557722010237 Type III secretion system regulator (LcrR); Region: LcrR; cl09838 557722010238 Type III secretory pathway, component EscV [Intracellular trafficking and secretion]; Region: EscV; COG4789 557722010239 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 557722010240 Type III secretion system YscX (type_III_YscX); Region: Type_III_YscX; cl09710 557722010241 type III secretion chaperone SycN; Region: type_III_SycN; TIGR02503 557722010242 TyeA; Region: TyeA; cl07611 557722010243 HrpJ-like domain; Region: HrpJ; cl15454 557722010244 type III secretion system ATPase; Provisional; Region: PRK06936 557722010245 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 557722010246 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 557722010247 Walker A motif/ATP binding site; other site 557722010248 Walker B motif; other site 557722010249 Type III secretion protein YscO; Region: YscO; pfam07321 557722010250 type III secretion system protein; Validated; Region: PRK06933 557722010251 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 557722010252 FliP family; Region: FliP; cl00593 557722010253 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 557722010254 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 557722010255 Type III secretory pathway, component EscU [Intracellular trafficking and secretion]; Region: EscU; COG4792 557722010256 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 557722010257 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 557722010258 Sulfatase; Region: Sulfatase; cl10460 557722010259 Uncharacterized conserved protein [Function unknown]; Region: COG3391 557722010260 Strictosidine synthase; Region: Str_synth; pfam03088 557722010261 spermidine synthase; Provisional; Region: PRK00811 557722010262 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722010263 S-adenosylmethionine binding site [chemical binding]; other site 557722010264 AlkA N-terminal domain; Region: AlkA_N; cl05528 557722010265 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 557722010266 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557722010267 minor groove reading motif; other site 557722010268 helix-hairpin-helix signature motif; other site 557722010269 substrate binding pocket [chemical binding]; other site 557722010270 active site 557722010271 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 557722010272 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722010273 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1791 557722010274 Cupin domain; Region: Cupin_2; cl09118 557722010275 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 557722010276 intersubunit interface [polypeptide binding]; other site 557722010277 active site 557722010278 Zn2+ binding site [ion binding]; other site 557722010279 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010280 putative substrate translocation pore; other site 557722010281 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 557722010282 Tetramer interface [polypeptide binding]; other site 557722010283 active site 557722010284 FMN-binding site [chemical binding]; other site 557722010285 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722010286 HemK family putative methylases; Region: hemK_fam; TIGR00536 557722010287 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722010288 S-adenosylmethionine binding site [chemical binding]; other site 557722010289 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 557722010290 Isochorismatase family; Region: Isochorismatase; pfam00857 557722010291 catalytic triad [active] 557722010292 conserved cis-peptide bond; other site 557722010293 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 557722010294 Smr domain; Region: Smr; cl02619 557722010295 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 557722010296 homodecamer interface [polypeptide binding]; other site 557722010297 GTP cyclohydrolase I; Provisional; Region: PLN03044 557722010298 active site 557722010299 putative catalytic site residues [active] 557722010300 zinc binding site [ion binding]; other site 557722010301 GTP-CH-I/GFRP interaction surface; other site 557722010302 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cd00522 557722010303 octamerization interface [polypeptide binding]; other site 557722010304 diferric-oxygen binding site [ion binding]; other site 557722010305 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 557722010306 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722010307 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 557722010308 Catalytic domain of Protein Kinases; Region: PKc; cd00180 557722010309 active site 557722010310 ATP binding site [chemical binding]; other site 557722010311 substrate binding site [chemical binding]; other site 557722010312 activation loop (A-loop); other site 557722010313 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722010314 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 557722010315 Protein phosphatase 2C; Region: PP2C; pfam00481 557722010316 active site 557722010317 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 557722010318 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 557722010319 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 557722010320 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 557722010321 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 557722010322 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 557722010323 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 557722010324 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 557722010325 type VI secretion system FHA domain protein; Region: VI_FHA; TIGR03354 557722010326 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 557722010327 phosphopeptide binding site; other site 557722010328 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 557722010329 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 557722010330 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722010331 Walker A motif; other site 557722010332 ATP binding site [chemical binding]; other site 557722010333 Walker B motif; other site 557722010334 arginine finger; other site 557722010335 Helix-turn-helix domains; Region: HTH; cl00088 557722010336 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 557722010337 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722010338 Walker A motif; other site 557722010339 ATP binding site [chemical binding]; other site 557722010340 Walker B motif; other site 557722010341 arginine finger; other site 557722010342 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722010343 Walker A motif; other site 557722010344 ATP binding site [chemical binding]; other site 557722010345 Walker B motif; other site 557722010346 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722010347 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 557722010348 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 557722010349 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557722010350 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 557722010351 Protein of unknown function (DUF877); Region: DUF877; pfam05943 557722010352 Protein of unknown function (DUF770); Region: DUF770; cl01402 557722010353 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3515 557722010354 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 557722010355 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 557722010356 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722010357 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 557722010358 putative C-terminal domain interface [polypeptide binding]; other site 557722010359 putative GSH binding site (G-site) [chemical binding]; other site 557722010360 putative dimer interface [polypeptide binding]; other site 557722010361 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 557722010362 N-terminal domain interface [polypeptide binding]; other site 557722010363 dimer interface [polypeptide binding]; other site 557722010364 substrate binding pocket (H-site) [chemical binding]; other site 557722010365 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 557722010366 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722010367 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722010368 homodimer interface [polypeptide binding]; other site 557722010369 catalytic residue [active] 557722010370 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557722010371 Helix-turn-helix domains; Region: HTH; cl00088 557722010372 benzoate transporter; Region: benE; TIGR00843 557722010373 Benzoate membrane transport protein; Region: BenE; pfam03594 557722010374 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 557722010375 Membrane transport protein; Region: Mem_trans; cl09117 557722010376 short chain dehydrogenase; Provisional; Region: PRK12939 557722010377 classical (c) SDRs; Region: SDR_c; cd05233 557722010378 NAD(P) binding site [chemical binding]; other site 557722010379 active site 557722010380 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 557722010381 Prostaglandin dehydrogenases; Region: PGDH; cd05288 557722010382 NAD(P) binding site [chemical binding]; other site 557722010383 substrate binding site [chemical binding]; other site 557722010384 dimer interface [polypeptide binding]; other site 557722010385 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 557722010386 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722010387 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722010388 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 557722010389 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722010390 dimerization interface [polypeptide binding]; other site 557722010391 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722010392 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722010393 dimer interface [polypeptide binding]; other site 557722010394 putative CheW interface [polypeptide binding]; other site 557722010395 Flavin Reductases; Region: FlaRed; cl00801 557722010396 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 557722010397 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 557722010398 active site residue [active] 557722010399 selenophosphate synthetase; Provisional; Region: PRK00943 557722010400 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 557722010401 dimerization interface [polypeptide binding]; other site 557722010402 putative ATP binding site [chemical binding]; other site 557722010403 hypothetical protein; Provisional; Region: PRK10279 557722010404 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 557722010405 active site 557722010406 nucleophile elbow; other site 557722010407 Glutaminase; Region: Glutaminase; cl00907 557722010408 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 557722010409 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722010410 active site 557722010411 phosphorylation site [posttranslational modification] 557722010412 intermolecular recognition site; other site 557722010413 dimerization interface [polypeptide binding]; other site 557722010414 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722010415 DNA binding site [nucleotide binding] 557722010416 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 557722010417 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 557722010418 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 557722010419 Ligand Binding Site [chemical binding]; other site 557722010420 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 557722010421 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722010422 dimer interface [polypeptide binding]; other site 557722010423 phosphorylation site [posttranslational modification] 557722010424 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722010425 ATP binding site [chemical binding]; other site 557722010426 Mg2+ binding site [ion binding]; other site 557722010427 G-X-G motif; other site 557722010428 K+-transporting ATPase, c chain; Region: KdpC; cl00944 557722010429 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 557722010430 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722010431 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722010432 Potassium-transporting ATPase A subunit; Region: KdpA; cl00903 557722010433 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722010434 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722010435 active site 557722010436 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722010437 Helix-turn-helix domains; Region: HTH; cl00088 557722010438 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722010439 enoyl-CoA hydratase; Provisional; Region: PRK08138 557722010440 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722010441 substrate binding site [chemical binding]; other site 557722010442 oxyanion hole (OAH) forming residues; other site 557722010443 trimer interface [polypeptide binding]; other site 557722010444 Transcriptional regulators [Transcription]; Region: FadR; COG2186 557722010445 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722010446 DNA-binding site [nucleotide binding]; DNA binding site 557722010447 FCD domain; Region: FCD; cl11656 557722010448 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010449 putative substrate translocation pore; other site 557722010450 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 557722010451 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 557722010452 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 557722010453 C-terminal domain interface [polypeptide binding]; other site 557722010454 GSH binding site (G-site) [chemical binding]; other site 557722010455 dimer interface [polypeptide binding]; other site 557722010456 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 557722010457 N-terminal domain interface [polypeptide binding]; other site 557722010458 dimer interface [polypeptide binding]; other site 557722010459 substrate binding pocket (H-site) [chemical binding]; other site 557722010460 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722010461 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722010462 LysE type translocator; Region: LysE; cl00565 557722010463 Cupin domain; Region: Cupin_2; cl09118 557722010464 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722010465 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722010466 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722010467 CoenzymeA binding site [chemical binding]; other site 557722010468 subunit interaction site [polypeptide binding]; other site 557722010469 PHB binding site; other site 557722010470 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 557722010471 AMP-binding enzyme; Region: AMP-binding; cl15778 557722010472 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 557722010473 catalytic core [active] 557722010474 Domain of unknown function (DUF4389); Region: DUF4389; pfam14333 557722010475 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 557722010476 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010477 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 557722010478 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 557722010479 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 557722010480 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722010481 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722010482 dimer interface [polypeptide binding]; other site 557722010483 phosphorylation site [posttranslational modification] 557722010484 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722010485 ATP binding site [chemical binding]; other site 557722010486 Mg2+ binding site [ion binding]; other site 557722010487 G-X-G motif; other site 557722010488 Response regulator receiver domain; Region: Response_reg; pfam00072 557722010489 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722010490 active site 557722010491 phosphorylation site [posttranslational modification] 557722010492 intermolecular recognition site; other site 557722010493 dimerization interface [polypeptide binding]; other site 557722010494 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 557722010495 active site 1 [active] 557722010496 dimer interface [polypeptide binding]; other site 557722010497 active site 2 [active] 557722010498 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 557722010499 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 557722010500 dimer interface [polypeptide binding]; other site 557722010501 active site 557722010502 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557722010503 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722010504 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722010505 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722010506 dimer interface [polypeptide binding]; other site 557722010507 putative CheW interface [polypeptide binding]; other site 557722010508 Helix-turn-helix domains; Region: HTH; cl00088 557722010509 Domain of unknown function (DUF3859); Region: DUF3859; pfam12975 557722010510 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 557722010511 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722010512 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557722010513 Helix-turn-helix domains; Region: HTH; cl00088 557722010514 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 557722010515 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 557722010516 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 557722010517 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 557722010518 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722010519 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 557722010520 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722010521 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722010522 Cytochrome c; Region: Cytochrom_C; cl11414 557722010523 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557722010524 Cytochrome c; Region: Cytochrom_C; cl11414 557722010525 Cupin domain; Region: Cupin_2; cl09118 557722010526 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722010527 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722010528 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 557722010529 oligomerization interface [polypeptide binding]; other site 557722010530 active site 557722010531 metal binding site [ion binding]; metal-binding site 557722010532 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 557722010533 heat shock protein 90; Provisional; Region: PRK05218 557722010534 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722010535 ATP binding site [chemical binding]; other site 557722010536 Mg2+ binding site [ion binding]; other site 557722010537 G-X-G motif; other site 557722010538 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 557722010539 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722010540 CoenzymeA binding site [chemical binding]; other site 557722010541 subunit interaction site [polypeptide binding]; other site 557722010542 PHB binding site; other site 557722010543 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722010544 CoenzymeA binding site [chemical binding]; other site 557722010545 subunit interaction site [polypeptide binding]; other site 557722010546 PHB binding site; other site 557722010547 Protein of unknown function, DUF599; Region: DUF599; cl01575 557722010548 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 557722010549 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 557722010550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010551 CoA-ligase; Region: Ligase_CoA; cl02894 557722010552 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 557722010553 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722010554 CoA-ligase; Region: Ligase_CoA; cl02894 557722010555 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 557722010556 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010557 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722010558 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722010559 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 557722010560 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722010561 E3 interaction surface; other site 557722010562 lipoyl attachment site [posttranslational modification]; other site 557722010563 e3 binding domain; Region: E3_binding; pfam02817 557722010564 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 557722010565 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 557722010566 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 557722010567 TPP-binding site [chemical binding]; other site 557722010568 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 557722010569 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 557722010570 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 557722010571 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010572 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK05675 557722010573 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 557722010574 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 557722010575 SdhC subunit interface [polypeptide binding]; other site 557722010576 proximal heme binding site [chemical binding]; other site 557722010577 cardiolipin binding site; other site 557722010578 Iron-sulfur protein interface; other site 557722010579 proximal quinone binding site [chemical binding]; other site 557722010580 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 557722010581 Iron-sulfur protein interface; other site 557722010582 proximal quinone binding site [chemical binding]; other site 557722010583 SdhD (CybS) interface [polypeptide binding]; other site 557722010584 proximal heme binding site [chemical binding]; other site 557722010585 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 557722010586 dimer interface [polypeptide binding]; other site 557722010587 Citrate synthase; Region: Citrate_synt; pfam00285 557722010588 active site 557722010589 citrylCoA binding site [chemical binding]; other site 557722010590 NADH binding [chemical binding]; other site 557722010591 cationic pore residues; other site 557722010592 oxalacetate/citrate binding site [chemical binding]; other site 557722010593 coenzyme A binding site [chemical binding]; other site 557722010594 catalytic triad [active] 557722010595 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family; Region: START_1; cd08876 557722010596 putative lipid binding site [chemical binding]; other site 557722010597 Flagellin N-methylase; Region: FliB; cl00497 557722010598 Protein of unknown function, DUF486; Region: DUF486; cl01236 557722010599 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557722010600 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010601 DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; Region: ERI-1_3'hExo_like; cd06133 557722010602 active site 557722010603 substrate binding site [chemical binding]; other site 557722010604 catalytic site [active] 557722010605 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 557722010606 Domain of unknown function (DUF1287); Region: DUF1287; cl01519 557722010607 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 557722010608 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 557722010609 Helix-turn-helix domains; Region: HTH; cl00088 557722010610 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722010611 dimerization interface [polypeptide binding]; other site 557722010612 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 557722010613 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010614 putative substrate translocation pore; other site 557722010615 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010616 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 557722010617 homotrimer interaction site [polypeptide binding]; other site 557722010618 putative active site [active] 557722010619 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010620 FAD dependent oxidoreductase; Region: DAO; pfam01266 557722010621 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722010622 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722010623 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010624 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722010625 SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A...; Region: SirA; cd03423 557722010626 CPxP motif; other site 557722010627 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 557722010628 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722010629 aconitate hydratase; Validated; Region: PRK09277 557722010630 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 557722010631 substrate binding site [chemical binding]; other site 557722010632 ligand binding site [chemical binding]; other site 557722010633 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 557722010634 substrate binding site [chemical binding]; other site 557722010635 PAS domain; Region: PAS_9; pfam13426 557722010636 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722010637 putative active site [active] 557722010638 heme pocket [chemical binding]; other site 557722010639 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722010640 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722010641 dimer interface [polypeptide binding]; other site 557722010642 putative CheW interface [polypeptide binding]; other site 557722010643 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010644 NAD(P) binding site [chemical binding]; other site 557722010645 active site 557722010646 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 557722010647 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722010648 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 557722010649 Low-spin heme binding site [chemical binding]; other site 557722010650 Putative water exit pathway; other site 557722010651 Binuclear center (active site) [active] 557722010652 Putative proton exit pathway; other site 557722010653 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 557722010654 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 557722010655 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 557722010656 Cytochrome c; Region: Cytochrom_C; cl11414 557722010657 Cytochrome c; Region: Cytochrom_C; cl11414 557722010658 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 557722010659 Low-spin heme binding site [chemical binding]; other site 557722010660 Putative water exit pathway; other site 557722010661 Binuclear center (active site) [active] 557722010662 Putative proton exit pathway; other site 557722010663 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 557722010664 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 557722010665 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 557722010666 Cytochrome c; Region: Cytochrom_C; cl11414 557722010667 Cytochrome c; Region: Cytochrom_C; cl11414 557722010668 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 557722010669 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557722010670 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 557722010671 FixH; Region: FixH; cl01254 557722010672 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 557722010673 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557722010674 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 557722010675 metal-binding site [ion binding] 557722010676 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722010677 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722010678 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 557722010679 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 557722010680 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 557722010681 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722010682 FeS/SAM binding site; other site 557722010683 HemN C-terminal domain; Region: HemN_C; pfam06969 557722010684 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 557722010685 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722010686 ligand binding site [chemical binding]; other site 557722010687 flexible hinge region; other site 557722010688 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 557722010689 putative switch regulator; other site 557722010690 non-specific DNA interactions [nucleotide binding]; other site 557722010691 DNA binding site [nucleotide binding] 557722010692 sequence specific DNA binding site [nucleotide binding]; other site 557722010693 putative cAMP binding site [chemical binding]; other site 557722010694 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 557722010695 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722010696 active site 557722010697 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 557722010698 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 557722010699 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722010700 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722010701 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 557722010702 Helix-turn-helix domains; Region: HTH; cl00088 557722010703 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 557722010704 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010705 short chain dehydrogenase; Provisional; Region: PRK06181 557722010706 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010707 NAD(P) binding site [chemical binding]; other site 557722010708 active site 557722010709 Uncharacterized protein family (UPF0167); Region: UPF0167; cl01252 557722010710 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722010711 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722010712 active site 557722010713 recombination protein RecR; Reviewed; Region: recR; PRK00076 557722010714 RecR protein; Region: RecR; pfam02132 557722010715 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 557722010716 putative active site [active] 557722010717 putative metal-binding site [ion binding]; other site 557722010718 tetramer interface [polypeptide binding]; other site 557722010719 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 557722010720 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 557722010721 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722010722 Walker A motif; other site 557722010723 ATP binding site [chemical binding]; other site 557722010724 Walker B motif; other site 557722010725 arginine finger; other site 557722010726 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 557722010727 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 557722010728 potential protein location (hypothetical protein PLES_37971 [Pseudomonas aeruginosa LESB58]) that overlaps RNA (4.5S ribosomal RNA) 557722010729 potential protein location (hypothetical protein PLES_37981 [Pseudomonas aeruginosa LESB58]) that overlaps RNA (4.5S ribosomal RNA) 557722010730 Ligase N family; Region: LIGANc; smart00532 557722010731 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 557722010732 nucleotide binding pocket [chemical binding]; other site 557722010733 K-X-D-G motif; other site 557722010734 catalytic site [active] 557722010735 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 557722010736 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 557722010737 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 557722010738 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 557722010739 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 557722010740 Dimer interface [polypeptide binding]; other site 557722010741 BRCT sequence motif; other site 557722010742 Cell division protein [Cell division and chromosome partitioning]; Region: ZipA; COG3115 557722010743 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cd00231 557722010744 FtsZ protein binding site [polypeptide binding]; other site 557722010745 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557722010746 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 557722010747 Walker A/P-loop; other site 557722010748 ATP binding site [chemical binding]; other site 557722010749 Q-loop/lid; other site 557722010750 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 557722010751 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 557722010752 ABC transporter signature motif; other site 557722010753 Walker B; other site 557722010754 D-loop; other site 557722010755 H-loop/switch region; other site 557722010756 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557722010757 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722010758 DNA-binding site [nucleotide binding]; DNA binding site 557722010759 FCD domain; Region: FCD; cl11656 557722010760 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 557722010761 Fatty acid desaturase; Region: FA_desaturase; pfam00487 557722010762 Di-iron ligands [ion binding]; other site 557722010763 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 557722010764 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722010765 catalytic loop [active] 557722010766 iron binding site [ion binding]; other site 557722010767 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 557722010768 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 557722010769 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 557722010770 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 557722010771 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722010772 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 557722010773 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 557722010774 XdhC Rossmann domain; Region: XdhC_C; pfam13478 557722010775 guanine deaminase; Provisional; Region: PRK09228 557722010776 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 557722010777 active site 557722010778 putative acetyltransferase YhhY; Provisional; Region: PRK10140 557722010779 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722010780 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 557722010781 Isocitrate dehydrogenase kinase/phosphatase (AceK); Region: AceK; cl01891 557722010782 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 557722010783 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010784 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 557722010785 Helix-turn-helix domains; Region: HTH; cl00088 557722010786 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 557722010787 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 557722010788 dimer interface [polypeptide binding]; other site 557722010789 active site 557722010790 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 557722010791 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722010792 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 557722010793 Fic/DOC family; Region: Fic; cl00960 557722010794 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722010795 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722010796 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722010797 N-terminal plug; other site 557722010798 ligand-binding site [chemical binding]; other site 557722010799 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722010800 FecR protein; Region: FecR; pfam04773 557722010801 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 557722010802 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722010803 DNA binding residues [nucleotide binding] 557722010804 multidrug efflux protein; Reviewed; Region: PRK01766 557722010805 MatE; Region: MatE; cl10513 557722010806 MatE; Region: MatE; cl10513 557722010807 threonine and homoserine efflux system; Provisional; Region: PRK10532 557722010808 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722010809 non-specific DNA binding site [nucleotide binding]; other site 557722010810 salt bridge; other site 557722010811 sequence-specific DNA binding site [nucleotide binding]; other site 557722010812 Cupin domain; Region: Cupin_2; cl09118 557722010813 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 557722010814 dimer interface [polypeptide binding]; other site 557722010815 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722010816 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 557722010817 putative deacylase active site [active] 557722010818 Ubiquitin-like proteins; Region: UBQ; cl00155 557722010819 YCII-related domain; Region: YCII; cl00999 557722010820 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722010821 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 557722010822 dimer interface [polypeptide binding]; other site 557722010823 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]; Region: COG4941 557722010824 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722010825 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722010826 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722010827 YCII-related domain; Region: YCII; cl00999 557722010828 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722010829 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722010830 DNA binding residues [nucleotide binding] 557722010831 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 557722010832 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 557722010833 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722010834 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 557722010835 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 557722010836 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 557722010837 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722010838 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722010839 short chain dehydrogenase; Provisional; Region: PRK06523 557722010840 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722010841 NAD(P) binding site [chemical binding]; other site 557722010842 active site 557722010843 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 557722010844 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722010845 substrate binding pocket [chemical binding]; other site 557722010846 membrane-bound complex binding site; other site 557722010847 hinge residues; other site 557722010848 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722010849 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722010850 dimer interface [polypeptide binding]; other site 557722010851 conserved gate region; other site 557722010852 putative PBP binding loops; other site 557722010853 ABC-ATPase subunit interface; other site 557722010854 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722010855 dimer interface [polypeptide binding]; other site 557722010856 conserved gate region; other site 557722010857 putative PBP binding loops; other site 557722010858 ABC-ATPase subunit interface; other site 557722010859 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557722010860 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722010861 Walker A/P-loop; other site 557722010862 ATP binding site [chemical binding]; other site 557722010863 Q-loop/lid; other site 557722010864 ABC transporter signature motif; other site 557722010865 Walker B; other site 557722010866 D-loop; other site 557722010867 H-loop/switch region; other site 557722010868 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 557722010869 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 557722010870 Bacterial L-asparaginases and related enzymes; Region: L-asparaginase_like; cl00216 557722010871 homodimer interface [polypeptide binding]; other site 557722010872 active site 557722010873 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 557722010874 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 557722010875 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722010876 ATP binding site [chemical binding]; other site 557722010877 Mg2+ binding site [ion binding]; other site 557722010878 G-X-G motif; other site 557722010879 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722010880 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722010881 active site 557722010882 phosphorylation site [posttranslational modification] 557722010883 intermolecular recognition site; other site 557722010884 dimerization interface [polypeptide binding]; other site 557722010885 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722010886 Walker A motif; other site 557722010887 ATP binding site [chemical binding]; other site 557722010888 Walker B motif; other site 557722010889 arginine finger; other site 557722010890 Helix-turn-helix domains; Region: HTH; cl00088 557722010891 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 557722010892 FMN binding site [chemical binding]; other site 557722010893 active site 557722010894 substrate binding site [chemical binding]; other site 557722010895 catalytic residue [active] 557722010896 Integral membrane protein TerC family; Region: TerC; cl10468 557722010897 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 557722010898 Transporter associated domain; Region: CorC_HlyC; cl08393 557722010899 short chain dehydrogenase; Provisional; Region: PRK09291 557722010900 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 557722010901 NADP binding site [chemical binding]; other site 557722010902 active site 557722010903 steroid binding site; other site 557722010904 Domain of unknown function (DUF336); Region: DUF336; cl01249 557722010905 transcriptional activator TtdR; Provisional; Region: PRK09801 557722010906 Helix-turn-helix domains; Region: HTH; cl00088 557722010907 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 557722010908 putative effector binding pocket; other site 557722010909 putative dimerization interface [polypeptide binding]; other site 557722010910 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 557722010911 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cd00091 557722010912 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 557722010913 active site 557722010914 substrate binding site [chemical binding]; other site 557722010915 Mg2+ binding site [ion binding]; other site 557722010916 threonine dehydratase; Reviewed; Region: PRK09224 557722010917 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 557722010918 tetramer interface [polypeptide binding]; other site 557722010919 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722010920 catalytic residue [active] 557722010921 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 557722010922 putative Ile/Val binding site [chemical binding]; other site 557722010923 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 557722010924 putative Ile/Val binding site [chemical binding]; other site 557722010925 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722010926 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 557722010927 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 557722010928 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722010929 N-terminal plug; other site 557722010930 ligand-binding site [chemical binding]; other site 557722010931 UbiA prenyltransferase family; Region: UbiA; cl00337 557722010932 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 557722010933 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 557722010934 Subunit I/III interface [polypeptide binding]; other site 557722010935 Subunit III/IV interface [polypeptide binding]; other site 557722010936 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 557722010937 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 557722010938 D-pathway; other site 557722010939 Putative ubiquinol binding site [chemical binding]; other site 557722010940 Low-spin heme (heme b) binding site [chemical binding]; other site 557722010941 Putative water exit pathway; other site 557722010942 Binuclear center (heme o3/CuB) [ion binding]; other site 557722010943 K-pathway; other site 557722010944 Putative proton exit pathway; other site 557722010945 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 557722010946 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722010947 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 557722010948 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557722010949 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010950 putative substrate translocation pore; other site 557722010951 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 557722010952 Helix-turn-helix domains; Region: HTH; cl00088 557722010953 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4460 557722010954 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010955 putative substrate translocation pore; other site 557722010956 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722010957 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722010958 Helix-turn-helix domains; Region: HTH; cl00088 557722010959 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722010960 putative effector binding pocket; other site 557722010961 dimerization interface [polypeptide binding]; other site 557722010962 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 557722010963 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722010964 motif II; other site 557722010965 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 557722010966 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722010967 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722010968 catalytic residue [active] 557722010969 Helix-turn-helix domains; Region: HTH; cl00088 557722010970 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 557722010971 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722010972 dimerization interface [polypeptide binding]; other site 557722010973 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 557722010974 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 557722010975 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 557722010976 putative active site [active] 557722010977 putative dimer interface [polypeptide binding]; other site 557722010978 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 557722010979 nucleotide binding site/active site [active] 557722010980 HIT family signature motif; other site 557722010981 catalytic residue [active] 557722010982 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 557722010983 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722010984 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 557722010985 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 557722010986 Catalytic site [active] 557722010987 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722010988 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 557722010989 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722010990 N-terminal plug; other site 557722010991 ligand-binding site [chemical binding]; other site 557722010992 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722010993 FecR protein; Region: FecR; pfam04773 557722010994 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722010995 RNA polymerase sigma factor; Reviewed; Region: PRK12527 557722010996 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722010997 Flagellin N-methylase; Region: FliB; cl00497 557722010998 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 557722010999 putative metal binding site [ion binding]; other site 557722011000 putative homotetramer interface [polypeptide binding]; other site 557722011001 putative homodimer interface [polypeptide binding]; other site 557722011002 putative homodimer-homodimer interface [polypeptide binding]; other site 557722011003 putative allosteric switch controlling residues; other site 557722011004 Cation efflux family; Region: Cation_efflux; cl00316 557722011005 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 557722011006 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011007 YcgL domain; Region: YcgL; cl01189 557722011008 ribonuclease D; Region: rnd; TIGR01388 557722011009 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 557722011010 putative active site [active] 557722011011 catalytic site [active] 557722011012 putative substrate binding site [chemical binding]; other site 557722011013 HRDC domain; Region: HRDC; cl02578 557722011014 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 557722011015 Strictosidine synthase; Region: Str_synth; pfam03088 557722011016 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557722011017 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722011018 DNA-binding site [nucleotide binding]; DNA binding site 557722011019 FCD domain; Region: FCD; cl11656 557722011020 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 557722011021 Sulfate transporter family; Region: Sulfate_transp; cl15842 557722011022 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 557722011023 active site 557722011024 homotetramer interface [polypeptide binding]; other site 557722011025 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 557722011026 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 557722011027 active site 557722011028 catalytic site [active] 557722011029 tetramer interface [polypeptide binding]; other site 557722011030 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 557722011031 allantoicase; Provisional; Region: PRK13257 557722011032 Allantoicase repeat; Region: Allantoicase; pfam03561 557722011033 Allantoicase repeat; Region: Allantoicase; pfam03561 557722011034 Ureidoglycolate hydrolase [Nucleotide transport and metabolism]; Region: DAL3; COG3194 557722011035 Ureidoglycolate hydrolase; Region: Ureidogly_hydro; cl01250 557722011036 Predicted membrane protein [Function unknown]; Region: COG3748 557722011037 Protein of unknown function (DUF989); Region: DUF989; pfam06181 557722011038 Cytochrome c; Region: Cytochrom_C; cl11414 557722011039 Protein of unknown function (DUF796); Region: DUF796; cl01226 557722011040 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722011041 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722011042 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722011043 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 557722011044 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 557722011045 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722011046 PAAR motif; Region: PAAR_motif; cl15808 557722011047 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 557722011048 xanthine permease; Region: pbuX; TIGR03173 557722011049 Low molecular weight phosphatase family; Region: LMWPc; cl00105 557722011050 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 557722011051 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722011052 FeS/SAM binding site; other site 557722011053 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 557722011054 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 557722011055 Helix-turn-helix domains; Region: HTH; cl00088 557722011056 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 557722011057 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011058 Domain of unknown function (DUF336); Region: DUF336; cl01249 557722011059 glyoxylate carboligase; Provisional; Region: PRK11269 557722011060 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722011061 PYR/PP interface [polypeptide binding]; other site 557722011062 dimer interface [polypeptide binding]; other site 557722011063 TPP binding site [chemical binding]; other site 557722011064 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722011065 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 557722011066 TPP-binding site [chemical binding]; other site 557722011067 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 557722011068 tartronate semialdehyde reductase; Provisional; Region: PRK15059 557722011069 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011070 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 557722011071 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 557722011072 MOFRL family; Region: MOFRL; pfam05161 557722011073 pyruvate kinase; Provisional; Region: PRK06247 557722011074 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722011075 domain interfaces; other site 557722011076 active site 557722011077 Urea transporter; Region: UT; cl01829 557722011078 Ion transport protein; Region: Ion_trans; pfam00520 557722011079 Ion channel; Region: Ion_trans_2; cl11596 557722011080 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722011081 conserved hypothetical protein; Region: TIGR02231 557722011082 N-terminal domain of unknown function (DUF4140); Region: DUF4140; pfam13600 557722011083 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 557722011084 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 557722011085 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722011086 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 557722011087 TIR domain; Region: TIR_2; cl15770 557722011088 Ethanolamine utilisation protein, EutH; Region: EutH; cl01248 557722011089 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 557722011090 Helix-turn-helix domains; Region: HTH; cl00088 557722011091 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722011092 Predicted dehydrogenase [General function prediction only]; Region: COG0579 557722011093 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 557722011094 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011095 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 557722011096 proteobacterial glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_GK_like_proteobact; cd07794 557722011097 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 557722011098 putative N- and C-terminal domain interface [polypeptide binding]; other site 557722011099 putative active site [active] 557722011100 putative MgATP binding site [chemical binding]; other site 557722011101 catalytic site [active] 557722011102 metal binding site [ion binding]; metal-binding site 557722011103 putative homotetramer interface [polypeptide binding]; other site 557722011104 putative homodimer interface [polypeptide binding]; other site 557722011105 putative glycerol binding site [chemical binding]; other site 557722011106 L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active...; Region: DmpA; cd02253 557722011107 homodimer interface [polypeptide binding]; other site 557722011108 homotetramer interface [polypeptide binding]; other site 557722011109 active site pocket [active] 557722011110 cleavage site 557722011111 Spore germination protein; Region: Spore_permease; cl15802 557722011112 amino acid transporter; Region: 2A0306; TIGR00909 557722011113 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 557722011114 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722011115 DNA binding residues [nucleotide binding] 557722011116 dimerization interface [polypeptide binding]; other site 557722011117 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 557722011118 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 557722011119 Cytochrome C biogenesis protein; Region: CcmH; cl01179 557722011120 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 557722011121 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 557722011122 catalytic residues [active] 557722011123 central insert; other site 557722011124 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557722011125 CcmE; Region: CcmE; cl00994 557722011126 Heme exporter protein D (CcmD); Region: CcmD; cl11475 557722011127 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557722011128 CcmB protein; Region: CcmB; cl01016 557722011129 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 557722011130 CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE...; Region: ABC_CcmA_heme_exporter; cd03231 557722011131 Walker A/P-loop; other site 557722011132 ATP binding site [chemical binding]; other site 557722011133 Q-loop/lid; other site 557722011134 ABC transporter signature motif; other site 557722011135 Walker B; other site 557722011136 D-loop; other site 557722011137 H-loop/switch region; other site 557722011138 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 557722011139 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 557722011140 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 557722011141 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722011142 short chain dehydrogenase; Provisional; Region: PRK12937 557722011143 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 557722011144 NADP binding site [chemical binding]; other site 557722011145 homodimer interface [polypeptide binding]; other site 557722011146 active site 557722011147 substrate binding site [chemical binding]; other site 557722011148 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 557722011149 Predicted transcriptional regulator [Transcription]; Region: COG2378 557722011150 Helix-turn-helix domains; Region: HTH; cl00088 557722011151 WYL domain; Region: WYL; cl14852 557722011152 glutathionine S-transferase; Provisional; Region: PRK10542 557722011153 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 557722011154 C-terminal domain interface [polypeptide binding]; other site 557722011155 GSH binding site (G-site) [chemical binding]; other site 557722011156 dimer interface [polypeptide binding]; other site 557722011157 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 557722011158 N-terminal domain interface [polypeptide binding]; other site 557722011159 dimer interface [polypeptide binding]; other site 557722011160 substrate binding pocket (H-site) [chemical binding]; other site 557722011161 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 557722011162 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 557722011163 putative CheA interaction surface; other site 557722011164 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 557722011165 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 557722011166 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722011167 P-loop; other site 557722011168 Magnesium ion binding site [ion binding]; other site 557722011169 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722011170 Magnesium ion binding site [ion binding]; other site 557722011171 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 557722011172 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 557722011173 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722011174 ligand binding site [chemical binding]; other site 557722011175 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 557722011176 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722011177 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 557722011178 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011179 active site 557722011180 phosphorylation site [posttranslational modification] 557722011181 intermolecular recognition site; other site 557722011182 dimerization interface [polypeptide binding]; other site 557722011183 CheB methylesterase; Region: CheB_methylest; pfam01339 557722011184 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 557722011185 putative binding surface; other site 557722011186 active site 557722011187 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 557722011188 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011189 ATP binding site [chemical binding]; other site 557722011190 Mg2+ binding site [ion binding]; other site 557722011191 G-X-G motif; other site 557722011192 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 557722011193 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 557722011194 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 557722011195 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011196 active site 557722011197 phosphorylation site [posttranslational modification] 557722011198 intermolecular recognition site; other site 557722011199 dimerization interface [polypeptide binding]; other site 557722011200 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 557722011201 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722011202 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557722011203 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722011204 DNA binding residues [nucleotide binding] 557722011205 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 557722011206 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 557722011207 P-loop; other site 557722011208 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 557722011209 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011210 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 557722011211 FHIPEP family; Region: FHIPEP; pfam00771 557722011212 Repair protein; Region: Repair_PSII; cl01535 557722011213 Repair protein; Region: Repair_PSII; cl01535 557722011214 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 557722011215 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 557722011216 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 557722011217 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 557722011218 FliP family; Region: FliP; cl00593 557722011219 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 557722011220 flagellar motor switch protein; Validated; Region: fliN; PRK05698 557722011221 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 557722011222 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 557722011223 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 557722011224 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 557722011225 Flagellar hook-length control protein [Cell motility and secretion]; Region: FliK; COG3144 557722011226 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 557722011227 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 557722011228 Protein of unknown function (DUF454); Region: DUF454; cl01063 557722011229 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 557722011230 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722011231 dimer interface [polypeptide binding]; other site 557722011232 phosphorylation site [posttranslational modification] 557722011233 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011234 ATP binding site [chemical binding]; other site 557722011235 Mg2+ binding site [ion binding]; other site 557722011236 G-X-G motif; other site 557722011237 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 557722011238 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011239 active site 557722011240 phosphorylation site [posttranslational modification] 557722011241 intermolecular recognition site; other site 557722011242 dimerization interface [polypeptide binding]; other site 557722011243 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722011244 DNA binding site [nucleotide binding] 557722011245 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 557722011246 multidrug efflux system subunit MdtA; Provisional; Region: PRK11556 557722011247 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011248 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011249 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 557722011250 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722011251 metal binding site [ion binding]; metal-binding site 557722011252 active site 557722011253 I-site; other site 557722011254 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722011255 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722011256 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 557722011257 Autoinducer binding domain; Region: Autoind_bind; pfam03472 557722011258 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722011259 DNA binding residues [nucleotide binding] 557722011260 dimerization interface [polypeptide binding]; other site 557722011261 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 557722011262 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 557722011263 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722011264 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 557722011265 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722011266 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 557722011267 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722011268 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 557722011269 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011270 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011271 Walker A/P-loop; other site 557722011272 Walker A/P-loop; other site 557722011273 ATP binding site [chemical binding]; other site 557722011274 ATP binding site [chemical binding]; other site 557722011275 Q-loop/lid; other site 557722011276 ABC transporter signature motif; other site 557722011277 Walker B; other site 557722011278 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722011279 DTW domain; Region: DTW; cl01221 557722011280 PAS domain; Region: PAS_9; pfam13426 557722011281 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722011282 putative active site [active] 557722011283 heme pocket [chemical binding]; other site 557722011284 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722011285 PAS domain; Region: PAS_9; pfam13426 557722011286 putative active site [active] 557722011287 heme pocket [chemical binding]; other site 557722011288 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722011289 dimer interface [polypeptide binding]; other site 557722011290 putative CheW interface [polypeptide binding]; other site 557722011291 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011292 Helix-turn-helix domains; Region: HTH; cl00088 557722011293 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722011294 dimerization interface [polypeptide binding]; other site 557722011295 Arginase family; Region: Arginase; cl00306 557722011296 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722011297 Sodium:solute symporter family; Region: SSF; cl00456 557722011298 Sodium:solute symporter family; Region: SSF; cl00456 557722011299 hypothetical protein; Provisional; Region: PRK07524 557722011300 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722011301 PYR/PP interface [polypeptide binding]; other site 557722011302 dimer interface [polypeptide binding]; other site 557722011303 TPP binding site [chemical binding]; other site 557722011304 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722011305 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 557722011306 TPP-binding site [chemical binding]; other site 557722011307 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557722011308 FAD binding domain; Region: FAD_binding_4; pfam01565 557722011309 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722011310 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011311 Helix-turn-helix domains; Region: HTH; cl00088 557722011312 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 557722011313 putative dimerization interface [polypeptide binding]; other site 557722011314 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 557722011315 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 557722011316 EamA-like transporter family; Region: EamA; cl01037 557722011317 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 557722011318 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722011319 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 557722011320 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 557722011321 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 557722011322 Protein of unknown function (DUF3772); Region: DUF3772; pfam12607 557722011323 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722011324 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 557722011325 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722011326 S-adenosylmethionine binding site [chemical binding]; other site 557722011327 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 557722011328 active site 557722011329 NTP binding site [chemical binding]; other site 557722011330 metal binding triad [ion binding]; metal-binding site 557722011331 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 557722011332 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 557722011333 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 557722011334 Family description; Region: UvrD_C_2; cl15862 557722011335 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722011336 Helix-turn-helix domains; Region: HTH; cl00088 557722011337 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011338 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722011339 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 557722011340 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722011341 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722011342 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557722011343 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 557722011344 carboxyltransferase (CT) interaction site; other site 557722011345 biotinylation site [posttranslational modification]; other site 557722011346 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 557722011347 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 557722011348 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011349 Helix-turn-helix domains; Region: HTH; cl00088 557722011350 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 557722011351 substrate binding pocket [chemical binding]; other site 557722011352 dimerization interface [polypeptide binding]; other site 557722011353 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722011354 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011355 active site 557722011356 phosphorylation site [posttranslational modification] 557722011357 intermolecular recognition site; other site 557722011358 dimerization interface [polypeptide binding]; other site 557722011359 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722011360 DNA binding residues [nucleotide binding] 557722011361 dimerization interface [polypeptide binding]; other site 557722011362 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722011363 dimer interface [polypeptide binding]; other site 557722011364 phosphorylation site [posttranslational modification] 557722011365 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 557722011366 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011367 ATP binding site [chemical binding]; other site 557722011368 Mg2+ binding site [ion binding]; other site 557722011369 G-X-G motif; other site 557722011370 Response regulator receiver domain; Region: Response_reg; pfam00072 557722011371 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011372 active site 557722011373 phosphorylation site [posttranslational modification] 557722011374 intermolecular recognition site; other site 557722011375 dimerization interface [polypeptide binding]; other site 557722011376 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 557722011377 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 557722011378 active site residue [active] 557722011379 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 557722011380 active site residue [active] 557722011381 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 557722011382 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722011383 Helix-turn-helix domains; Region: HTH; cl00088 557722011384 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722011385 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 557722011386 catalytic residues [active] 557722011387 dimer interface [polypeptide binding]; other site 557722011388 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011389 Helix-turn-helix domains; Region: HTH; cl00088 557722011390 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722011391 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722011392 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722011393 active site 557722011394 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722011395 Helix-turn-helix domains; Region: HTH; cl00088 557722011396 methyl viologen resistance protein SmvA; Provisional; Region: PRK14995 557722011397 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011398 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 557722011399 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 557722011400 catalytic core [active] 557722011401 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 557722011402 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 557722011403 putative dimer interface [polypeptide binding]; other site 557722011404 active site pocket [active] 557722011405 putative cataytic base [active] 557722011406 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 557722011407 homotrimer interface [polypeptide binding]; other site 557722011408 Walker A motif; other site 557722011409 GTP binding site [chemical binding]; other site 557722011410 Walker B motif; other site 557722011411 cobyric acid synthase; Provisional; Region: PRK00784 557722011412 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011413 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011414 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 557722011415 catalytic triad [active] 557722011416 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 557722011417 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722011418 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722011419 catalytic residue [active] 557722011420 CobD/Cbib protein; Region: CobD_Cbib; cl00561 557722011421 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 557722011422 FMN binding site [chemical binding]; other site 557722011423 dimer interface [polypeptide binding]; other site 557722011424 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 557722011425 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 557722011426 conserved cys residue [active] 557722011427 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011428 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 557722011429 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 557722011430 homodimer interface [polypeptide binding]; other site 557722011431 Walker A motif; other site 557722011432 ATP binding site [chemical binding]; other site 557722011433 hydroxycobalamin binding site [chemical binding]; other site 557722011434 Walker B motif; other site 557722011435 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 557722011436 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722011437 N-terminal plug; other site 557722011438 ligand-binding site [chemical binding]; other site 557722011439 Fusaric acid resistance protein family; Region: FUSC; pfam04632 557722011440 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 557722011441 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557722011442 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722011443 DNA-binding site [nucleotide binding]; DNA binding site 557722011444 FCD domain; Region: FCD; cl11656 557722011445 hydroxyproline-2-epimerase; Provisional; Region: PRK13970 557722011446 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 557722011447 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557722011448 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 557722011449 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 557722011450 EamA-like transporter family; Region: EamA; cl01037 557722011451 Helix-turn-helix domains; Region: HTH; cl00088 557722011452 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722011453 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722011454 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011455 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557722011456 putative substrate translocation pore; other site 557722011457 PAS fold; Region: PAS_4; pfam08448 557722011458 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722011459 putative active site [active] 557722011460 heme pocket [chemical binding]; other site 557722011461 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722011462 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722011463 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722011464 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722011465 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722011466 substrate binding pocket [chemical binding]; other site 557722011467 membrane-bound complex binding site; other site 557722011468 hinge residues; other site 557722011469 Putative Aconitase X swivel domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure...; Region: AcnX_swivel; cd01356 557722011470 substrate binding site [chemical binding]; other site 557722011471 Protein of unknown function (DUF521); Region: DUF521; pfam04412 557722011472 Putative Aconitase X catalytic domain; Region: AcnX; cd01355 557722011473 substrate binding site [chemical binding]; other site 557722011474 ligand binding site [chemical binding]; other site 557722011475 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722011476 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722011477 dimer interface [polypeptide binding]; other site 557722011478 conserved gate region; other site 557722011479 putative PBP binding loops; other site 557722011480 ABC-ATPase subunit interface; other site 557722011481 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722011482 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722011483 dimer interface [polypeptide binding]; other site 557722011484 conserved gate region; other site 557722011485 putative PBP binding loops; other site 557722011486 ABC-ATPase subunit interface; other site 557722011487 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557722011488 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722011489 Walker A/P-loop; other site 557722011490 ATP binding site [chemical binding]; other site 557722011491 Q-loop/lid; other site 557722011492 ABC transporter signature motif; other site 557722011493 Walker B; other site 557722011494 D-loop; other site 557722011495 H-loop/switch region; other site 557722011496 Proline racemase [Amino acid transport and metabolism]; Region: COG3938 557722011497 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 557722011498 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 557722011499 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 557722011500 inhibitor site; inhibition site 557722011501 active site 557722011502 dimer interface [polypeptide binding]; other site 557722011503 catalytic residue [active] 557722011504 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 557722011505 dimer interface [polypeptide binding]; other site 557722011506 NADP binding site [chemical binding]; other site 557722011507 catalytic residues [active] 557722011508 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 557722011509 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557722011510 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722011511 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722011512 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722011513 dimer interface [polypeptide binding]; other site 557722011514 putative CheW interface [polypeptide binding]; other site 557722011515 Protease inhibitor Inh; Region: Inh; pfam02974 557722011516 Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not...; Region: ZnMc_serralysin_like; cd04277 557722011517 active site 557722011518 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 557722011519 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 557722011520 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 557722011521 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011522 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011523 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 557722011524 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722011525 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011526 Walker A/P-loop; other site 557722011527 ATP binding site [chemical binding]; other site 557722011528 Q-loop/lid; other site 557722011529 ABC transporter signature motif; other site 557722011530 Walker B; other site 557722011531 D-loop; other site 557722011532 H-loop/switch region; other site 557722011533 GAF domain; Region: GAF_2; pfam13185 557722011534 GAF domain; Region: GAF; cl15785 557722011535 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722011536 PAS domain; Region: PAS_9; pfam13426 557722011537 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 557722011538 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722011539 dimer interface [polypeptide binding]; other site 557722011540 phosphorylation site [posttranslational modification] 557722011541 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011542 ATP binding site [chemical binding]; other site 557722011543 Mg2+ binding site [ion binding]; other site 557722011544 G-X-G motif; other site 557722011545 Response regulator receiver domain; Region: Response_reg; pfam00072 557722011546 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011547 active site 557722011548 phosphorylation site [posttranslational modification] 557722011549 intermolecular recognition site; other site 557722011550 dimerization interface [polypeptide binding]; other site 557722011551 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cd00306 557722011552 active site 557722011553 catalytic residues [active] 557722011554 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722011555 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 557722011556 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011557 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722011558 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011559 putative substrate translocation pore; other site 557722011560 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011561 Cupin domain; Region: Cupin_2; cl09118 557722011562 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722011563 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722011564 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722011565 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 557722011566 Fusaric acid resistance protein family; Region: FUSC; pfam04632 557722011567 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 557722011568 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011569 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722011570 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722011571 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722011572 substrate binding site [chemical binding]; other site 557722011573 Helix-turn-helix domains; Region: HTH; cl00088 557722011574 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722011575 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722011576 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011577 Helix-turn-helix domains; Region: HTH; cl00088 557722011578 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_3; cd08461 557722011579 putative substrate binding pocket [chemical binding]; other site 557722011580 putative dimerization interface [polypeptide binding]; other site 557722011581 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 557722011582 MltA specific insert domain; Region: MltA; cl08398 557722011583 3D domain; Region: 3D; cl01439 557722011584 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 557722011585 AMP-binding enzyme; Region: AMP-binding; cl15778 557722011586 AMP-binding enzyme; Region: AMP-binding; cl15778 557722011587 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722011588 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722011589 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 557722011590 active site 557722011591 catalytic residues [active] 557722011592 metal binding site [ion binding]; metal-binding site 557722011593 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722011594 S-adenosylmethionine binding site [chemical binding]; other site 557722011595 O-succinylbenzoate-CoA ligase; Region: menE; TIGR01923 557722011596 AMP-binding enzyme; Region: AMP-binding; cl15778 557722011597 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 557722011598 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 557722011599 active site 557722011600 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557722011601 Ligand Binding Site [chemical binding]; other site 557722011602 Molecular Tunnel; other site 557722011603 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cd00250 557722011604 substrate binding pocket [chemical binding]; other site 557722011605 active site 557722011606 iron coordination sites [ion binding]; other site 557722011607 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011608 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722011609 putative substrate translocation pore; other site 557722011610 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722011611 Cupin domain; Region: Cupin_2; cl09118 557722011612 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 557722011613 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 557722011614 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557722011615 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 557722011616 active site residue [active] 557722011617 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 557722011618 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011619 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011620 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 557722011621 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557722011622 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011623 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 557722011624 putative hydrophobic ligand binding site [chemical binding]; other site 557722011625 Pirin-related protein [General function prediction only]; Region: COG1741 557722011626 Cupin domain; Region: Cupin_2; cl09118 557722011627 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 557722011628 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722011629 OsmC-like protein; Region: OsmC; cl00767 557722011630 Isochorismatase family; Region: Isochorismatase; pfam00857 557722011631 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 557722011632 catalytic triad [active] 557722011633 dimer interface [polypeptide binding]; other site 557722011634 conserved cis-peptide bond; other site 557722011635 transcriptional regulator; Provisional; Region: PRK10632 557722011636 Helix-turn-helix domains; Region: HTH; cl00088 557722011637 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722011638 putative effector binding pocket; other site 557722011639 dimerization interface [polypeptide binding]; other site 557722011640 O-methyltransferase; Region: Methyltransf_3; pfam01596 557722011641 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011642 NlpC/P60 family; Region: NLPC_P60; cl11438 557722011643 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722011644 outer membrane lipoprotein; Provisional; Region: spr; PRK10838 557722011645 NlpC/P60 family; Region: NLPC_P60; cl11438 557722011646 NAD-dependent deacetylase; Provisional; Region: PRK00481 557722011647 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 557722011648 NAD+ binding site [chemical binding]; other site 557722011649 substrate binding site [chemical binding]; other site 557722011650 Zn binding site [ion binding]; other site 557722011651 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 557722011652 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722011653 Walker A motif; other site 557722011654 ATP binding site [chemical binding]; other site 557722011655 Walker B motif; other site 557722011656 arginine finger; other site 557722011657 Helix-turn-helix domains; Region: HTH; cl00088 557722011658 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 557722011659 Amidinotransferase; Region: Amidinotransf; cl12043 557722011660 arginine/ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557722011661 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 557722011662 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 557722011663 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 557722011664 Ligand Binding Site [chemical binding]; other site 557722011665 LES prophage 6 557722011666 integrase; Provisional; Region: int; PHA02601 557722011667 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722011668 DNA binding site [nucleotide binding] 557722011669 Int/Topo IB signature motif; other site 557722011670 active site 557722011671 Replication initiation factor; Region: Rep_trans; pfam02486 557722011672 putative assembly protein; Region: PHA00350 557722011673 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011674 hypothetical protein; Region: PHA01159 557722011675 Protein of unknown function (DUF2813); Region: DUF2813; pfam11398 557722011676 AAA domain; Region: AAA_21; pfam13304 557722011677 DNA-J related protein; Region: DNAJ_related; pfam12339 557722011678 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cl02542 557722011679 Yip1 domain; Region: Yip1; cl12048 557722011680 hypothetical protein; Provisional; Region: PRK04860 557722011681 SprT homologues; Region: SprT; cl01182 557722011682 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 557722011683 CoA-transferase family III; Region: CoA_transf_3; pfam02515 557722011684 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722011685 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722011686 active site 557722011687 luciferase-type oxidoreductase, BA3436 family; Region: lucif_BA3436; TIGR03571 557722011688 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 557722011689 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 557722011690 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 557722011691 C-terminal domain interface [polypeptide binding]; other site 557722011692 GSH binding site (G-site) [chemical binding]; other site 557722011693 dimer interface [polypeptide binding]; other site 557722011694 C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins; Region: GST_C_Ure2p_like; cd03178 557722011695 dimer interface [polypeptide binding]; other site 557722011696 N-terminal domain interface [polypeptide binding]; other site 557722011697 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722011698 Helix-turn-helix domains; Region: HTH; cl00088 557722011699 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 557722011700 dimerization interface [polypeptide binding]; other site 557722011701 substrate binding pocket [chemical binding]; other site 557722011702 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 557722011703 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557722011704 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722011705 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722011706 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722011707 MASE1; Region: MASE1; pfam05231 557722011708 putative diguanylate cyclase; Provisional; Region: PRK09776 557722011709 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722011710 putative active site [active] 557722011711 heme pocket [chemical binding]; other site 557722011712 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722011713 putative active site [active] 557722011714 heme pocket [chemical binding]; other site 557722011715 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722011716 putative active site [active] 557722011717 heme pocket [chemical binding]; other site 557722011718 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722011719 metal binding site [ion binding]; metal-binding site 557722011720 active site 557722011721 I-site; other site 557722011722 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722011723 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722011724 dimer interface [polypeptide binding]; other site 557722011725 phosphorylation site [posttranslational modification] 557722011726 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011727 ATP binding site [chemical binding]; other site 557722011728 G-X-G motif; other site 557722011729 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 557722011730 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011731 active site 557722011732 phosphorylation site [posttranslational modification] 557722011733 intermolecular recognition site; other site 557722011734 dimerization interface [polypeptide binding]; other site 557722011735 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722011736 DNA binding site [nucleotide binding] 557722011737 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722011738 Periplasmic nitrate reductase protein NapE; Region: NapE; cl01848 557722011739 ferredoxin-type protein; Provisional; Region: PRK10194 557722011740 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 557722011741 NapD protein; Region: NapD; cl01163 557722011742 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 557722011743 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 557722011744 [4Fe-4S] binding site [ion binding]; other site 557722011745 molybdopterin cofactor binding site; other site 557722011746 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 557722011747 molybdopterin cofactor binding site; other site 557722011748 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 557722011749 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 557722011750 Transglycosylase SLT domain; Region: SLT_2; pfam13406 557722011751 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722011752 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722011753 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 557722011754 Integral membrane protein TerC family; Region: TerC; cl10468 557722011755 Lipoxygenase; Region: Lipoxygenase; pfam00305 557722011756 Alginate lyase; Region: Alginate_lyase2; pfam08787 557722011757 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 557722011758 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722011759 Phosphopantetheinyl transferase component of siderophore synthetase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntD; COG2977 557722011760 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 557722011761 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 557722011762 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 557722011763 putative ATP binding site [chemical binding]; other site 557722011764 putative substrate interface [chemical binding]; other site 557722011765 Glycosyl hydrolases family 17; Region: Glyco_hydro_17; cl02191 557722011766 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557722011767 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722011768 active site 557722011769 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 557722011770 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 557722011771 metal binding site [ion binding]; metal-binding site 557722011772 dimer interface [polypeptide binding]; other site 557722011773 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 557722011774 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722011775 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557722011776 DNA-binding site [nucleotide binding]; DNA binding site 557722011777 RNA-binding motif; other site 557722011778 sensor protein RstB; Provisional; Region: PRK10604 557722011779 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722011780 dimerization interface [polypeptide binding]; other site 557722011781 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722011782 dimer interface [polypeptide binding]; other site 557722011783 phosphorylation site [posttranslational modification] 557722011784 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011785 ATP binding site [chemical binding]; other site 557722011786 Mg2+ binding site [ion binding]; other site 557722011787 G-X-G motif; other site 557722011788 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 557722011789 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011790 active site 557722011791 phosphorylation site [posttranslational modification] 557722011792 intermolecular recognition site; other site 557722011793 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722011794 DNA binding site [nucleotide binding] 557722011795 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 557722011796 ATP cone domain; Region: ATP-cone; pfam03477 557722011797 ATP cone domain; Region: ATP-cone; pfam03477 557722011798 Class I ribonucleotide reductase; Region: RNR_I; cd01679 557722011799 active site 557722011800 dimer interface [polypeptide binding]; other site 557722011801 catalytic residues [active] 557722011802 effector binding site; other site 557722011803 R2 peptide binding site; other site 557722011804 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 557722011805 dimer interface [polypeptide binding]; other site 557722011806 putative radical transfer pathway; other site 557722011807 diiron center [ion binding]; other site 557722011808 tyrosyl radical; other site 557722011809 Transposase IS200 like; Region: Y1_Tnp; cl00848 557722011810 Prophage antirepressor [Transcription]; Region: COG3617 557722011811 BRO family, N-terminal domain; Region: Bro-N; cl10591 557722011812 Colicin-like bacteriocin tRNase domain; Region: Cloacin; pfam03515 557722011813 S-type Pyocin; Region: Pyocin_S; pfam06958 557722011814 Colicin D; Region: Colicin_D; pfam11429 557722011815 Uncharacterized protein conserved in bacteria (DUF2195); Region: DUF2195; cl02042 557722011816 Exotoxin A binding; Region: Exotox-A_bind; pfam09101 557722011817 Exotoxin A, targeting; Region: Exotox-A_target; pfam09102 557722011818 Mono-ADP-ribosylating toxins catalyze the transfer of ADP_ribose from NAD+ to eukaryotic Elongation Factor 2, halting protein synthesis. A single molecule of delivered toxin is sufficient to kill a cell. These toxins share mono-ADP-ribosylating activity...; Region: Dipth_tox_like; cd01436 557722011819 nad+ binding pocket [chemical binding]; other site 557722011820 Spore germination protein; Region: Spore_permease; cl15802 557722011821 Amino acid permease; Region: AA_permease_2; pfam13520 557722011822 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 557722011823 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 557722011824 putative active site [active] 557722011825 metal binding site [ion binding]; metal-binding site 557722011826 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011827 Helix-turn-helix domains; Region: HTH; cl00088 557722011828 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722011829 dimerization interface [polypeptide binding]; other site 557722011830 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 557722011831 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011832 putative substrate translocation pore; other site 557722011833 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 557722011834 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722011835 transcriptional regulator protein; Region: phnR; TIGR03337 557722011836 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722011837 DNA-binding site [nucleotide binding]; DNA binding site 557722011838 UTRA domain; Region: UTRA; cl01230 557722011839 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011840 Helix-turn-helix domains; Region: HTH; cl00088 557722011841 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722011842 dimerization interface [polypeptide binding]; other site 557722011843 hypothetical protein; Provisional; Region: PRK11171 557722011844 Cupin domain; Region: Cupin_2; cl09118 557722011845 Cupin domain; Region: Cupin_2; cl09118 557722011846 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 557722011847 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 557722011848 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011849 Helix-turn-helix domains; Region: HTH; cl00088 557722011850 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722011851 dimerization interface [polypeptide binding]; other site 557722011852 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 557722011853 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 557722011854 NAD(P) binding site [chemical binding]; other site 557722011855 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 557722011856 Autoinducer binding domain; Region: Autoind_bind; pfam03472 557722011857 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722011858 DNA binding residues [nucleotide binding] 557722011859 dimerization interface [polypeptide binding]; other site 557722011860 chaperone protein HchA; Provisional; Region: PRK04155 557722011861 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 557722011862 conserved cys residue [active] 557722011863 Protein of unknown function, DUF393; Region: DUF393; cl01136 557722011864 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl11420 557722011865 RfbF is a putative dTDP-rhamnosyl transferase; Region: GT2_RfbF_like; cd02526 557722011866 Ligand binding site [chemical binding]; other site 557722011867 FosA, a Fosfomycin resistance protein, catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive; Region: FosA; cd07244 557722011868 dimer interface [polypeptide binding]; other site 557722011869 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722011870 Mn binding site [ion binding]; other site 557722011871 K binding site; other site 557722011872 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722011873 Helix-turn-helix domains; Region: HTH; cl00088 557722011874 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 557722011875 putative effector binding pocket; other site 557722011876 putative dimerization interface [polypeptide binding]; other site 557722011877 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 557722011878 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722011879 active site 557722011880 catalytic tetrad [active] 557722011881 Domain of unknown function (DUF4234); Region: DUF4234; pfam14018 557722011882 NAD-dependent deacetylase; Provisional; Region: PRK00481 557722011883 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 557722011884 NAD+ binding site [chemical binding]; other site 557722011885 substrate binding site [chemical binding]; other site 557722011886 Zn binding site [ion binding]; other site 557722011887 deoxyguanosinetriphosphate triphosphohydrolase; Provisional; Region: dgt; PRK04926 557722011888 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722011889 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 557722011890 Protein of unknown function (DUF2025); Region: DUF2025; pfam09634 557722011891 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 557722011892 active site 557722011893 catalytic residues [active] 557722011894 metal binding site [ion binding]; metal-binding site 557722011895 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 557722011896 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 557722011897 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722011898 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722011899 metal binding site [ion binding]; metal-binding site 557722011900 active site 557722011901 I-site; other site 557722011902 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722011903 ligand binding site [chemical binding]; other site 557722011904 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 557722011905 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557722011906 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557722011907 Sulfatase; Region: Sulfatase; cl10460 557722011908 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 557722011909 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 557722011910 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722011911 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722011912 Walker A/P-loop; other site 557722011913 ATP binding site [chemical binding]; other site 557722011914 Q-loop/lid; other site 557722011915 ABC transporter signature motif; other site 557722011916 Walker B; other site 557722011917 D-loop; other site 557722011918 H-loop/switch region; other site 557722011919 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 557722011920 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 557722011921 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 557722011922 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 557722011923 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722011924 RNA binding surface [nucleotide binding]; other site 557722011925 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSSA_1; cd02555 557722011926 active site 557722011927 Cupin domain; Region: Cupin_2; cl09118 557722011928 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557722011929 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722011930 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722011931 metal binding site [ion binding]; metal-binding site 557722011932 active site 557722011933 I-site; other site 557722011934 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 557722011935 flagellar biosynthesis chaperone; Validated; Region: fliJ; cl09161 557722011936 Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliJ; COG2882 557722011937 flagellum-specific ATP synthase; Validated; Region: fliI; PRK05688 557722011938 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 557722011939 Walker A motif/ATP binding site; other site 557722011940 Walker B motif; other site 557722011941 flagellar assembly protein H; Validated; Region: fliH; PRK05687 557722011942 Flagellar assembly protein FliH; Region: FliH; pfam02108 557722011943 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 557722011944 MgtE intracellular N domain; Region: MgtE_N; cl15244 557722011945 FliG C-terminal domain; Region: FliG_C; pfam01706 557722011946 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 557722011947 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 557722011948 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 557722011949 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 557722011950 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722011951 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722011952 active site 557722011953 phosphorylation site [posttranslational modification] 557722011954 intermolecular recognition site; other site 557722011955 dimerization interface [polypeptide binding]; other site 557722011956 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722011957 Walker A motif; other site 557722011958 ATP binding site [chemical binding]; other site 557722011959 Walker B motif; other site 557722011960 arginine finger; other site 557722011961 Helix-turn-helix domains; Region: HTH; cl00088 557722011962 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557722011963 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722011964 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722011965 dimer interface [polypeptide binding]; other site 557722011966 phosphorylation site [posttranslational modification] 557722011967 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722011968 ATP binding site [chemical binding]; other site 557722011969 Mg2+ binding site [ion binding]; other site 557722011970 G-X-G motif; other site 557722011971 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722011972 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 557722011973 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722011974 Walker A motif; other site 557722011975 ATP binding site [chemical binding]; other site 557722011976 Walker B motif; other site 557722011977 arginine finger; other site 557722011978 Helix-turn-helix domains; Region: HTH; cl00088 557722011979 Flagellar protein FliS; Region: FliS; cl00654 557722011980 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 557722011981 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 557722011982 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 557722011983 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 557722011984 FlaG protein; Region: FlaG; cl00591 557722011985 flagellin; Provisional; Region: PRK12806 557722011986 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 557722011987 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 557722011988 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 557722011989 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 557722011990 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722011991 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557722011992 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722011993 active site 557722011994 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722011995 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722011996 active site 557722011997 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 557722011998 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722011999 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557722012000 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722012001 S-adenosylmethionine binding site [chemical binding]; other site 557722012002 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722012003 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 557722012004 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 557722012005 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 557722012006 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK05683 557722012007 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 557722012008 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 557722012009 Rod binding protein; Region: Rod-binding; cl01626 557722012010 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 557722012011 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 557722012012 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 557722012013 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 557722012014 Flagellar L-ring protein; Region: FlgH; cl00905 557722012015 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 557722012016 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 557722012017 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 557722012018 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 557722012019 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 557722012020 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 557722012021 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 557722012022 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 557722012023 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 557722012024 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 557722012025 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 557722012026 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 557722012027 FlgD Ig-like domain; Region: FlgD_ig; cl15790 557722012028 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 557722012029 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 557722012030 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 557722012031 flagellar basal-body rod protein FlgB; Region: FlgB; TIGR01396 557722012032 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 557722012033 Protein of unknown function (DUF2288); Region: DUF2288; cl02399 557722012034 leucine ABC transporter subunit substrate-binding protein LivK; Provisional; Region: PRK15404 557722012035 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 557722012036 dimerization interface [polypeptide binding]; other site 557722012037 ligand binding site [chemical binding]; other site 557722012038 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 557722012039 TM-ABC transporter signature motif; other site 557722012040 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 557722012041 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 557722012042 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 557722012043 TM-ABC transporter signature motif; other site 557722012044 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 557722012045 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 557722012046 Walker A/P-loop; other site 557722012047 ATP binding site [chemical binding]; other site 557722012048 Q-loop/lid; other site 557722012049 ABC transporter signature motif; other site 557722012050 Walker B; other site 557722012051 D-loop; other site 557722012052 H-loop/switch region; other site 557722012053 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livF; PRK11614 557722012054 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 557722012055 Walker A/P-loop; other site 557722012056 ATP binding site [chemical binding]; other site 557722012057 Q-loop/lid; other site 557722012058 ABC transporter signature motif; other site 557722012059 Walker B; other site 557722012060 D-loop; other site 557722012061 H-loop/switch region; other site 557722012062 NMDA receptor-regulated protein 1; Region: NARP1; pfam12569 557722012063 Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]; Region: HtpG; COG0326 557722012064 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 557722012065 LysR family transcriptional regulator; Provisional; Region: PRK14997 557722012066 Helix-turn-helix domains; Region: HTH; cl00088 557722012067 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722012068 putative effector binding pocket; other site 557722012069 dimerization interface [polypeptide binding]; other site 557722012070 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722012071 NAD(P) binding site [chemical binding]; other site 557722012072 active site 557722012073 Protein of unknown function, DUF488; Region: DUF488; cl01246 557722012074 Predicted membrane protein [Function unknown]; Region: COG3650 557722012075 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722012076 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557722012077 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 557722012078 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722012079 catalytic residue [active] 557722012080 EamA-like transporter family; Region: EamA; cl01037 557722012081 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557722012082 EamA-like transporter family; Region: EamA; cl01037 557722012083 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 557722012084 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 557722012085 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 557722012086 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 557722012087 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 557722012088 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 557722012089 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 557722012090 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 557722012091 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 557722012092 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 557722012093 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 557722012094 Glycerate kinase family; Region: Gly_kinase; cl00841 557722012095 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 557722012096 Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]; Region: CdaR; COG3835 557722012097 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 557722012098 Helix-turn-helix domains; Region: HTH; cl00088 557722012099 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 557722012100 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557722012101 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 557722012102 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722012103 ligand binding site [chemical binding]; other site 557722012104 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722012105 Beta-galactosidase; Region: Glyco_hydro_42; cl03154 557722012106 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 557722012107 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012108 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012109 Copper resistance protein D; Region: CopD; cl00563 557722012110 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 557722012111 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722012112 ligand binding site [chemical binding]; other site 557722012113 hypothetical protein; Provisional; Region: PRK00183 557722012114 SEC-C motif; Region: SEC-C; pfam02810 557722012115 Predicted membrane protein [Function unknown]; Region: COG2860 557722012116 UPF0126 domain; Region: UPF0126; pfam03458 557722012117 UPF0126 domain; Region: UPF0126; pfam03458 557722012118 LEA14-like dessication related protein [Defense mechanisms]; Region: COG5608 557722012119 Late embryogenesis abundant protein; Region: LEA_2; cl12118 557722012120 SEC-C motif; Region: SEC-C; pfam02810 557722012121 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 557722012122 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 557722012123 C-terminal domain interface [polypeptide binding]; other site 557722012124 GSH binding site (G-site) [chemical binding]; other site 557722012125 dimer interface [polypeptide binding]; other site 557722012126 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 557722012127 N-terminal domain interface [polypeptide binding]; other site 557722012128 putative dimer interface [polypeptide binding]; other site 557722012129 active site 557722012130 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 557722012131 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 557722012132 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 557722012133 active site 557722012134 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 557722012135 RmuC family; Region: RmuC; pfam02646 557722012136 RES domain; Region: RES; cl02411 557722012137 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722012138 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 557722012139 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722012140 FAD dependent oxidoreductase; Region: DAO; pfam01266 557722012141 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722012142 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 557722012143 tetrameric interface [polypeptide binding]; other site 557722012144 NAD binding site [chemical binding]; other site 557722012145 catalytic residues [active] 557722012146 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557722012147 outer membrane porin, OprD family; Region: OprD; pfam03573 557722012148 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 557722012149 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 557722012150 FMN binding site [chemical binding]; other site 557722012151 substrate binding site [chemical binding]; other site 557722012152 putative catalytic residue [active] 557722012153 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK06463 557722012154 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722012155 NAD(P) binding site [chemical binding]; other site 557722012156 active site 557722012157 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 557722012158 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722012159 active site 557722012160 enoyl-CoA hydratase; Provisional; Region: PRK06688 557722012161 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722012162 substrate binding site [chemical binding]; other site 557722012163 oxyanion hole (OAH) forming residues; other site 557722012164 trimer interface [polypeptide binding]; other site 557722012165 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 557722012166 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722012167 active site 557722012168 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722012169 CoenzymeA binding site [chemical binding]; other site 557722012170 subunit interaction site [polypeptide binding]; other site 557722012171 PHB binding site; other site 557722012172 benzoate transport; Region: 2A0115; TIGR00895 557722012173 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722012174 putative substrate translocation pore; other site 557722012175 enoyl-CoA hydratase; Region: PLN02864 557722012176 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557722012177 HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit; Region: HDE_HSD; cd03448 557722012178 dimer interaction site [polypeptide binding]; other site 557722012179 substrate-binding tunnel; other site 557722012180 active site 557722012181 catalytic site [active] 557722012182 substrate binding site [chemical binding]; other site 557722012183 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 557722012184 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722012185 CoA-ligase; Region: Ligase_CoA; cl02894 557722012186 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722012187 thiolase; Provisional; Region: PRK06158 557722012188 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 557722012189 active site 557722012190 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722012191 Helix-turn-helix domains; Region: HTH; cl00088 557722012192 Bacterial transcriptional regulator; Region: IclR; pfam01614 557722012193 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 557722012194 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 557722012195 active site 557722012196 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 557722012197 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 557722012198 ATP binding site [chemical binding]; other site 557722012199 active site 557722012200 substrate binding site [chemical binding]; other site 557722012201 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722012202 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 557722012203 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 557722012204 dihydrodipicolinate synthase; Region: dapA; TIGR00674 557722012205 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 557722012206 dimer interface [polypeptide binding]; other site 557722012207 active site 557722012208 catalytic residue [active] 557722012209 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 557722012210 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 557722012211 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 557722012212 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 557722012213 catalytic triad [active] 557722012214 Domain of unknown function DUF20; Region: UPF0118; pfam01594 557722012215 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 557722012216 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 557722012217 CPxP motif; other site 557722012218 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 557722012219 Peptidase family M48; Region: Peptidase_M48; cl12018 557722012220 Quinolinate synthetase A protein; Region: NadA; cl00420 557722012221 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722012222 Helix-turn-helix domains; Region: HTH; cl00088 557722012223 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722012224 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557722012225 Glutamine amidotransferase class-I; Region: GATase; pfam00117 557722012226 glutamine binding [chemical binding]; other site 557722012227 catalytic triad [active] 557722012228 anthranilate synthase component I; Provisional; Region: PRK13564 557722012229 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 557722012230 chorismate binding enzyme; Region: Chorismate_bind; cl10555 557722012231 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722012232 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 557722012233 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 557722012234 dimer interface [polypeptide binding]; other site 557722012235 active site 557722012236 CoA binding pocket [chemical binding]; other site 557722012237 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 557722012238 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 557722012239 active site 557722012240 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 557722012241 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 557722012242 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 557722012243 AMP-binding enzyme; Region: AMP-binding; cl15778 557722012244 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 557722012245 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 557722012246 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 557722012247 DNA binding site [nucleotide binding] 557722012248 active site 557722012249 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 557722012250 PapC N-terminal domain; Region: PapC_N; pfam13954 557722012251 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 557722012252 PapC C-terminal domain; Region: PapC_C; pfam13953 557722012253 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 557722012254 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722012255 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 557722012256 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722012257 Hydrolase of X-linked nucleoside diphosphate N terminal; Region: Nudix_N; pfam12535 557722012258 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_14; cd04672 557722012259 nudix motif; other site 557722012260 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722012261 active site 557722012262 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 557722012263 Ligand Binding Site [chemical binding]; other site 557722012264 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Region: rSAM_QueE_Clost; TIGR03963 557722012265 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722012266 FeS/SAM binding site; other site 557722012267 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 557722012268 Tetratricopeptide repeat; Region: TPR_6; pfam13174 557722012269 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722012270 ligand binding site [chemical binding]; other site 557722012271 translocation protein TolB; Provisional; Region: tolB; PRK00178 557722012272 TolB amino-terminal domain; Region: TolB_N; cl00639 557722012273 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557722012274 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557722012275 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557722012276 TolA protein; Region: tolA_full; TIGR02794 557722012277 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557722012278 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557722012279 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722012280 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722012281 active site 557722012282 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 557722012283 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722012284 Walker A motif; other site 557722012285 ATP binding site [chemical binding]; other site 557722012286 Walker B motif; other site 557722012287 arginine finger; other site 557722012288 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 557722012289 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 557722012290 RuvA N terminal domain; Region: RuvA_N; pfam01330 557722012291 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 557722012292 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 557722012293 active site 557722012294 putative DNA-binding cleft [nucleotide binding]; other site 557722012295 dimer interface [polypeptide binding]; other site 557722012296 Transcriptional regulator; Region: Transcrip_reg; cl00361 557722012297 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 557722012298 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 557722012299 dimer interface [polypeptide binding]; other site 557722012300 anticodon binding site; other site 557722012301 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 557722012302 homodimer interface [polypeptide binding]; other site 557722012303 motif 1; other site 557722012304 active site 557722012305 motif 2; other site 557722012306 GAD domain; Region: GAD; pfam02938 557722012307 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 557722012308 active site 557722012309 motif 3; other site 557722012310 Ferritin-like domain; Region: Ferritin; pfam00210 557722012311 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 557722012312 dimerization interface [polypeptide binding]; other site 557722012313 DPS ferroxidase diiron center [ion binding]; other site 557722012314 ion pore; other site 557722012315 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 557722012316 DNA-binding site [nucleotide binding]; DNA binding site 557722012317 RNA-binding motif; other site 557722012318 SlyX; Region: SlyX; cl01090 557722012319 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 557722012320 outer membrane porin, OprD family; Region: OprD; pfam03573 557722012321 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722012322 CoenzymeA binding site [chemical binding]; other site 557722012323 subunit interaction site [polypeptide binding]; other site 557722012324 PHB binding site; other site 557722012325 prolyl-tRNA synthetase; Provisional; Region: PRK09194 557722012326 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 557722012327 dimer interface [polypeptide binding]; other site 557722012328 motif 1; other site 557722012329 active site 557722012330 motif 2; other site 557722012331 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 557722012332 putative deacylase active site [active] 557722012333 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 557722012334 active site 557722012335 motif 3; other site 557722012336 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 557722012337 anticodon binding site; other site 557722012338 Acylphosphatase; Region: Acylphosphatase; cl00551 557722012339 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 557722012340 catalytic residues [active] 557722012341 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 557722012342 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 557722012343 ArsC family; Region: ArsC; pfam03960 557722012344 catalytic residues [active] 557722012345 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722012346 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 557722012347 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012348 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 557722012349 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 557722012350 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 557722012351 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 557722012352 dimerization interface [polypeptide binding]; other site 557722012353 putative ATP binding site [chemical binding]; other site 557722012354 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 557722012355 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 557722012356 active site 557722012357 substrate binding site [chemical binding]; other site 557722012358 cosubstrate binding site; other site 557722012359 catalytic site [active] 557722012360 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 557722012361 Transcriptional regulators [Transcription]; Region: MarR; COG1846 557722012362 Helix-turn-helix domains; Region: HTH; cl00088 557722012363 Helix-turn-helix domains; Region: HTH; cl00088 557722012364 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557722012365 Domain of unknown function (DUF2024); Region: DUF2024; pfam09630 557722012366 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 557722012367 Chain length determinant protein [Cell envelope biogenesis, outer membrane]; Region: WzzB; COG3765 557722012368 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 557722012369 Cupin domain; Region: Cupin_2; cl09118 557722012370 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 557722012371 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 557722012372 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 557722012373 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 557722012374 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722012375 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 557722012376 synthetase active site [active] 557722012377 NTP binding site [chemical binding]; other site 557722012378 metal binding site [ion binding]; metal-binding site 557722012379 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 557722012380 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 557722012381 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 557722012382 TRAM domain; Region: TRAM; cl01282 557722012383 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722012384 cysteine synthase B; Region: cysM; TIGR01138 557722012385 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 557722012386 dimer interface [polypeptide binding]; other site 557722012387 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722012388 catalytic residue [active] 557722012389 outer membrane receptor FepA; Provisional; Region: PRK13528 557722012390 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722012391 N-terminal plug; other site 557722012392 ligand-binding site [chemical binding]; other site 557722012393 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722012394 dimerization interface [polypeptide binding]; other site 557722012395 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722012396 dimer interface [polypeptide binding]; other site 557722012397 phosphorylation site [posttranslational modification] 557722012398 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722012399 ATP binding site [chemical binding]; other site 557722012400 G-X-G motif; other site 557722012401 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722012402 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722012403 active site 557722012404 phosphorylation site [posttranslational modification] 557722012405 intermolecular recognition site; other site 557722012406 dimerization interface [polypeptide binding]; other site 557722012407 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722012408 DNA binding site [nucleotide binding] 557722012409 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 557722012410 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722012411 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722012412 dimer interface [polypeptide binding]; other site 557722012413 phosphorylation site [posttranslational modification] 557722012414 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722012415 ATP binding site [chemical binding]; other site 557722012416 Mg2+ binding site [ion binding]; other site 557722012417 G-X-G motif; other site 557722012418 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722012419 active site 557722012420 phosphorylation site [posttranslational modification] 557722012421 intermolecular recognition site; other site 557722012422 dimerization interface [polypeptide binding]; other site 557722012423 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 557722012424 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 557722012425 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722012426 META domain; Region: META; cl01245 557722012427 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 557722012428 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 557722012429 Sulfatase; Region: Sulfatase; cl10460 557722012430 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 557722012431 active site 557722012432 DNA polymerase IV; Validated; Region: PRK02406 557722012433 DNA binding site [nucleotide binding] 557722012434 Replication protein A C terminal; Region: RPA_C; pfam08784 557722012435 Predicted integral membrane protein [Function unknown]; Region: COG0392 557722012436 Uncharacterized conserved protein [Function unknown]; Region: COG2898 557722012437 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 557722012438 Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]; Region: VirJ; COG3946 557722012439 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 557722012440 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557722012441 K+ potassium transporter; Region: K_trans; cl15781 557722012442 potassium uptake protein; Region: kup; TIGR00794 557722012443 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 557722012444 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 557722012445 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 557722012446 FeS/SAM binding site; other site 557722012447 TRAM domain; Region: TRAM; cl01282 557722012448 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 557722012449 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 557722012450 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 557722012451 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 557722012452 MgtE intracellular N domain; Region: MgtE_N; cl15244 557722012453 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 557722012454 Divalent cation transporter; Region: MgtE; cl00786 557722012455 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557722012456 Protein of unknown function (DUF754); Region: DUF754; pfam05449 557722012457 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722012458 non-specific DNA binding site [nucleotide binding]; other site 557722012459 Predicted transcriptional regulator [Transcription]; Region: COG2932 557722012460 salt bridge; other site 557722012461 sequence-specific DNA binding site [nucleotide binding]; other site 557722012462 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 557722012463 Catalytic site [active] 557722012464 Global regulator protein family; Region: CsrA; cl00670 557722012465 aspartate kinase; Reviewed; Region: PRK06635 557722012466 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 557722012467 putative nucleotide binding site [chemical binding]; other site 557722012468 putative catalytic residues [active] 557722012469 putative Mg ion binding site [ion binding]; other site 557722012470 putative aspartate binding site [chemical binding]; other site 557722012471 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 557722012472 putative allosteric regulatory site; other site 557722012473 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 557722012474 putative allosteric regulatory residue; other site 557722012475 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 557722012476 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 557722012477 motif 1; other site 557722012478 active site 557722012479 motif 2; other site 557722012480 motif 3; other site 557722012481 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 557722012482 DHHA1 domain; Region: DHHA1; pfam02272 557722012483 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 557722012484 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 557722012485 tetramer interface [polypeptide binding]; other site 557722012486 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722012487 catalytic residue [active] 557722012488 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 557722012489 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 557722012490 putative active site [active] 557722012491 Zn binding site [ion binding]; other site 557722012492 Succinylarginine dihydrolase; Region: AstB; cl01511 557722012493 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722012494 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 557722012495 NAD(P) binding site [chemical binding]; other site 557722012496 catalytic residues [active] 557722012497 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 557722012498 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 557722012499 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 557722012500 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722012501 inhibitor-cofactor binding pocket; inhibition site 557722012502 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722012503 catalytic residue [active] 557722012504 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 557722012505 conserved cys residue [active] 557722012506 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012507 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722012508 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012509 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 557722012510 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722012511 Walker A/P-loop; other site 557722012512 ATP binding site [chemical binding]; other site 557722012513 Q-loop/lid; other site 557722012514 ABC transporter signature motif; other site 557722012515 Walker B; other site 557722012516 D-loop; other site 557722012517 H-loop/switch region; other site 557722012518 Predicted deacylase [General function prediction only]; Region: COG3608 557722012519 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 557722012520 active site 557722012521 Zn binding site [ion binding]; other site 557722012522 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722012523 dimer interface [polypeptide binding]; other site 557722012524 conserved gate region; other site 557722012525 putative PBP binding loops; other site 557722012526 ABC-ATPase subunit interface; other site 557722012527 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722012528 dimer interface [polypeptide binding]; other site 557722012529 conserved gate region; other site 557722012530 putative PBP binding loops; other site 557722012531 ABC-ATPase subunit interface; other site 557722012532 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 557722012533 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722012534 substrate binding pocket [chemical binding]; other site 557722012535 membrane-bound complex binding site; other site 557722012536 hinge residues; other site 557722012537 acetyl-CoA synthetase; Provisional; Region: PRK00174 557722012538 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 557722012539 AMP-binding enzyme; Region: AMP-binding; cl15778 557722012540 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722012541 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 557722012542 DctM-like transporters; Region: DctM; pfam06808 557722012543 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 557722012544 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 557722012545 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 557722012546 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722012547 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 557722012548 CoA-transferase family III; Region: CoA_transf_3; pfam02515 557722012549 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 557722012550 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_2; cd07253 557722012551 dimer interface [polypeptide binding]; other site 557722012552 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722012553 metal binding site [ion binding]; metal-binding site 557722012554 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722012555 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722012556 active site 557722012557 Uncharacterized conserved protein [Function unknown]; Region: COG3777 557722012558 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557722012559 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557722012560 active site 2 [active] 557722012561 active site 1 [active] 557722012562 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722012563 Helix-turn-helix domains; Region: HTH; cl00088 557722012564 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 557722012565 putative dimerization interface [polypeptide binding]; other site 557722012566 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722012567 Helix-turn-helix domains; Region: HTH; cl00088 557722012568 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 557722012569 putative effector binding pocket; other site 557722012570 dimerization interface [polypeptide binding]; other site 557722012571 Fusaric acid resistance protein family; Region: FUSC; pfam04632 557722012572 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 557722012573 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 557722012574 Protein of unknown function (DUF2790); Region: DUF2790; pfam10976 557722012575 Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]; Region: TyrR; COG3283 557722012576 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 557722012577 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722012578 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722012579 Walker A motif; other site 557722012580 ATP binding site [chemical binding]; other site 557722012581 Walker B motif; other site 557722012582 arginine finger; other site 557722012583 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 557722012584 cofactor binding site; other site 557722012585 metal binding site [ion binding]; metal-binding site 557722012586 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 557722012587 aromatic arch; other site 557722012588 DCoH dimer interaction site [polypeptide binding]; other site 557722012589 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 557722012590 DCoH tetramer interaction site [polypeptide binding]; other site 557722012591 substrate binding site [chemical binding]; other site 557722012592 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 557722012593 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722012594 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722012595 homodimer interface [polypeptide binding]; other site 557722012596 catalytic residue [active] 557722012597 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 557722012598 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722012599 RF-1 domain; Region: RF-1; cl02875 557722012600 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 557722012601 aromatic amino acid transporter; Provisional; Region: PRK10238 557722012602 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 557722012603 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 557722012604 dimer interface [polypeptide binding]; other site 557722012605 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 557722012606 active site 557722012607 Fe binding site [ion binding]; other site 557722012608 Cupin domain; Region: Cupin_2; cl09118 557722012609 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722012610 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012611 Protein of unknown function (DUF1427); Region: DUF1427; cl01771 557722012612 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 557722012613 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 557722012614 putative NAD(P) binding site [chemical binding]; other site 557722012615 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 557722012616 PAS domain S-box; Region: sensory_box; TIGR00229 557722012617 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722012618 putative active site [active] 557722012619 heme pocket [chemical binding]; other site 557722012620 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722012621 metal binding site [ion binding]; metal-binding site 557722012622 active site 557722012623 I-site; other site 557722012624 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722012625 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722012626 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012627 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557722012628 Walker A/P-loop; other site 557722012629 ATP binding site [chemical binding]; other site 557722012630 Q-loop/lid; other site 557722012631 ABC transporter signature motif; other site 557722012632 Walker B; other site 557722012633 D-loop; other site 557722012634 H-loop/switch region; other site 557722012635 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 557722012636 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 557722012637 catalytic residues [active] 557722012638 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 557722012639 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 557722012640 active site residue [active] 557722012641 BolA-like protein; Region: BolA; cl00386 557722012642 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 557722012643 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 557722012644 fumarate hydratase; Provisional; Region: PRK12425 557722012645 Class II fumarases; Region: Fumarase_classII; cd01362 557722012646 active site 557722012647 tetramer interface [polypeptide binding]; other site 557722012648 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722012649 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3397 557722012650 Chitin binding domain; Region: Chitin_bind_3; cl03871 557722012651 N-acetylglucosamine-binding protein A; Reviewed; Region: PRK13211 557722012652 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 557722012653 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 557722012654 tetramer interface [polypeptide binding]; other site 557722012655 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722012656 catalytic residue [active] 557722012657 MAPEG family; Region: MAPEG; cl09190 557722012658 thioredoxin reductase; Provisional; Region: PRK10262 557722012659 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722012660 peroxidase; Provisional; Region: PRK15000 557722012661 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 557722012662 dimer interface [polypeptide binding]; other site 557722012663 decamer (pentamer of dimers) interface [polypeptide binding]; other site 557722012664 catalytic triad [active] 557722012665 peroxidatic and resolving cysteines [active] 557722012666 CHASE4 domain; Region: CHASE4; cl01308 557722012667 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722012668 PAS domain S-box; Region: sensory_box; TIGR00229 557722012669 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722012670 putative active site [active] 557722012671 heme pocket [chemical binding]; other site 557722012672 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722012673 metal binding site [ion binding]; metal-binding site 557722012674 active site 557722012675 I-site; other site 557722012676 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 557722012677 Neutral/alkaline non-lysosomal ceramidase; Region: Ceramidase_alk; cl04712 557722012678 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 557722012679 Phosphoesterase family; Region: Phosphoesterase; cl15450 557722012680 Domain of unknown function (DUF756); Region: DUF756; pfam05506 557722012681 Domain of unknown function (DUF756); Region: DUF756; pfam05506 557722012682 phospholipase C accessory protein PlcR; Region: plc_access_R; TIGR03398 557722012683 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722012684 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 557722012685 Uncharacterized protein, DegV family COG1307; Region: DegV; cl00577 557722012686 Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_5_FMN; cd04747 557722012687 putative active site [active] 557722012688 putative FMN binding site [chemical binding]; other site 557722012689 putative substrate binding site [chemical binding]; other site 557722012690 putative catalytic residue [active] 557722012691 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557722012692 Helix-turn-helix domains; Region: HTH; cl00088 557722012693 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 557722012694 catalytic residues [active] 557722012695 dimer interface [polypeptide binding]; other site 557722012696 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722012697 Acetokinase family; Region: Acetate_kinase; cl01029 557722012698 propionate/acetate kinase; Provisional; Region: PRK12379 557722012699 phosphate acetyltransferase; Reviewed; Region: PRK05632 557722012700 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012701 DRTGG domain; Region: DRTGG; cl12147 557722012702 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 557722012703 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 557722012704 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 557722012705 putative acyl-acceptor binding pocket; other site 557722012706 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722012707 ligand binding site [chemical binding]; other site 557722012708 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722012709 LESGI-5 557722012710 integrase; Provisional; Region: int; PHA02601 557722012711 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722012712 DNA binding site [nucleotide binding] 557722012713 Int/Topo IB signature motif; other site 557722012714 active site 557722012715 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 557722012716 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722012717 Coenzyme A binding pocket [chemical binding]; other site 557722012718 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722012719 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012720 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 557722012721 Catalytic domain of Protein Kinases; Region: PKc; cd00180 557722012722 active site 557722012723 ATP binding site [chemical binding]; other site 557722012724 substrate binding site [chemical binding]; other site 557722012725 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722012726 activation loop (A-loop); other site 557722012727 activation loop (A-loop); other site 557722012728 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 557722012729 putative transposase OrfB; Reviewed; Region: PHA02517 557722012730 HTH-like domain; Region: HTH_21; pfam13276 557722012731 Integrase core domain; Region: rve; cl01316 557722012732 Integrase core domain; Region: rve_3; cl15866 557722012733 Helix-turn-helix domains; Region: HTH; cl00088 557722012734 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 557722012735 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 557722012736 TraX protein; Region: TraX; cl05434 557722012737 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 557722012738 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722012739 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012740 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 557722012741 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 557722012742 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722012743 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722012744 mycofactocin system transcriptional regulator; Region: mycofact_TetR; TIGR03968 557722012745 Helix-turn-helix domains; Region: HTH; cl00088 557722012746 TM2 domain; Region: TM2; cl00984 557722012747 PAAR motif; Region: PAAR_motif; cl15808 557722012748 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 557722012749 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 557722012750 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722012751 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_18; cd08357 557722012752 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722012753 putative metal binding site [ion binding]; other site 557722012754 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722012755 Helix-turn-helix domains; Region: HTH; cl00088 557722012756 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 557722012757 putative dimerization interface [polypeptide binding]; other site 557722012758 cell density-dependent motility repressor; Provisional; Region: PRK10082 557722012759 Helix-turn-helix domains; Region: HTH; cl00088 557722012760 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722012761 dimerization interface [polypeptide binding]; other site 557722012762 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 557722012763 homotrimer interaction site [polypeptide binding]; other site 557722012764 putative active site [active] 557722012765 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 557722012766 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722012767 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722012768 catalytic residue [active] 557722012769 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl15827 557722012770 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722012771 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722012772 putative substrate translocation pore; other site 557722012773 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 557722012774 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722012775 motif II; other site 557722012776 manganese transport protein MntH; Reviewed; Region: PRK00701; cl15845 557722012777 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 557722012778 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_8; cd08901 557722012779 putative hydrophobic ligand binding site [chemical binding]; other site 557722012780 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 557722012781 amidase catalytic site [active] 557722012782 Zn binding residues [ion binding]; other site 557722012783 substrate binding site [chemical binding]; other site 557722012784 Predicted membrane protein [Function unknown]; Region: COG4270 557722012785 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722012786 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 557722012787 active site 557722012788 catalytic tetrad [active] 557722012789 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_14; cd08355 557722012790 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722012791 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 557722012792 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722012793 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722012794 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722012795 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 557722012796 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722012797 ATP binding site [chemical binding]; other site 557722012798 putative Mg++ binding site [ion binding]; other site 557722012799 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722012800 nucleotide binding region [chemical binding]; other site 557722012801 ATP-binding site [chemical binding]; other site 557722012802 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557722012803 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722012804 S-adenosylmethionine binding site [chemical binding]; other site 557722012805 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557722012806 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722012807 DNA-binding site [nucleotide binding]; DNA binding site 557722012808 FCD domain; Region: FCD; cl11656 557722012809 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 557722012810 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 557722012811 tetramer interface [polypeptide binding]; other site 557722012812 active site 557722012813 Mg2+/Mn2+ binding site [ion binding]; other site 557722012814 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 557722012815 dimer interface [polypeptide binding]; other site 557722012816 Citrate synthase; Region: Citrate_synt; pfam00285 557722012817 active site 557722012818 citrylCoA binding site [chemical binding]; other site 557722012819 oxalacetate/citrate binding site [chemical binding]; other site 557722012820 coenzyme A binding site [chemical binding]; other site 557722012821 catalytic triad [active] 557722012822 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 557722012823 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 557722012824 substrate binding site [chemical binding]; other site 557722012825 ligand binding site [chemical binding]; other site 557722012826 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 557722012827 substrate binding site [chemical binding]; other site 557722012828 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 557722012829 PrpF protein; Region: PrpF; pfam04303 557722012830 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 557722012831 Cupin domain; Region: Cupin_2; cl09118 557722012832 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722012833 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012834 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557722012835 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 557722012836 Spore germination protein; Region: Spore_permease; cl15802 557722012837 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 557722012838 Transglycosylase; Region: Transgly; cl07896 557722012839 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722012840 Predicted ATPase [General function prediction only]; Region: COG4637 557722012841 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722012842 Walker A/P-loop; other site 557722012843 ATP binding site [chemical binding]; other site 557722012844 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722012845 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722012846 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722012847 Helix-turn-helix domains; Region: HTH; cl00088 557722012848 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722012849 dimerization interface [polypeptide binding]; other site 557722012850 Sodium:solute symporter family; Region: SSF; cl00456 557722012851 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557722012852 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 557722012853 Proline dehydrogenase; Region: Pro_dh; cl03282 557722012854 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 557722012855 Glutamate binding site [chemical binding]; other site 557722012856 NAD binding site [chemical binding]; other site 557722012857 catalytic residues [active] 557722012858 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 557722012859 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722012860 N-terminal plug; other site 557722012861 ligand-binding site [chemical binding]; other site 557722012862 Cupin domain; Region: Cupin_2; cl09118 557722012863 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012864 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722012865 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722012866 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 557722012867 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722012868 Walker A motif; other site 557722012869 ATP binding site [chemical binding]; other site 557722012870 Walker B motif; other site 557722012871 arginine finger; other site 557722012872 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 557722012873 Chagasin family peptidase inhibitor I42; Region: Inhibitor_I42; cl02325 557722012874 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl15306 557722012875 substrate binding pocket [chemical binding]; other site 557722012876 membrane-bound complex binding site; other site 557722012877 hinge residues; other site 557722012878 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722012879 S-adenosylmethionine binding site [chemical binding]; other site 557722012880 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557722012881 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722012882 S-adenosylmethionine binding site [chemical binding]; other site 557722012883 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 557722012884 active site 557722012885 hydrophilic channel; other site 557722012886 dimerization interface [polypeptide binding]; other site 557722012887 catalytic residues [active] 557722012888 active site lid [active] 557722012889 Recombination protein O N terminal; Region: RecO_N; cl15812 557722012890 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 557722012891 Recombination protein O C terminal; Region: RecO_C; pfam02565 557722012892 GTPase Era; Reviewed; Region: era; PRK00089 557722012893 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 557722012894 G1 box; other site 557722012895 GTP/Mg2+ binding site [chemical binding]; other site 557722012896 Switch I region; other site 557722012897 G2 box; other site 557722012898 Switch II region; other site 557722012899 G3 box; other site 557722012900 G4 box; other site 557722012901 G5 box; other site 557722012902 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 557722012903 ribonuclease III; Reviewed; Region: rnc; PRK00102 557722012904 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 557722012905 dimerization interface [polypeptide binding]; other site 557722012906 active site 557722012907 metal binding site [ion binding]; metal-binding site 557722012908 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 557722012909 dsRNA binding site [nucleotide binding]; other site 557722012910 signal peptidase I; Provisional; Region: PRK10861 557722012911 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 557722012912 Catalytic site [active] 557722012913 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 557722012914 GTP-binding protein LepA; Provisional; Region: PRK05433 557722012915 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 557722012916 G1 box; other site 557722012917 putative GEF interaction site [polypeptide binding]; other site 557722012918 GTP/Mg2+ binding site [chemical binding]; other site 557722012919 Switch I region; other site 557722012920 G2 box; other site 557722012921 G3 box; other site 557722012922 Switch II region; other site 557722012923 G4 box; other site 557722012924 G5 box; other site 557722012925 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 557722012926 lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits...; Region: lepA_C; cd03709 557722012927 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 557722012928 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 557722012929 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 557722012930 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 557722012931 protein binding site [polypeptide binding]; other site 557722012932 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 557722012933 protein binding site [polypeptide binding]; other site 557722012934 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 557722012935 MucB/RseB family; Region: MucB_RseB; pfam03888 557722012936 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 557722012937 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseA; COG3073 557722012938 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 557722012939 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 557722012940 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 557722012941 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722012942 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 557722012943 DNA binding residues [nucleotide binding] 557722012944 L-aspartate oxidase; Provisional; Region: PRK09077 557722012945 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722012946 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 557722012947 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 557722012948 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 557722012949 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 557722012950 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 557722012951 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 557722012952 sensor protein PhoQ; Provisional; Region: PRK10815 557722012953 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722012954 dimer interface [polypeptide binding]; other site 557722012955 phosphorylation site [posttranslational modification] 557722012956 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722012957 ATP binding site [chemical binding]; other site 557722012958 G-X-G motif; other site 557722012959 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 557722012960 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722012961 active site 557722012962 phosphorylation site [posttranslational modification] 557722012963 intermolecular recognition site; other site 557722012964 dimerization interface [polypeptide binding]; other site 557722012965 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722012966 DNA binding site [nucleotide binding] 557722012967 outer membrane porin, OprD family; Region: OprD; pfam03573 557722012968 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 557722012969 NMT1-like family; Region: NMT1_2; cl15260 557722012970 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 557722012971 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 557722012972 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 557722012973 Putative ammonia monooxygenase; Region: AmoA; pfam05145 557722012974 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 557722012975 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 557722012976 ligand binding site [chemical binding]; other site 557722012977 active site 557722012978 UGI interface [polypeptide binding]; other site 557722012979 catalytic site [active] 557722012980 Uncharacterized vancomycin resistance protein [Defense mechanisms]; Region: COG2720 557722012981 VanW like protein; Region: VanW; pfam04294 557722012982 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 557722012983 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722012984 tetrameric interface [polypeptide binding]; other site 557722012985 NAD binding site [chemical binding]; other site 557722012986 catalytic residues [active] 557722012987 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722012988 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 557722012989 substrate binding pocket [chemical binding]; other site 557722012990 FAD binding site [chemical binding]; other site 557722012991 catalytic base [active] 557722012992 enoyl-CoA hydratase; Provisional; Region: PRK09076 557722012993 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722012994 substrate binding site [chemical binding]; other site 557722012995 oxyanion hole (OAH) forming residues; other site 557722012996 trimer interface [polypeptide binding]; other site 557722012997 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 557722012998 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722012999 substrate binding site [chemical binding]; other site 557722013000 oxyanion hole (OAH) forming residues; other site 557722013001 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 557722013002 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013003 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 557722013004 Ion channel; Region: Ion_trans_2; cl11596 557722013005 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 557722013006 NADH(P)-binding; Region: NAD_binding_10; pfam13460 557722013007 NAD binding site [chemical binding]; other site 557722013008 substrate binding site [chemical binding]; other site 557722013009 putative active site [active] 557722013010 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 557722013011 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722013012 SCP-2 sterol transfer family; Region: SCP2; cl01225 557722013013 Helix-turn-helix domains; Region: HTH; cl00088 557722013014 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 557722013015 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722013016 dimerization interface [polypeptide binding]; other site 557722013017 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 557722013018 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 557722013019 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 557722013020 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722013021 RNA binding surface [nucleotide binding]; other site 557722013022 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 557722013023 active site 557722013024 uracil binding [chemical binding]; other site 557722013025 hypothetical protein; Provisional; Region: PRK06132 557722013026 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 557722013027 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 557722013028 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722013029 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 557722013030 Uncharacterized protein conserved in bacteria (DUF2084); Region: DUF2084; cl01566 557722013031 Predicted acetyltransferase [General function prediction only]; Region: COG3153 557722013032 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722013033 Coenzyme A binding pocket [chemical binding]; other site 557722013034 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722013035 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 557722013036 dimer interface [polypeptide binding]; other site 557722013037 active site 557722013038 metal binding site [ion binding]; metal-binding site 557722013039 glutathione binding site [chemical binding]; other site 557722013040 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 557722013041 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722013042 Helix-turn-helix domains; Region: HTH; cl00088 557722013043 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722013044 dimerization interface [polypeptide binding]; other site 557722013045 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 557722013046 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 557722013047 active site 557722013048 substrate binding site [chemical binding]; other site 557722013049 trimer interface [polypeptide binding]; other site 557722013050 CoA binding site [chemical binding]; other site 557722013051 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557722013052 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 557722013053 active site 557722013054 amidase; Provisional; Region: PRK07042 557722013055 Amidase; Region: Amidase; cl11426 557722013056 citrate-proton symporter; Provisional; Region: PRK15075 557722013057 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722013058 putative substrate translocation pore; other site 557722013059 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 557722013060 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722013061 Helix-turn-helix domains; Region: HTH; cl00088 557722013062 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722013063 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK02998 557722013064 PPIC-type PPIASE domain; Region: Rotamase; cl08278 557722013065 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 557722013066 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 557722013067 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557722013068 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 557722013069 Domain of unknown function (DUF2341); Region: DUF2341; pfam10102 557722013070 Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of...; Region: LamG; cl00102 557722013071 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722013072 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722013073 Surface antigen; Region: Bac_surface_Ag; cl03097 557722013074 haemagglutination activity domain; Region: Haemagg_act; cl05436 557722013075 Filamentous haemagglutinin family outer membrane protein; Region: DUF3739; pfam12545 557722013076 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722013077 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722013078 general secretion pathway protein F; Region: GspF; TIGR02120 557722013079 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722013080 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722013081 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 557722013082 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 557722013083 Walker A motif; other site 557722013084 ATP binding site [chemical binding]; other site 557722013085 Walker B motif; other site 557722013086 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 557722013087 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722013088 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722013089 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722013090 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 557722013091 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722013092 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 557722013093 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 557722013094 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722013095 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 557722013096 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 557722013097 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 557722013098 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 557722013099 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722013100 general secretion pathway protein H; Region: typeII_sec_gspH; TIGR01708 557722013101 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 557722013102 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722013103 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 557722013104 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722013105 FecR protein; Region: FecR; pfam04773 557722013106 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 557722013107 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722013108 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722013109 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557722013110 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 557722013111 heme binding pocket [chemical binding]; other site 557722013112 heme ligand [chemical binding]; other site 557722013113 Cell division inhibitor SulA; Region: SulA; cl01880 557722013114 DNA Polymerase Y-family; Region: PolY_like; cd03468 557722013115 active site 557722013116 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 557722013117 DNA binding site [nucleotide binding] 557722013118 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 557722013119 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 557722013120 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 557722013121 generic binding surface II; other site 557722013122 generic binding surface I; other site 557722013123 exonuclease subunit SbcD; Provisional; Region: PRK10966 557722013124 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 557722013125 active site 557722013126 metal binding site [ion binding]; metal-binding site 557722013127 DNA binding site [nucleotide binding] 557722013128 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 557722013129 exonuclease subunit SbcC; Provisional; Region: PRK10246 557722013130 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722013131 Walker A/P-loop; other site 557722013132 ATP binding site [chemical binding]; other site 557722013133 Q-loop/lid; other site 557722013134 exonuclease subunit SbcC; Provisional; Region: PRK10246 557722013135 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722013136 ABC transporter signature motif; other site 557722013137 Walker B; other site 557722013138 D-loop; other site 557722013139 H-loop/switch region; other site 557722013140 exodeoxyribonuclease V, alpha subunit; Region: recD; TIGR01447 557722013141 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722013142 Family description; Region: UvrD_C_2; cl15862 557722013143 exodeoxyribonuclease V, beta subunit; Region: recB; TIGR00609 557722013144 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722013145 exodeoxyribonuclease V, beta subunit; Region: recB; TIGR00609 557722013146 Family description; Region: UvrD_C_2; cl15862 557722013147 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 557722013148 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 557722013149 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 557722013150 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 557722013151 EamA-like transporter family; Region: EamA; cl01037 557722013152 Cupin domain; Region: Cupin_2; cl09118 557722013153 Helix-turn-helix domain; Region: HTH_18; pfam12833 557722013154 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722013155 Chromate transporter; Region: Chromate_transp; pfam02417 557722013156 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 557722013157 Chromate transporter; Region: Chromate_transp; pfam02417 557722013158 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722013159 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722013160 dimer interface [polypeptide binding]; other site 557722013161 putative CheW interface [polypeptide binding]; other site 557722013162 Phosphate transporter family; Region: PHO4; cl00396 557722013163 Phosphate transporter family; Region: PHO4; cl00396 557722013164 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722013165 PAS fold; Region: PAS_3; pfam08447 557722013166 putative active site [active] 557722013167 heme pocket [chemical binding]; other site 557722013168 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722013169 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722013170 putative active site [active] 557722013171 heme pocket [chemical binding]; other site 557722013172 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722013173 dimer interface [polypeptide binding]; other site 557722013174 phosphorylation site [posttranslational modification] 557722013175 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722013176 ATP binding site [chemical binding]; other site 557722013177 Mg2+ binding site [ion binding]; other site 557722013178 G-X-G motif; other site 557722013179 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 557722013180 TadE-like protein; Region: TadE; cl10688 557722013181 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 557722013182 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557722013183 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722013184 active site 557722013185 phosphorylation site [posttranslational modification] 557722013186 intermolecular recognition site; other site 557722013187 dimerization interface [polypeptide binding]; other site 557722013188 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722013189 DNA binding residues [nucleotide binding] 557722013190 dimerization interface [polypeptide binding]; other site 557722013191 Predicted membrane protein [Function unknown]; Region: COG4655 557722013192 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 557722013193 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 557722013194 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722013195 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 557722013196 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722013197 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 557722013198 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 557722013199 ATP binding site [chemical binding]; other site 557722013200 Walker A motif; other site 557722013201 hexamer interface [polypeptide binding]; other site 557722013202 Walker B motif; other site 557722013203 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 557722013204 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722013205 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 557722013206 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722013207 SAF domain; Region: SAF; cl00555 557722013208 Flp/Fap pilin component; Region: Flp_Fap; cl01585 557722013209 putative diguanylate cyclase YedQ; Provisional; Region: PRK15426 557722013210 Cache domain; Region: Cache_1; pfam02743 557722013211 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 557722013212 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722013213 dimerization interface [polypeptide binding]; other site 557722013214 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722013215 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722013216 dimer interface [polypeptide binding]; other site 557722013217 putative CheW interface [polypeptide binding]; other site 557722013218 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722013219 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 557722013220 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; Region: CE4_u10; cd11374 557722013221 Predicted deacetylase [General function prediction only]; Region: COG3233 557722013222 putative active site [active] 557722013223 putative Zn binding site [ion binding]; other site 557722013224 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 557722013225 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 557722013226 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 557722013227 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 557722013228 putative active site [active] 557722013229 putative substrate binding site [chemical binding]; other site 557722013230 putative cosubstrate binding site; other site 557722013231 catalytic site [active] 557722013232 exonuclease I; Provisional; Region: sbcB; PRK11779 557722013233 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 557722013234 active site 557722013235 substrate binding site [chemical binding]; other site 557722013236 catalytic site [active] 557722013237 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 557722013238 Protein of unknown function (DUF975); Region: DUF975; cl10504 557722013239 RDD family; Region: RDD; cl00746 557722013240 Integral membrane protein DUF95; Region: DUF95; cl00572 557722013241 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 557722013242 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722013243 Walker A motif; other site 557722013244 ATP binding site [chemical binding]; other site 557722013245 Walker B motif; other site 557722013246 Mg-chelatase subunit ChlI [Coenzyme metabolism]; Region: ChlI; COG1239 557722013247 arginine finger; other site 557722013248 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 557722013249 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722013250 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 557722013251 PilZ domain; Region: PilZ; cl01260 557722013252 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557722013253 universal stress protein UspE; Provisional; Region: PRK11175 557722013254 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722013255 Ligand Binding Site [chemical binding]; other site 557722013256 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 557722013257 pyruvate kinase; Provisional; Region: PRK05826 557722013258 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 557722013259 domain interfaces; other site 557722013260 active site 557722013261 enoyl-CoA hydratase; Provisional; Region: PRK06688 557722013262 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722013263 substrate binding site [chemical binding]; other site 557722013264 oxyanion hole (OAH) forming residues; other site 557722013265 trimer interface [polypeptide binding]; other site 557722013266 hypothetical protein; Provisional; Region: PRK05713 557722013267 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722013268 catalytic loop [active] 557722013269 iron binding site [ion binding]; other site 557722013270 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 557722013271 FAD binding pocket [chemical binding]; other site 557722013272 conserved FAD binding motif [chemical binding]; other site 557722013273 phosphate binding motif [ion binding]; other site 557722013274 beta-alpha-beta structure motif; other site 557722013275 NAD binding pocket [chemical binding]; other site 557722013276 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722013277 metal binding site [ion binding]; metal-binding site 557722013278 active site 557722013279 I-site; other site 557722013280 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 557722013281 Fumarase C-terminus; Region: Fumerase_C; cl00795 557722013282 manganese transport protein MntH; Reviewed; Region: PRK00701; cl15845 557722013283 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 557722013284 Ribbon-helix-helix domain; Region: RHH_4; cl01775 557722013285 intracellular protease, PfpI family; Region: PfpI; TIGR01382 557722013286 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 557722013287 conserved cys residue [active] 557722013288 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 557722013289 OpgC protein; Region: OpgC_C; cl00792 557722013290 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 557722013291 putative active site [active] 557722013292 catalytic site [active] 557722013293 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 557722013294 PLD-like domain; Region: PLDc_2; pfam13091 557722013295 putative active site [active] 557722013296 catalytic site [active] 557722013297 YceI-like domain; Region: YceI; cl01001 557722013298 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557722013299 Helix-turn-helix domains; Region: HTH; cl00088 557722013300 amidase; Provisional; Region: PRK07486 557722013301 Amidase; Region: Amidase; cl11426 557722013302 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722013303 metabolite-proton symporter; Region: 2A0106; TIGR00883 557722013304 putative substrate translocation pore; other site 557722013305 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 557722013306 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 557722013307 metal binding site [ion binding]; metal-binding site 557722013308 putative dimer interface [polypeptide binding]; other site 557722013309 YceI-like domain; Region: YceI; cl01001 557722013310 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 557722013311 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722013312 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 557722013313 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722013314 active site 557722013315 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722013316 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 557722013317 putative acyl-acceptor binding pocket; other site 557722013318 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722013319 Ligand Binding Site [chemical binding]; other site 557722013320 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722013321 Ligand Binding Site [chemical binding]; other site 557722013322 Protein of unknown function, DUF479; Region: DUF479; cl01203 557722013323 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 557722013324 dimerization interface [polypeptide binding]; other site 557722013325 putative DNA binding site [nucleotide binding]; other site 557722013326 putative Zn2+ binding site [ion binding]; other site 557722013327 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722013328 putative substrate translocation pore; other site 557722013329 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 557722013330 FMN binding site [chemical binding]; other site 557722013331 active site 557722013332 substrate binding site [chemical binding]; other site 557722013333 catalytic residue [active] 557722013334 Helix-turn-helix domains; Region: HTH; cl00088 557722013335 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 557722013336 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 557722013337 G1 box; other site 557722013338 GTP/Mg2+ binding site [chemical binding]; other site 557722013339 Switch I region; other site 557722013340 G2 box; other site 557722013341 G3 box; other site 557722013342 Switch II region; other site 557722013343 G4 box; other site 557722013344 G5 box; other site 557722013345 Nucleoside recognition; Region: Gate; cl00486 557722013346 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 557722013347 Nucleoside recognition; Region: Gate; cl00486 557722013348 FeoA domain; Region: FeoA; cl00838 557722013349 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557722013350 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557722013351 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013352 NAD(P) binding site [chemical binding]; other site 557722013353 active site 557722013354 Uncharacterized conserved protein [Function unknown]; Region: COG3268 557722013355 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013356 NAD(P) binding site [chemical binding]; other site 557722013357 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 557722013358 Helix-turn-helix domains; Region: HTH; cl00088 557722013359 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722013360 dimerization interface [polypeptide binding]; other site 557722013361 ACT domain; Region: ACT_3; pfam10000 557722013362 LysE type translocator; Region: LysE; cl00565 557722013363 superoxide dismutase; Provisional; Region: PRK10543 557722013364 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 557722013365 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 557722013366 biofilm formation regulator HmsP; Provisional; Region: PRK11829 557722013367 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722013368 metal binding site [ion binding]; metal-binding site 557722013369 active site 557722013370 I-site; other site 557722013371 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722013372 E3 Ubiquitin ligase; Region: GIDE; pfam12483 557722013373 LemA family; Region: LemA; cl00742 557722013374 Imelysin; Region: Peptidase_M75; cl09159 557722013375 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 557722013376 Imelysin; Region: Peptidase_M75; cl09159 557722013377 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3490 557722013378 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722013379 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722013380 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722013381 multidrug efflux protein; Reviewed; Region: PRK09579 557722013382 Protein export membrane protein; Region: SecD_SecF; cl14618 557722013383 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 557722013384 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 557722013385 active site 557722013386 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722013387 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722013388 S-adenosylmethionine binding site [chemical binding]; other site 557722013389 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722013390 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722013391 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722013392 dimer interface [polypeptide binding]; other site 557722013393 phosphorylation site [posttranslational modification] 557722013394 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722013395 ATP binding site [chemical binding]; other site 557722013396 Mg2+ binding site [ion binding]; other site 557722013397 G-X-G motif; other site 557722013398 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557722013399 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722013400 active site 557722013401 phosphorylation site [posttranslational modification] 557722013402 intermolecular recognition site; other site 557722013403 dimerization interface [polypeptide binding]; other site 557722013404 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722013405 DNA binding site [nucleotide binding] 557722013406 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_6; cd03396 557722013407 active site 557722013408 CrcB-like protein; Region: CRCB; cl09114 557722013409 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4318 557722013410 Putative ParB-like nuclease; Region: ParBc_2; pfam08857 557722013411 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 557722013412 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 557722013413 ring oligomerisation interface [polypeptide binding]; other site 557722013414 ATP/Mg binding site [chemical binding]; other site 557722013415 stacking interactions; other site 557722013416 hinge regions; other site 557722013417 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 557722013418 oligomerisation interface [polypeptide binding]; other site 557722013419 mobile loop; other site 557722013420 roof hairpin; other site 557722013421 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 557722013422 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 557722013423 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 557722013424 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 557722013425 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722013426 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013427 NAD(P) binding site [chemical binding]; other site 557722013428 active site 557722013429 Protein of unknown function, DUF481; Region: DUF481; cl01213 557722013430 Protein of unknown function, DUF481; Region: DUF481; cl01213 557722013431 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 557722013432 DNA binding site [nucleotide binding] 557722013433 active site 557722013434 muropeptide transporter; Validated; Region: ampG; PRK11010 557722013435 muropeptide transporter; Validated; Region: ampG; PRK11010 557722013436 mechanosensitive channel MscS; Provisional; Region: PRK10334 557722013437 Conserved TM helix; Region: TM_helix; pfam05552 557722013438 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722013439 Protein of unknown function (DUF520); Region: DUF520; cl00723 557722013440 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 557722013441 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722013442 active site 557722013443 phosphorylation site [posttranslational modification] 557722013444 intermolecular recognition site; other site 557722013445 dimerization interface [polypeptide binding]; other site 557722013446 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 557722013447 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013448 2-dehydropantoate 2-reductase; Region: apbA_panE; TIGR00745 557722013449 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 557722013450 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 557722013451 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722013452 dimerization interface [polypeptide binding]; other site 557722013453 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722013454 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 557722013455 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722013456 dimer interface [polypeptide binding]; other site 557722013457 phosphorylation site [posttranslational modification] 557722013458 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722013459 ATP binding site [chemical binding]; other site 557722013460 Mg2+ binding site [ion binding]; other site 557722013461 G-X-G motif; other site 557722013462 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 557722013463 hypothetical protein; Provisional; Region: PRK08999 557722013464 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 557722013465 active site 557722013466 8-oxo-dGMP binding site [chemical binding]; other site 557722013467 nudix motif; other site 557722013468 metal binding site [ion binding]; metal-binding site 557722013469 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 557722013470 thiamine phosphate binding site [chemical binding]; other site 557722013471 active site 557722013472 pyrophosphate binding site [ion binding]; other site 557722013473 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 557722013474 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557722013475 putative C-terminal domain interface [polypeptide binding]; other site 557722013476 putative GSH binding site (G-site) [chemical binding]; other site 557722013477 putative dimer interface [polypeptide binding]; other site 557722013478 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 557722013479 putative N-terminal domain interface [polypeptide binding]; other site 557722013480 putative dimer interface [polypeptide binding]; other site 557722013481 putative substrate binding pocket (H-site) [chemical binding]; other site 557722013482 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 557722013483 heterotetramer interface [polypeptide binding]; other site 557722013484 active site pocket [active] 557722013485 cleavage site 557722013486 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK13103 557722013487 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 557722013488 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722013489 nucleotide binding region [chemical binding]; other site 557722013490 ATP-binding site [chemical binding]; other site 557722013491 SEC-C motif; Region: SEC-C; pfam02810 557722013492 Peptidase family M23; Region: Peptidase_M23; pfam01551 557722013493 Protein of unknown function (DUF721); Region: DUF721; cl02324 557722013494 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 557722013495 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 557722013496 cell division protein FtsZ; Validated; Region: PRK09330 557722013497 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 557722013498 nucleotide binding site [chemical binding]; other site 557722013499 SulA interaction site; other site 557722013500 cell division protein FtsA; Region: ftsA; TIGR01174 557722013501 Cell division protein FtsA; Region: FtsA; cl11496 557722013502 Cell division protein FtsA; Region: FtsA; cl11496 557722013503 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 557722013504 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 557722013505 Cell division protein FtsQ; Region: FtsQ; pfam03799 557722013506 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 557722013507 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 557722013508 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722013509 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 557722013510 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557722013511 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557722013512 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557722013513 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 557722013514 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 557722013515 active site 557722013516 homodimer interface [polypeptide binding]; other site 557722013517 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 557722013518 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 557722013519 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013520 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557722013521 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 557722013522 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 557722013523 Mg++ binding site [ion binding]; other site 557722013524 putative catalytic motif [active] 557722013525 putative substrate binding site [chemical binding]; other site 557722013526 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557722013527 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 557722013528 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557722013529 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557722013530 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 557722013531 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557722013532 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557722013533 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557722013534 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 557722013535 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557722013536 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722013537 Septum formation initiator; Region: DivIC; cl11433 557722013538 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 557722013539 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722013540 cell division protein MraZ; Reviewed; Region: PRK00326 557722013541 MraZ protein; Region: MraZ; pfam02381 557722013542 MraZ protein; Region: MraZ; pfam02381 557722013543 Predicted methyltransferases [General function prediction only]; Region: COG0313 557722013544 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 557722013545 LppC putative lipoprotein; Region: LppC; pfam04348 557722013546 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 557722013547 putative ligand binding site [chemical binding]; other site 557722013548 Restriction endonuclease; Region: Mrr_cat; cl00516 557722013549 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 557722013550 dimer interface [polypeptide binding]; other site 557722013551 active site 557722013552 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 557722013553 BON domain; Region: BON; cl02771 557722013554 Stringent starvation protein B; Region: SspB; cl01120 557722013555 stringent starvation protein A; Provisional; Region: sspA; PRK09481 557722013556 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 557722013557 C-terminal domain interface [polypeptide binding]; other site 557722013558 putative GSH binding site (G-site) [chemical binding]; other site 557722013559 dimer interface [polypeptide binding]; other site 557722013560 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 557722013561 dimer interface [polypeptide binding]; other site 557722013562 N-terminal domain interface [polypeptide binding]; other site 557722013563 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 557722013564 cytochrome b; Provisional; Region: CYTB; MTH00145 557722013565 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 557722013566 Qi binding site; other site 557722013567 intrachain domain interface; other site 557722013568 interchain domain interface [polypeptide binding]; other site 557722013569 heme bH binding site [chemical binding]; other site 557722013570 heme bL binding site [chemical binding]; other site 557722013571 Qo binding site; other site 557722013572 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cl00193 557722013573 interchain domain interface [polypeptide binding]; other site 557722013574 intrachain domain interface; other site 557722013575 Qi binding site; other site 557722013576 Qo binding site; other site 557722013577 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 557722013578 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 557722013579 [2Fe-2S] cluster binding site [ion binding]; other site 557722013580 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 557722013581 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the...; Region: Ribosomal_L13; cd00392 557722013582 23S rRNA interface [nucleotide binding]; other site 557722013583 L3 interface [polypeptide binding]; other site 557722013584 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 557722013585 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722013586 active site 557722013587 catalytic tetrad [active] 557722013588 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722013589 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722013590 active site 557722013591 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 557722013592 conserved cys residue [active] 557722013593 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722013594 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722013595 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722013596 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 557722013597 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK12284 557722013598 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 557722013599 active site 557722013600 HIGH motif; other site 557722013601 dimer interface [polypeptide binding]; other site 557722013602 KMSKS motif; other site 557722013603 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 557722013604 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 557722013605 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 557722013606 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 557722013607 CysD dimerization site [polypeptide binding]; other site 557722013608 G1 box; other site 557722013609 putative GEF interaction site [polypeptide binding]; other site 557722013610 GTP/Mg2+ binding site [chemical binding]; other site 557722013611 Switch I region; other site 557722013612 G2 box; other site 557722013613 G3 box; other site 557722013614 Switch II region; other site 557722013615 G4 box; other site 557722013616 G5 box; other site 557722013617 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 557722013618 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 557722013619 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation of...; Region: APSK; cd02027 557722013620 ligand-binding site [chemical binding]; other site 557722013621 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 557722013622 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 557722013623 Active Sites [active] 557722013624 Transglycosylase SLT domain; Region: SLT_2; pfam13406 557722013625 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 557722013626 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557722013627 catalytic residue [active] 557722013628 Uncharacterized conserved protein [Function unknown]; Region: COG0327 557722013629 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 557722013630 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 557722013631 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 557722013632 protein binding site [polypeptide binding]; other site 557722013633 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 557722013634 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722013635 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722013636 homodimer interface [polypeptide binding]; other site 557722013637 catalytic residue [active] 557722013638 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 557722013639 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 557722013640 NAD binding site [chemical binding]; other site 557722013641 dimerization interface [polypeptide binding]; other site 557722013642 product binding site; other site 557722013643 substrate binding site [chemical binding]; other site 557722013644 zinc binding site [ion binding]; other site 557722013645 catalytic residues [active] 557722013646 ATP phosphoribosyltransferase; Region: HisG; cl15266 557722013647 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 557722013648 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 557722013649 hinge; other site 557722013650 active site 557722013651 BolA-like protein; Region: BolA; cl00386 557722013652 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 557722013653 anti sigma factor interaction site; other site 557722013654 regulatory phosphorylation site [posttranslational modification]; other site 557722013655 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 557722013656 mce related protein; Region: MCE; pfam02470 557722013657 Permease; Region: Permease; cl00510 557722013658 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 557722013659 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 557722013660 Walker A/P-loop; other site 557722013661 ATP binding site [chemical binding]; other site 557722013662 Q-loop/lid; other site 557722013663 ABC transporter signature motif; other site 557722013664 Walker B; other site 557722013665 D-loop; other site 557722013666 H-loop/switch region; other site 557722013667 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 557722013668 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 557722013669 putative active site [active] 557722013670 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 557722013671 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 557722013672 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722013673 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 557722013674 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 557722013675 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 557722013676 OstA-like protein; Region: OstA; cl00844 557722013677 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 557722013678 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 557722013679 Walker A/P-loop; other site 557722013680 ATP binding site [chemical binding]; other site 557722013681 Q-loop/lid; other site 557722013682 ABC transporter signature motif; other site 557722013683 Walker B; other site 557722013684 D-loop; other site 557722013685 H-loop/switch region; other site 557722013686 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 557722013687 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 557722013688 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 557722013689 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 557722013690 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 557722013691 30S subunit binding site; other site 557722013692 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 557722013693 active site 557722013694 phosphorylation site [posttranslational modification] 557722013695 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 557722013696 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 557722013697 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 557722013698 dimerization domain swap beta strand [polypeptide binding]; other site 557722013699 regulatory protein interface [polypeptide binding]; other site 557722013700 active site 557722013701 regulatory phosphorylation site [posttranslational modification]; other site 557722013702 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 557722013703 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 557722013704 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 557722013705 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 557722013706 Protein of unknown function (DUF2753); Region: DUF2753; pfam10952 557722013707 fumarate hydratase; Reviewed; Region: fumC; PRK00485 557722013708 Class II fumarases; Region: Fumarase_classII; cd01362 557722013709 active site 557722013710 tetramer interface [polypeptide binding]; other site 557722013711 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557722013712 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 557722013713 Protein of unknown function (DUF615); Region: DUF615; cl01147 557722013714 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 557722013715 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 557722013716 Predicted amidohydrolase [General function prediction only]; Region: COG0388 557722013717 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 557722013718 putative active site [active] 557722013719 catalytic triad [active] 557722013720 dimer interface [polypeptide binding]; other site 557722013721 Predicted membrane protein [Function unknown]; Region: COG3164 557722013722 AsmA-like C-terminal region; Region: AsmA_2; cl15864 557722013723 ribonuclease G; Provisional; Region: PRK11712 557722013724 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 557722013725 homodimer interface [polypeptide binding]; other site 557722013726 oligonucleotide binding site [chemical binding]; other site 557722013727 Maf-like protein; Region: Maf; pfam02545 557722013728 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 557722013729 active site 557722013730 dimer interface [polypeptide binding]; other site 557722013731 rod shape-determining protein MreD; Region: MreD; cl01087 557722013732 rod shape-determining protein MreC; Region: MreC; pfam04085 557722013733 rod shape-determining protein MreB; Provisional; Region: PRK13927 557722013734 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 557722013735 ATP binding site [chemical binding]; other site 557722013736 profilin binding site; other site 557722013737 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 557722013738 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 557722013739 Amidase; Region: Amidase; cl11426 557722013740 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 557722013741 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 557722013742 GatB domain; Region: GatB_Yqey; cl11497 557722013743 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 557722013744 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557722013745 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 557722013746 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 557722013747 putative metal binding site [ion binding]; other site 557722013748 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 557722013749 Predicted secreted protein [Function unknown]; Region: COG5445 557722013750 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 557722013751 Predicted secreted protein [Function unknown]; Region: COG5445 557722013752 Stage II sporulation protein; Region: SpoIID; pfam08486 557722013753 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 557722013754 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 557722013755 MG2 domain; Region: A2M_N; pfam01835 557722013756 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 557722013757 Alpha-2-macroglobulin family; Region: A2M; pfam00207 557722013758 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 557722013759 surface patch; other site 557722013760 thioester region; other site 557722013761 Protein of unknown function (DUF1175); Region: DUF1175; cl14898 557722013762 Uncharacterized protein conserved in bacteria (DUF2138); Region: DUF2138; cl01916 557722013763 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 557722013764 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 557722013765 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 557722013766 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722013767 active site 557722013768 phosphorylation site [posttranslational modification] 557722013769 intermolecular recognition site; other site 557722013770 dimerization interface [polypeptide binding]; other site 557722013771 Helix-turn-helix domains; Region: HTH; cl00088 557722013772 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557722013773 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722013774 phosphorylation site [posttranslational modification] 557722013775 dimer interface [polypeptide binding]; other site 557722013776 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 557722013777 Protein of unknown function (DUF541); Region: SIMPL; cl01077 557722013778 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557722013779 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557722013780 peptide binding site [polypeptide binding]; other site 557722013781 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557722013782 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 557722013783 peptide binding site [polypeptide binding]; other site 557722013784 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 557722013785 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 557722013786 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cl00279 557722013787 active site 557722013788 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722013789 non-specific DNA binding site [nucleotide binding]; other site 557722013790 salt bridge; other site 557722013791 sequence-specific DNA binding site [nucleotide binding]; other site 557722013792 Cupin domain; Region: Cupin_2; cl09118 557722013793 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557722013794 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557722013795 peptide binding site [polypeptide binding]; other site 557722013796 outer membrane porin, OprD family; Region: OprD; pfam03573 557722013797 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557722013798 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557722013799 peptide binding site [polypeptide binding]; other site 557722013800 dipeptide transporter permease DppB; Provisional; Region: PRK10914 557722013801 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722013802 dimer interface [polypeptide binding]; other site 557722013803 conserved gate region; other site 557722013804 putative PBP binding loops; other site 557722013805 ABC-ATPase subunit interface; other site 557722013806 dipeptide transporter; Provisional; Region: PRK10913 557722013807 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 557722013808 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722013809 putative PBP binding loops; other site 557722013810 dimer interface [polypeptide binding]; other site 557722013811 ABC-ATPase subunit interface; other site 557722013812 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 557722013813 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722013814 Walker A/P-loop; other site 557722013815 ATP binding site [chemical binding]; other site 557722013816 Q-loop/lid; other site 557722013817 ABC transporter signature motif; other site 557722013818 Walker B; other site 557722013819 D-loop; other site 557722013820 H-loop/switch region; other site 557722013821 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722013822 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 557722013823 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 557722013824 Walker A/P-loop; other site 557722013825 ATP binding site [chemical binding]; other site 557722013826 Q-loop/lid; other site 557722013827 ABC transporter signature motif; other site 557722013828 Walker B; other site 557722013829 D-loop; other site 557722013830 H-loop/switch region; other site 557722013831 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557722013832 LysE type translocator; Region: LysE; cl00565 557722013833 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 557722013834 Helix-turn-helix domains; Region: HTH; cl00088 557722013835 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 557722013836 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 557722013837 LamB/YcsF family; Region: LamB_YcsF; cl00664 557722013838 Cupin domain; Region: Cupin_2; cl09118 557722013839 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 557722013840 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722013841 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 557722013842 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 557722013843 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722013844 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like1; cd06200 557722013845 FAD binding pocket [chemical binding]; other site 557722013846 FAD binding motif [chemical binding]; other site 557722013847 catalytic residues [active] 557722013848 NAD binding pocket [chemical binding]; other site 557722013849 phosphate binding motif [ion binding]; other site 557722013850 beta-alpha-beta structure motif; other site 557722013851 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 557722013852 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722013853 N-terminal plug; other site 557722013854 ligand-binding site [chemical binding]; other site 557722013855 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 557722013856 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 557722013857 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722013858 Sel1 repeat; Region: Sel1; cl02723 557722013859 Sel1 repeat; Region: Sel1; cl02723 557722013860 hypothetical protein; Provisional; Region: PRK10649 557722013861 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 557722013862 Sulfatase; Region: Sulfatase; cl10460 557722013863 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 557722013864 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722013865 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 557722013866 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 557722013867 dimer interface [polypeptide binding]; other site 557722013868 active site 557722013869 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722013870 catalytic residues [active] 557722013871 substrate binding site [chemical binding]; other site 557722013872 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557722013873 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722013874 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722013875 dimer interface [polypeptide binding]; other site 557722013876 putative CheW interface [polypeptide binding]; other site 557722013877 CobD/Cbib protein; Region: CobD_Cbib; cl00561 557722013878 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 557722013879 amidase catalytic site [active] 557722013880 Zn binding residues [ion binding]; other site 557722013881 substrate binding site [chemical binding]; other site 557722013882 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 557722013883 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05742 557722013884 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 557722013885 dimerization interface [polypeptide binding]; other site 557722013886 active site 557722013887 O-Antigen ligase; Region: Wzy_C; cl04850 557722013888 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 557722013889 Pilin (bacterial filament); Region: Pilin; pfam00114 557722013890 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 557722013891 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 557722013892 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 557722013893 Walker A motif; other site 557722013894 ATP binding site [chemical binding]; other site 557722013895 Walker B motif; other site 557722013896 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 557722013897 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722013898 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 557722013899 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 557722013900 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 557722013901 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 557722013902 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 557722013903 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 557722013904 CoA-binding site [chemical binding]; other site 557722013905 ATP-binding [chemical binding]; other site 557722013906 Domain of unknown function (DUF329); Region: DUF329; cl01144 557722013907 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 557722013908 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557722013909 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722013910 Coenzyme A binding pocket [chemical binding]; other site 557722013911 Protein of unknown function (DUF1780); Region: DUF1780; pfam08682 557722013912 MOSC domain; Region: MOSC; pfam03473 557722013913 Protein of unknown function (DUF3094); Region: DUF3094; pfam11293 557722013914 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 557722013915 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722013916 AFG1-like ATPase; Region: AFG1_ATPase; pfam03969 557722013917 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 557722013918 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722013919 Surface antigen; Region: Bac_surface_Ag; cl03097 557722013920 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 557722013921 haemagglutination activity domain; Region: Haemagg_act; cl05436 557722013922 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 557722013923 Clp amino terminal domain; Region: Clp_N; pfam02861 557722013924 Clp amino terminal domain; Region: Clp_N; pfam02861 557722013925 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722013926 Walker A motif; other site 557722013927 ATP binding site [chemical binding]; other site 557722013928 Walker B motif; other site 557722013929 arginine finger; other site 557722013930 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722013931 Walker A motif; other site 557722013932 ATP binding site [chemical binding]; other site 557722013933 Walker B motif; other site 557722013934 arginine finger; other site 557722013935 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722013936 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 557722013937 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 557722013938 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 557722013939 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722013940 RNA binding surface [nucleotide binding]; other site 557722013941 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 557722013942 active site 557722013943 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 557722013944 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 557722013945 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722013946 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722013947 dimer interface [polypeptide binding]; other site 557722013948 phosphorylation site [posttranslational modification] 557722013949 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722013950 ATP binding site [chemical binding]; other site 557722013951 Mg2+ binding site [ion binding]; other site 557722013952 G-X-G motif; other site 557722013953 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722013954 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722013955 active site 557722013956 phosphorylation site [posttranslational modification] 557722013957 intermolecular recognition site; other site 557722013958 dimerization interface [polypeptide binding]; other site 557722013959 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722013960 Walker A motif; other site 557722013961 ATP binding site [chemical binding]; other site 557722013962 Walker B motif; other site 557722013963 arginine finger; other site 557722013964 Helix-turn-helix domains; Region: HTH; cl00088 557722013965 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 557722013966 Type II transport protein GspH; Region: GspH; pfam12019 557722013967 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 557722013968 Type II transport protein GspH; Region: GspH; pfam12019 557722013969 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722013970 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 557722013971 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 557722013972 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557722013973 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 557722013974 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 557722013975 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 557722013976 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 557722013977 LytB protein; Region: LYTB; cl00507 557722013978 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 557722013979 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722013980 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 557722013981 lipoprotein signal peptidase; Provisional; Region: PRK14787 557722013982 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 557722013983 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722013984 active site 557722013985 HIGH motif; other site 557722013986 nucleotide binding site [chemical binding]; other site 557722013987 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 557722013988 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 557722013989 active site 557722013990 KMSKS motif; other site 557722013991 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 557722013992 tRNA binding surface [nucleotide binding]; other site 557722013993 anticodon binding site; other site 557722013994 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 557722013995 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 557722013996 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 557722013997 active site 557722013998 Riboflavin kinase; Region: Flavokinase; cl03312 557722013999 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 557722014000 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 557722014001 CreA protein; Region: CreA; pfam05981 557722014002 gamma-glutamyl kinase; Provisional; Region: PRK05429 557722014003 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 557722014004 nucleotide binding site [chemical binding]; other site 557722014005 homotetrameric interface [polypeptide binding]; other site 557722014006 putative phosphate binding site [ion binding]; other site 557722014007 putative allosteric binding site; other site 557722014008 PUA domain; Region: PUA; cl00607 557722014009 GTPase CgtA; Reviewed; Region: obgE; PRK12298 557722014010 GTP1/OBG; Region: GTP1_OBG; pfam01018 557722014011 Obg GTPase; Region: Obg; cd01898 557722014012 G1 box; other site 557722014013 GTP/Mg2+ binding site [chemical binding]; other site 557722014014 Switch I region; other site 557722014015 G2 box; other site 557722014016 G3 box; other site 557722014017 Switch II region; other site 557722014018 G4 box; other site 557722014019 G5 box; other site 557722014020 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 557722014021 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 557722014022 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 557722014023 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 557722014024 substrate binding pocket [chemical binding]; other site 557722014025 chain length determination region; other site 557722014026 substrate-Mg2+ binding site; other site 557722014027 catalytic residues [active] 557722014028 aspartate-rich region 1; other site 557722014029 active site lid residues [active] 557722014030 aspartate-rich region 2; other site 557722014031 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557722014032 Cytochrome c; Region: Cytochrom_C; cl11414 557722014033 Cytochrome c [Energy production and conversion]; Region: COG3258 557722014034 Cytochrome c; Region: Cytochrom_C; cl11414 557722014035 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 557722014036 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 557722014037 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722014038 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 557722014039 Ammonia monooxygenase; Region: AMO; cl03602 557722014040 AAA domain; Region: AAA_32; pfam13654 557722014041 ATP-dependent protease Lon; Provisional; Region: PRK13765 557722014042 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 557722014043 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557722014044 Protein of unknown function (DUF3015); Region: DUF3015; pfam11220 557722014045 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 557722014046 Domain of unknown function (DUF1768); Region: DUF1768; cl01271 557722014047 Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: RtcR; COG4650 557722014048 Regulator of RNA terminal phosphate cyclase; Region: RtcR; pfam06956 557722014049 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722014050 Walker A motif; other site 557722014051 ATP binding site [chemical binding]; other site 557722014052 Walker B motif; other site 557722014053 arginine finger; other site 557722014054 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 557722014055 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 557722014056 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl15780 557722014057 hypothetical protein; Reviewed; Region: PRK09588 557722014058 Predicted nucleotidyltransferase; Region: Nuc-transf; cl01417 557722014059 RNA 3'-terminal-phosphate cyclase; Provisional; Region: PRK04204 557722014060 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a...; Region: EPT_RTPC-like; cl00288 557722014061 putative active site [active] 557722014062 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 557722014063 glutamate dehydrogenase; Provisional; Region: PRK09414 557722014064 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 557722014065 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 557722014066 NAD(P) binding site [chemical binding]; other site 557722014067 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722014068 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722014069 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722014070 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722014071 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 557722014072 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 557722014073 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557722014074 FtsX-like permease family; Region: FtsX; cl15850 557722014075 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 557722014076 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 557722014077 Walker A/P-loop; other site 557722014078 ATP binding site [chemical binding]; other site 557722014079 Q-loop/lid; other site 557722014080 ABC transporter signature motif; other site 557722014081 Walker B; other site 557722014082 D-loop; other site 557722014083 H-loop/switch region; other site 557722014084 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 557722014085 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722014086 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722014087 ABC transporter; Region: ABC_tran_2; pfam12848 557722014088 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722014089 Helix-turn-helix domains; Region: HTH; cl00088 557722014090 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 557722014091 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 557722014092 Protein export membrane protein; Region: SecD_SecF; cl14618 557722014093 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 557722014094 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722014095 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722014096 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722014097 PAS domain; Region: PAS_9; pfam13426 557722014098 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722014099 PAS fold; Region: PAS_3; pfam08447 557722014100 putative active site [active] 557722014101 heme pocket [chemical binding]; other site 557722014102 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722014103 PAS domain; Region: PAS_9; pfam13426 557722014104 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 557722014105 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722014106 PAS domain; Region: PAS_9; pfam13426 557722014107 putative active site [active] 557722014108 heme pocket [chemical binding]; other site 557722014109 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722014110 metal binding site [ion binding]; metal-binding site 557722014111 active site 557722014112 I-site; other site 557722014113 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722014114 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 557722014115 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 557722014116 dimer interface [polypeptide binding]; other site 557722014117 glycine-pyridoxal phosphate binding site [chemical binding]; other site 557722014118 active site 557722014119 folate binding site [chemical binding]; other site 557722014120 putative GTP-binding protein YjiA; Provisional; Region: PRK11537 557722014121 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 557722014122 P-loop, Walker A motif; other site 557722014123 Base recognition motif; other site 557722014124 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 557722014125 Protein of unknown function (DUF466); Region: DUF466; cl01082 557722014126 carbon starvation protein A; Provisional; Region: PRK15015 557722014127 Carbon starvation protein CstA; Region: CstA; pfam02554 557722014128 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 557722014129 Protein of unknown function (DUF3015); Region: DUF3015; pfam11220 557722014130 PilZ domain; Region: PilZ; cl01260 557722014131 DNA repair protein RadA; Provisional; Region: PRK11823 557722014132 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 557722014133 Walker A motif/ATP binding site; other site 557722014134 ATP binding site [chemical binding]; other site 557722014135 Walker B motif; other site 557722014136 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 557722014137 Protein of unknown function (DUF465); Region: DUF465; cl01070 557722014138 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 557722014139 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 557722014140 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 557722014141 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 557722014142 Clade 1 of the heme-binding enzyme catalase; Region: catalase_clade_1; cd08154 557722014143 tetramer interface [polypeptide binding]; other site 557722014144 heme binding pocket [chemical binding]; other site 557722014145 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 557722014146 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 557722014147 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 557722014148 ferredoxin-NADP reductase; Provisional; Region: PRK10926 557722014149 FAD binding pocket [chemical binding]; other site 557722014150 FAD binding motif [chemical binding]; other site 557722014151 phosphate binding motif [ion binding]; other site 557722014152 beta-alpha-beta structure motif; other site 557722014153 NAD binding pocket [chemical binding]; other site 557722014154 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 557722014155 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 557722014156 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 557722014157 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722014158 S-adenosylmethionine binding site [chemical binding]; other site 557722014159 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 557722014160 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 557722014161 XdhC Rossmann domain; Region: XdhC_C; pfam13478 557722014162 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557722014163 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 557722014164 Cytochrome c; Region: Cytochrom_C; cl11414 557722014165 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 557722014166 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 557722014167 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722014168 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 557722014169 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 557722014170 enterobactin exporter EntS; Provisional; Region: PRK10489 557722014171 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 557722014172 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 557722014173 haemagglutination activity domain; Region: Haemagg_act; cl05436 557722014174 glycerate dehydrogenase; Provisional; Region: PRK06487 557722014175 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014176 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 557722014177 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 557722014178 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722014179 S-adenosylmethionine binding site [chemical binding]; other site 557722014180 lysine transporter; Provisional; Region: PRK10836 557722014181 Spore germination protein; Region: Spore_permease; cl15802 557722014182 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 557722014183 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 557722014184 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722014185 hopanoid-associated sugar epimerase; Region: HpnA; TIGR03466 557722014186 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014187 NAD(P) binding site [chemical binding]; other site 557722014188 active site 557722014189 Peptidase family M48; Region: Peptidase_M48; cl12018 557722014190 putative diguanylate cyclase YedQ; Provisional; Region: PRK15426 557722014191 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722014192 dimerization interface [polypeptide binding]; other site 557722014193 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722014194 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722014195 dimer interface [polypeptide binding]; other site 557722014196 putative CheW interface [polypeptide binding]; other site 557722014197 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 557722014198 MgtC family; Region: MgtC; pfam02308 557722014199 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 557722014200 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 557722014201 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722014202 putative acyl-acceptor binding pocket; other site 557722014203 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014204 Predicted dehydrogenase [General function prediction only]; Region: COG0579 557722014205 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 557722014206 dimer interface [polypeptide binding]; other site 557722014207 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722014208 Domain of unknown function (DUF1971); Region: DUF1971; cl01451 557722014209 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 557722014210 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722014211 active site 557722014212 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 557722014213 uracil-xanthine permease; Region: ncs2; TIGR00801 557722014214 Spore Coat Protein U domain; Region: SCPU; cl02253 557722014215 Spore Coat Protein U domain; Region: SCPU; cl02253 557722014216 Spore Coat Protein U domain; Region: SCPU; cl02253 557722014217 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557722014218 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 557722014219 PapC N-terminal domain; Region: PapC_N; pfam13954 557722014220 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 557722014221 PapC C-terminal domain; Region: PapC_C; pfam13953 557722014222 Spore Coat Protein U domain; Region: SCPU; cl02253 557722014223 Spore Coat Protein U domain; Region: SCPU; cl02253 557722014224 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722014225 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722014226 putative substrate translocation pore; other site 557722014227 ferrochelatase; Reviewed; Region: hemH; PRK00035 557722014228 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 557722014229 C-terminal domain interface [polypeptide binding]; other site 557722014230 active site 557722014231 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 557722014232 active site 557722014233 N-terminal domain interface [polypeptide binding]; other site 557722014234 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014235 TIGR01777 family protein; Region: yfcH 557722014236 NAD(P) binding site [chemical binding]; other site 557722014237 active site 557722014238 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 557722014239 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014240 Protein of unknown function (DUF523); Region: DUF523; cl00733 557722014241 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 557722014242 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 557722014243 DNA binding residues [nucleotide binding] 557722014244 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 557722014245 B12 binding domain; Region: B12-binding_2; cl03653 557722014246 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 557722014247 DNA photolyase; Region: DNA_photolyase; pfam00875 557722014248 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 557722014249 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 557722014250 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 557722014251 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 557722014252 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 557722014253 ATP binding site [chemical binding]; other site 557722014254 substrate interface [chemical binding]; other site 557722014255 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 557722014256 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014257 peptide chain release factor 1; Validated; Region: prfA; PRK00591 557722014258 RF-1 domain; Region: RF-1; cl02875 557722014259 RF-1 domain; Region: RF-1; cl02875 557722014260 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 557722014261 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 557722014262 tRNA; other site 557722014263 putative tRNA binding site [nucleotide binding]; other site 557722014264 putative NADP binding site [chemical binding]; other site 557722014265 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 557722014266 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 557722014267 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722014268 binding surface 557722014269 TPR motif; other site 557722014270 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722014271 binding surface 557722014272 TPR motif; other site 557722014273 TPR repeat; Region: TPR_11; pfam13414 557722014274 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722014275 binding surface 557722014276 TPR motif; other site 557722014277 Tetratricopeptide repeat; Region: TPR_12; pfam13424 557722014278 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 557722014279 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 557722014280 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 557722014281 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 557722014282 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 557722014283 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722014284 active site 557722014285 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 557722014286 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 557722014287 5S rRNA interface [nucleotide binding]; other site 557722014288 CTC domain interface [polypeptide binding]; other site 557722014289 L16 interface [polypeptide binding]; other site 557722014290 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 557722014291 metal binding site [ion binding]; metal-binding site 557722014292 Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through...; Region: PTH; cd00462 557722014293 putative active site [active] 557722014294 catalytic residue [active] 557722014295 GTP-binding protein YchF; Reviewed; Region: PRK09601 557722014296 YchF GTPase; Region: YchF; cd01900 557722014297 G1 box; other site 557722014298 GTP/Mg2+ binding site [chemical binding]; other site 557722014299 Switch I region; other site 557722014300 G2 box; other site 557722014301 Switch II region; other site 557722014302 G3 box; other site 557722014303 G4 box; other site 557722014304 G5 box; other site 557722014305 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 557722014306 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722014307 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 557722014308 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722014309 N-terminal plug; other site 557722014310 ligand-binding site [chemical binding]; other site 557722014311 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 557722014312 active site clefts [active] 557722014313 zinc binding site [ion binding]; other site 557722014314 dimer interface [polypeptide binding]; other site 557722014315 Dipeptidase [Amino acid transport and metabolism]; Region: PepD; COG4690 557722014316 Peptidase family C69; Region: Peptidase_C69; pfam03577 557722014317 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 557722014318 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722014319 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 557722014320 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557722014321 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 557722014322 mce related protein; Region: MCE; pfam02470 557722014323 mce related protein; Region: MCE; pfam02470 557722014324 mce related protein; Region: MCE; pfam02470 557722014325 mce related protein; Region: MCE; pfam02470 557722014326 mce related protein; Region: MCE; pfam02470 557722014327 mce related protein; Region: MCE; pfam02470 557722014328 Paraquat-inducible protein A; Region: PqiA; pfam04403 557722014329 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 557722014330 TMAO/DMSO reductase; Reviewed; Region: PRK05363 557722014331 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 557722014332 Moco binding site; other site 557722014333 metal coordination site [ion binding]; other site 557722014334 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 557722014335 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 557722014336 ketol-acid reductoisomerase; Provisional; Region: PRK05479 557722014337 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014338 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 557722014339 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 557722014340 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 557722014341 putative valine binding site [chemical binding]; other site 557722014342 dimer interface [polypeptide binding]; other site 557722014343 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 557722014344 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 557722014345 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722014346 PYR/PP interface [polypeptide binding]; other site 557722014347 dimer interface [polypeptide binding]; other site 557722014348 TPP binding site [chemical binding]; other site 557722014349 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722014350 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 557722014351 TPP-binding site [chemical binding]; other site 557722014352 dimer interface [polypeptide binding]; other site 557722014353 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557722014354 tRNA pseudouridine synthase C; Region: DUF446; cl01187 557722014355 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 557722014356 TPR motif; other site 557722014357 binding surface 557722014358 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 557722014359 Transglycosylase; Region: Transgly; cl07896 557722014360 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722014361 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 557722014362 Predicted kinase [General function prediction only]; Region: COG0645 557722014363 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 557722014364 ATP-binding site [chemical binding]; other site 557722014365 Gluconate-6-phosphate binding site [chemical binding]; other site 557722014366 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 557722014367 TfoX N-terminal domain; Region: TfoX_N; cl01167 557722014368 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 557722014369 ligand binding site [chemical binding]; other site 557722014370 flexible hinge region; other site 557722014371 Protein of unknown function, DUF399; Region: DUF399; cl01139 557722014372 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 557722014373 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 557722014374 Walker A/P-loop; other site 557722014375 ATP binding site [chemical binding]; other site 557722014376 Q-loop/lid; other site 557722014377 ABC transporter signature motif; other site 557722014378 Walker B; other site 557722014379 D-loop; other site 557722014380 H-loop/switch region; other site 557722014381 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 557722014382 ABC-ATPase subunit interface; other site 557722014383 dimer interface [polypeptide binding]; other site 557722014384 putative PBP binding regions; other site 557722014385 ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ChuT; COG4558 557722014386 Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a...; Region: HutB; cd01149 557722014387 putative hemin binding site; other site 557722014388 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 557722014389 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 557722014390 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 557722014391 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 557722014392 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722014393 N-terminal plug; other site 557722014394 ligand-binding site [chemical binding]; other site 557722014395 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 557722014396 iron-sulfur cluster [ion binding]; other site 557722014397 [2Fe-2S] cluster binding site [ion binding]; other site 557722014398 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 557722014399 Protein of unknown function, DUF; Region: DUF411; cl01142 557722014400 aminotransferase; Validated; Region: PRK08175 557722014401 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722014402 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722014403 homodimer interface [polypeptide binding]; other site 557722014404 catalytic residue [active] 557722014405 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 557722014406 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722014407 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 557722014408 Preprotein translocase subunit SecD [Intracellular trafficking and secretion]; Region: SecD; COG0342 557722014409 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 557722014410 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722014411 tRNA (uracil-5-)-methyltransferase; Region: trmA_only; TIGR02143 557722014412 Sugar fermentation stimulation protein; Region: SfsA; cl00647 557722014413 aminotransferase; Validated; Region: PRK07337 557722014414 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722014415 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722014416 homodimer interface [polypeptide binding]; other site 557722014417 catalytic residue [active] 557722014418 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557722014419 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722014420 active site 557722014421 HIGH motif; other site 557722014422 nucleotide binding site [chemical binding]; other site 557722014423 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722014424 KMSKS motif; other site 557722014425 Sodium:solute symporter family; Region: SSF; cl00456 557722014426 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557722014427 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722014428 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722014429 dimer interface [polypeptide binding]; other site 557722014430 phosphorylation site [posttranslational modification] 557722014431 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722014432 ATP binding site [chemical binding]; other site 557722014433 Mg2+ binding site [ion binding]; other site 557722014434 G-X-G motif; other site 557722014435 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722014436 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014437 active site 557722014438 phosphorylation site [posttranslational modification] 557722014439 intermolecular recognition site; other site 557722014440 dimerization interface [polypeptide binding]; other site 557722014441 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722014442 Walker A motif; other site 557722014443 ATP binding site [chemical binding]; other site 557722014444 Walker B motif; other site 557722014445 arginine finger; other site 557722014446 poly(A) polymerase; Region: pcnB; TIGR01942 557722014447 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 557722014448 active site 557722014449 NTP binding site [chemical binding]; other site 557722014450 metal binding triad [ion binding]; metal-binding site 557722014451 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 557722014452 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 557722014453 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 557722014454 catalytic center binding site [active] 557722014455 ATP binding site [chemical binding]; other site 557722014456 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 557722014457 oligomerization interface [polypeptide binding]; other site 557722014458 active site 557722014459 metal binding site [ion binding]; metal-binding site 557722014460 Pantoate-beta-alanine ligase; Region: PanC; cd00560 557722014461 pantoate--beta-alanine ligase; Region: panC; TIGR00018 557722014462 active site 557722014463 ATP-binding site [chemical binding]; other site 557722014464 pantoate-binding site; other site 557722014465 HXXH motif; other site 557722014466 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 557722014467 tetramerization interface [polypeptide binding]; other site 557722014468 active site 557722014469 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 557722014470 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 557722014471 active site 557722014472 dimer interface [polypeptide binding]; other site 557722014473 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 557722014474 dimer interface [polypeptide binding]; other site 557722014475 active site 557722014476 acetyl-CoA synthetase; Provisional; Region: PRK00174 557722014477 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 557722014478 AMP-binding enzyme; Region: AMP-binding; cl15778 557722014479 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722014480 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; cl01472 557722014481 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557722014482 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557722014483 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557722014484 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 557722014485 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 557722014486 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 557722014487 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 557722014488 CsbD-like; Region: CsbD; cl15799 557722014489 BON domain; Region: BON; cl02771 557722014490 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 557722014491 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 557722014492 RNase E interface [polypeptide binding]; other site 557722014493 trimer interface [polypeptide binding]; other site 557722014494 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 557722014495 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 557722014496 RNase E interface [polypeptide binding]; other site 557722014497 trimer interface [polypeptide binding]; other site 557722014498 active site 557722014499 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 557722014500 putative nucleic acid binding region [nucleotide binding]; other site 557722014501 G-X-X-G motif; other site 557722014502 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 557722014503 RNA binding site [nucleotide binding]; other site 557722014504 domain interface; other site 557722014505 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 557722014506 16S/18S rRNA binding site [nucleotide binding]; other site 557722014507 S13e-L30e interaction site [polypeptide binding]; other site 557722014508 25S rRNA binding site [nucleotide binding]; other site 557722014509 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 557722014510 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 557722014511 RNA binding site [nucleotide binding]; other site 557722014512 active site 557722014513 Ribosome-binding factor A; Region: RBFA; cl00542 557722014514 translation initiation factor IF-2; Validated; Region: infB; PRK05306 557722014515 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 557722014516 translation initiation factor IF-2; Region: IF-2; TIGR00487 557722014517 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 557722014518 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 557722014519 G1 box; other site 557722014520 putative GEF interaction site [polypeptide binding]; other site 557722014521 GTP/Mg2+ binding site [chemical binding]; other site 557722014522 Switch I region; other site 557722014523 G2 box; other site 557722014524 G3 box; other site 557722014525 Switch II region; other site 557722014526 G4 box; other site 557722014527 G5 box; other site 557722014528 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 557722014529 Translation-initiation factor 2; Region: IF-2; pfam11987 557722014530 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 557722014531 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 557722014532 NusA N-terminal domain; Region: NusA_N; pfam08529 557722014533 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 557722014534 RNA binding site [nucleotide binding]; other site 557722014535 homodimer interface [polypeptide binding]; other site 557722014536 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 557722014537 NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of...; Region: NusA_KH; cd02134 557722014538 G-X-X-G motif; other site 557722014539 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 557722014540 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 557722014541 ribosome maturation protein RimP; Reviewed; Region: PRK00092 557722014542 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 557722014543 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 557722014544 Sm1 motif; other site 557722014545 D3 - B interaction site; other site 557722014546 D1 - D2 interaction site; other site 557722014547 Hfq - Hfq interaction site; other site 557722014548 Sm2 motif; other site 557722014549 Preprotein translocase SecG subunit; Region: SecG; cl09123 557722014550 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 557722014551 substrate binding site [chemical binding]; other site 557722014552 dimer interface [polypeptide binding]; other site 557722014553 catalytic triad [active] 557722014554 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 557722014555 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 557722014556 active site 557722014557 substrate binding site [chemical binding]; other site 557722014558 metal binding site [ion binding]; metal-binding site 557722014559 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 557722014560 dihydropteroate synthase; Region: DHPS; TIGR01496 557722014561 substrate binding pocket [chemical binding]; other site 557722014562 dimer interface [polypeptide binding]; other site 557722014563 inhibitor binding site; inhibition site 557722014564 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 557722014565 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722014566 Walker A motif; other site 557722014567 ATP binding site [chemical binding]; other site 557722014568 Walker B motif; other site 557722014569 arginine finger; other site 557722014570 Peptidase family M41; Region: Peptidase_M41; pfam01434 557722014571 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722014572 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 557722014573 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 557722014574 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 557722014575 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 557722014576 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557722014577 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 557722014578 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722014579 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722014580 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 557722014581 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722014582 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722014583 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 557722014584 IMP binding site; other site 557722014585 dimer interface [polypeptide binding]; other site 557722014586 interdomain contacts; other site 557722014587 partial ornithine binding site; other site 557722014588 LysE type translocator; Region: LysE; cl00565 557722014589 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 557722014590 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 557722014591 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 557722014592 catalytic site [active] 557722014593 subunit interface [polypeptide binding]; other site 557722014594 dihydrodipicolinate reductase; Provisional; Region: PRK00048 557722014595 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014596 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 557722014597 chaperone protein DnaJ; Provisional; Region: PRK10767 557722014598 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 557722014599 HSP70 interaction site [polypeptide binding]; other site 557722014600 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 557722014601 substrate binding site [polypeptide binding]; other site 557722014602 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 557722014603 Zn binding sites [ion binding]; other site 557722014604 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 557722014605 dimer interface [polypeptide binding]; other site 557722014606 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 557722014607 GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding; Region: GrpE; cd00446 557722014608 dimer interface [polypeptide binding]; other site 557722014609 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 557722014610 recombination and repair protein; Provisional; Region: PRK10869 557722014611 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 557722014612 Walker A/P-loop; other site 557722014613 ATP binding site [chemical binding]; other site 557722014614 Q-loop/lid; other site 557722014615 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 557722014616 ABC transporter signature motif; other site 557722014617 Walker B; other site 557722014618 D-loop; other site 557722014619 H-loop/switch region; other site 557722014620 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 557722014621 metal binding site 2 [ion binding]; metal-binding site 557722014622 putative DNA binding helix; other site 557722014623 metal binding site 1 [ion binding]; metal-binding site 557722014624 dimer interface [polypeptide binding]; other site 557722014625 structural Zn2+ binding site [ion binding]; other site 557722014626 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 557722014627 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl15768 557722014628 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 557722014629 putative coenzyme Q binding site [chemical binding]; other site 557722014630 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 557722014631 SmpB-tmRNA interface; other site 557722014632 Transcriptional regulators [Transcription]; Region: FadR; COG2186 557722014633 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722014634 DNA-binding site [nucleotide binding]; DNA binding site 557722014635 FCD domain; Region: FCD; cl11656 557722014636 glycolate transporter; Provisional; Region: PRK09695 557722014637 L-lactate permease; Region: Lactate_perm; cl00701 557722014638 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 557722014639 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 557722014640 phosphate binding site [ion binding]; other site 557722014641 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557722014642 FAD binding domain; Region: FAD_binding_4; pfam01565 557722014643 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 557722014644 4Fe-4S dicluster domain; Region: Fer4_17; pfam13534 557722014645 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 557722014646 Cysteine-rich domain; Region: CCG; pfam02754 557722014647 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 557722014648 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722014649 spermidine synthase; Provisional; Region: PRK00811 557722014650 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 557722014651 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014652 active site 557722014653 phosphorylation site [posttranslational modification] 557722014654 intermolecular recognition site; other site 557722014655 dimerization interface [polypeptide binding]; other site 557722014656 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722014657 DNA binding site [nucleotide binding] 557722014658 sensor protein QseC; Provisional; Region: PRK10337 557722014659 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722014660 dimer interface [polypeptide binding]; other site 557722014661 phosphorylation site [posttranslational modification] 557722014662 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722014663 ATP binding site [chemical binding]; other site 557722014664 Mg2+ binding site [ion binding]; other site 557722014665 G-X-G motif; other site 557722014666 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 557722014667 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 557722014668 DNA binding residues [nucleotide binding] 557722014669 dimer interface [polypeptide binding]; other site 557722014670 copper binding site [ion binding]; other site 557722014671 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 557722014672 RIO kinase family; RIO1, RIO3 and similar proteins, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein...; Region: RIO1_like; cd05145 557722014673 ATP binding site [chemical binding]; other site 557722014674 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 557722014675 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014676 active site 557722014677 phosphorylation site [posttranslational modification] 557722014678 intermolecular recognition site; other site 557722014679 dimerization interface [polypeptide binding]; other site 557722014680 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557722014681 Zn2+ binding site [ion binding]; other site 557722014682 Mg2+ binding site [ion binding]; other site 557722014683 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 557722014684 EamA-like transporter family; Region: EamA; cl01037 557722014685 EamA-like transporter family; Region: EamA; cl01037 557722014686 Helix-turn-helix domains; Region: HTH; cl00088 557722014687 acetyl-CoA acetyltransferase; Provisional; Region: PRK09268 557722014688 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 557722014689 dimer interface [polypeptide binding]; other site 557722014690 active site 557722014691 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722014692 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722014693 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722014694 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557722014695 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 557722014696 active site 2 [active] 557722014697 active site 1 [active] 557722014698 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 557722014699 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722014700 S-adenosylmethionine binding site [chemical binding]; other site 557722014701 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 557722014702 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 557722014703 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial protein Rv2277c and similar proteins; Region: GDPD_Rv2277c_like; cd08580 557722014704 putative active site [active] 557722014705 catalytic site [active] 557722014706 putative metal binding site [ion binding]; other site 557722014707 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 557722014708 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 557722014709 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722014710 Coenzyme A binding pocket [chemical binding]; other site 557722014711 DsrE/DsrF-like family; Region: DrsE; cl00672 557722014712 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 557722014713 lipoyl attachment site [posttranslational modification]; other site 557722014714 Uncharacterized protein family (UPF0157); Region: UPF0157; cl00987 557722014715 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722014716 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722014717 S-adenosylmethionine binding site [chemical binding]; other site 557722014718 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 557722014719 active site 557722014720 catalytic triad [active] 557722014721 dimer interface [polypeptide binding]; other site 557722014722 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722014723 S-adenosylmethionine binding site [chemical binding]; other site 557722014724 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 557722014725 hypothetical protein; Provisional; Region: PRK07036 557722014726 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722014727 inhibitor-cofactor binding pocket; inhibition site 557722014728 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722014729 catalytic residue [active] 557722014730 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 557722014731 DNA binding residues [nucleotide binding] 557722014732 dimerization interface [polypeptide binding]; other site 557722014733 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 557722014734 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 557722014735 G1 box; other site 557722014736 putative GEF interaction site [polypeptide binding]; other site 557722014737 GTP/Mg2+ binding site [chemical binding]; other site 557722014738 Switch I region; other site 557722014739 G2 box; other site 557722014740 G3 box; other site 557722014741 Switch II region; other site 557722014742 G4 box; other site 557722014743 G5 box; other site 557722014744 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 557722014745 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 557722014746 Elongation factor SelB, winged helix; Region: SelB-wing_2; pfam09106 557722014747 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 557722014748 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722014749 Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]; Region: FdhE; COG3058 557722014750 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 557722014751 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557722014752 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 557722014753 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 557722014754 4Fe-4S binding domain; Region: Fer4; cl02805 557722014755 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 557722014756 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722014757 molybdopterin cofactor binding site; other site 557722014758 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 557722014759 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 557722014760 molybdopterin cofactor binding site; other site 557722014761 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 557722014762 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722014763 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 557722014764 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 557722014765 active site 557722014766 FMN binding site [chemical binding]; other site 557722014767 2,4-decadienoyl-CoA binding site; other site 557722014768 catalytic residue [active] 557722014769 4Fe-4S cluster binding site [ion binding]; other site 557722014770 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 557722014771 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722014772 Protein of unknown function, DUF606; Region: DUF606; cl01273 557722014773 Domain of unknown function (DUF1835); Region: DUF1835; pfam08874 557722014774 Flagellin N-methylase; Region: FliB; cl00497 557722014775 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 557722014776 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 557722014777 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 557722014778 Ligand binding site; other site 557722014779 Putative Catalytic site; other site 557722014780 DXD motif; other site 557722014781 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 557722014782 MatE; Region: MatE; cl10513 557722014783 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 557722014784 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 557722014785 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 557722014786 PhoU domain; Region: PhoU; pfam01895 557722014787 magnesium-transporting ATPase; Provisional; Region: PRK15122 557722014788 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 557722014789 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557722014790 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 557722014791 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722014792 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 557722014793 N-acetyltransferase; Region: Acetyltransf_2; cl00949 557722014794 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 557722014795 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06115 557722014796 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014797 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722014798 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557722014799 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722014800 CoenzymeA binding site [chemical binding]; other site 557722014801 subunit interaction site [polypeptide binding]; other site 557722014802 PHB binding site; other site 557722014803 Helix-turn-helix domains; Region: HTH; cl00088 557722014804 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 557722014805 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014806 NAD(P) binding site [chemical binding]; other site 557722014807 active site 557722014808 Haemolysin-III related; Region: HlyIII; cl03831 557722014809 EamA-like transporter family; Region: EamA; cl01037 557722014810 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557722014811 EamA-like transporter family; Region: EamA; cl01037 557722014812 Uncharacterized protein conserved in bacteria (DUF2338); Region: DUF2338; pfam10100 557722014813 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557722014814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722014815 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 557722014816 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 557722014817 N-terminal plug; other site 557722014818 ligand-binding site [chemical binding]; other site 557722014819 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 557722014820 arginine decarboxylase; Provisional; Region: PRK05354 557722014821 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 557722014822 dimer interface [polypeptide binding]; other site 557722014823 active site 557722014824 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722014825 catalytic residues [active] 557722014826 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 557722014827 translation initiation factor Sui1; Validated; Region: PRK06824 557722014828 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cd00474 557722014829 Predicted RNA interaction site [nucleotide binding]; other site 557722014830 putative binding site; other site 557722014831 Mutations affecting start-site selection; other site 557722014832 NUDIX hydrolase YfcD; Provisional; Region: PRK15393 557722014833 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_38; cd04697 557722014834 nudix motif; other site 557722014835 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 557722014836 Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]; Region: PleD; COG3706 557722014837 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014838 active site 557722014839 phosphorylation site [posttranslational modification] 557722014840 intermolecular recognition site; other site 557722014841 dimerization interface [polypeptide binding]; other site 557722014842 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722014843 metal binding site [ion binding]; metal-binding site 557722014844 active site 557722014845 I-site; other site 557722014846 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 557722014847 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722014848 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722014849 dimer interface [polypeptide binding]; other site 557722014850 putative CheW interface [polypeptide binding]; other site 557722014851 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 557722014852 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 557722014853 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 557722014854 DsbD alpha interface [polypeptide binding]; other site 557722014855 catalytic residues [active] 557722014856 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 557722014857 active site 557722014858 trimer interface [polypeptide binding]; other site 557722014859 dimer interface [polypeptide binding]; other site 557722014860 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 557722014861 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 557722014862 carboxyltransferase (CT) interaction site; other site 557722014863 biotinylation site [posttranslational modification]; other site 557722014864 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 557722014865 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722014866 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722014867 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557722014868 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 557722014869 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722014870 S-adenosylmethionine binding site [chemical binding]; other site 557722014871 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 557722014872 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 557722014873 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 557722014874 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 557722014875 FMN binding site [chemical binding]; other site 557722014876 active site 557722014877 catalytic residues [active] 557722014878 substrate binding site [chemical binding]; other site 557722014879 Helix-turn-helix domains; Region: HTH; cl00088 557722014880 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 557722014881 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 557722014882 purine monophosphate binding site [chemical binding]; other site 557722014883 dimer interface [polypeptide binding]; other site 557722014884 putative catalytic residues [active] 557722014885 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 557722014886 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 557722014887 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 557722014888 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 557722014889 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722014890 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 557722014891 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 557722014892 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 557722014893 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722014894 dimer interface [polypeptide binding]; other site 557722014895 phosphorylation site [posttranslational modification] 557722014896 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722014897 ATP binding site [chemical binding]; other site 557722014898 Mg2+ binding site [ion binding]; other site 557722014899 G-X-G motif; other site 557722014900 Response regulator receiver domain; Region: Response_reg; pfam00072 557722014901 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014902 active site 557722014903 phosphorylation site [posttranslational modification] 557722014904 intermolecular recognition site; other site 557722014905 dimerization interface [polypeptide binding]; other site 557722014906 Response regulator receiver domain; Region: Response_reg; pfam00072 557722014907 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014908 active site 557722014909 phosphorylation site [posttranslational modification] 557722014910 intermolecular recognition site; other site 557722014911 dimerization interface [polypeptide binding]; other site 557722014912 MarC family integral membrane protein; Region: MarC; cl00919 557722014913 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 557722014914 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 557722014915 putative ligand binding site [chemical binding]; other site 557722014916 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 557722014917 TM-ABC transporter signature motif; other site 557722014918 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 557722014919 TM-ABC transporter signature motif; other site 557722014920 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 557722014921 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 557722014922 Walker A/P-loop; other site 557722014923 ATP binding site [chemical binding]; other site 557722014924 Q-loop/lid; other site 557722014925 ABC transporter signature motif; other site 557722014926 Walker B; other site 557722014927 D-loop; other site 557722014928 H-loop/switch region; other site 557722014929 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 557722014930 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 557722014931 Walker A/P-loop; other site 557722014932 ATP binding site [chemical binding]; other site 557722014933 Q-loop/lid; other site 557722014934 ABC transporter signature motif; other site 557722014935 Walker B; other site 557722014936 D-loop; other site 557722014937 H-loop/switch region; other site 557722014938 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722014939 Coenzyme A binding pocket [chemical binding]; other site 557722014940 UreD urease accessory protein; Region: UreD; cl00530 557722014941 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 557722014942 alpha-gamma subunit interface [polypeptide binding]; other site 557722014943 beta-gamma subunit interface [polypeptide binding]; other site 557722014944 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 557722014945 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722014946 Coenzyme A binding pocket [chemical binding]; other site 557722014947 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 557722014948 gamma-beta subunit interface [polypeptide binding]; other site 557722014949 alpha-beta subunit interface [polypeptide binding]; other site 557722014950 urease subunit alpha; Reviewed; Region: ureC; PRK13207 557722014951 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 557722014952 subunit interactions [polypeptide binding]; other site 557722014953 active site 557722014954 flap region; other site 557722014955 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557722014956 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 557722014957 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 557722014958 tetramer interface [polypeptide binding]; other site 557722014959 active site 557722014960 Mg2+/Mn2+ binding site [ion binding]; other site 557722014961 putative chaperone; Provisional; Region: PRK11678 557722014962 psiF repeat; Region: PsiF_repeat; pfam07769 557722014963 psiF repeat; Region: PsiF_repeat; pfam07769 557722014964 psiF repeat; Region: PsiF_repeat; pfam07769 557722014965 MOSC domain; Region: MOSC; pfam03473 557722014966 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 557722014967 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 557722014968 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 557722014969 Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator; Region: HTH_BmrR; cd01107 557722014970 DNA binding residues [nucleotide binding] 557722014971 drug binding residues [chemical binding]; other site 557722014972 dimer interface [polypeptide binding]; other site 557722014973 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 557722014974 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 557722014975 AsmA-like C-terminal region; Region: AsmA_2; cl15864 557722014976 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 557722014977 dinuclear metal binding motif [ion binding]; other site 557722014978 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 557722014979 Moco binding site; other site 557722014980 metal coordination site [ion binding]; other site 557722014981 Thiosulfate reductase cytochrome B subunit (membrane anchoring protein) [Energy production and conversion]; Region: COG4117 557722014982 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 557722014983 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 557722014984 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722014985 active site 557722014986 phosphorylation site [posttranslational modification] 557722014987 intermolecular recognition site; other site 557722014988 dimerization interface [polypeptide binding]; other site 557722014989 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722014990 DNA binding site [nucleotide binding] 557722014991 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 557722014992 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722014993 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722014994 dimer interface [polypeptide binding]; other site 557722014995 phosphorylation site [posttranslational modification] 557722014996 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722014997 ATP binding site [chemical binding]; other site 557722014998 Mg2+ binding site [ion binding]; other site 557722014999 G-X-G motif; other site 557722015000 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722015001 putative MFS family transporter protein; Provisional; Region: PRK03633 557722015002 putative substrate translocation pore; other site 557722015003 The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases...; Region: Delta6-FADS-like; cd03506 557722015004 Fatty acid desaturase; Region: FA_desaturase; pfam00487 557722015005 putative di-iron ligands [ion binding]; other site 557722015006 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_2; cd06216 557722015007 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 557722015008 FAD binding pocket [chemical binding]; other site 557722015009 FAD binding motif [chemical binding]; other site 557722015010 phosphate binding motif [ion binding]; other site 557722015011 beta-alpha-beta structure motif; other site 557722015012 NAD binding pocket [chemical binding]; other site 557722015013 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722015014 catalytic loop [active] 557722015015 iron binding site [ion binding]; other site 557722015016 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 557722015017 Helix-turn-helix domains; Region: HTH; cl00088 557722015018 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 557722015019 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 557722015020 dimer interface [polypeptide binding]; other site 557722015021 catalytic residues [active] 557722015022 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 557722015023 UreF; Region: UreF; pfam01730 557722015024 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722015025 HupE / UreJ protein; Region: HupE_UreJ; cl01011 557722015026 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 557722015027 FecR protein; Region: FecR; pfam04773 557722015028 RNA polymerase sigma factor; Provisional; Region: PRK12529 557722015029 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557722015030 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722015031 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722015032 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 557722015033 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 557722015034 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 557722015035 outer membrane porin, OprD family; Region: OprD; pfam03573 557722015036 NADP+-dependent p-hydroxybenzaldehyde dehydrogenase-like; Region: ALDH_HBenzADH; cd07151 557722015037 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722015038 NAD(P) binding site [chemical binding]; other site 557722015039 catalytic residues [active] 557722015040 benzoate transport; Region: 2A0115; TIGR00895 557722015041 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722015042 putative substrate translocation pore; other site 557722015043 benzoylformate decarboxylase; Reviewed; Region: PRK07092 557722015044 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722015045 PYR/PP interface [polypeptide binding]; other site 557722015046 dimer interface [polypeptide binding]; other site 557722015047 TPP binding site [chemical binding]; other site 557722015048 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722015049 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 557722015050 TPP-binding site [chemical binding]; other site 557722015051 dimer interface [polypeptide binding]; other site 557722015052 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 557722015053 Helix-turn-helix domains; Region: HTH; cl00088 557722015054 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 557722015055 substrate binding pocket [chemical binding]; other site 557722015056 dimerization interface [polypeptide binding]; other site 557722015057 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722015058 putative substrate translocation pore; other site 557722015059 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 557722015060 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 557722015061 iron-sulfur cluster [ion binding]; other site 557722015062 [2Fe-2S] cluster binding site [ion binding]; other site 557722015063 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 557722015064 alpha subunit interface [polypeptide binding]; other site 557722015065 active site 557722015066 substrate binding site [chemical binding]; other site 557722015067 Fe binding site [ion binding]; other site 557722015068 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 557722015069 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 557722015070 FMN-binding pocket [chemical binding]; other site 557722015071 flavin binding motif; other site 557722015072 phosphate binding motif [ion binding]; other site 557722015073 beta-alpha-beta structure motif; other site 557722015074 NAD binding pocket [chemical binding]; other site 557722015075 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722015076 catalytic loop [active] 557722015077 iron binding site [ion binding]; other site 557722015078 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722015079 phosphonate utilization associated transcriptional regulator; Region: phnR_burk; TIGR03338 557722015080 DNA-binding site [nucleotide binding]; DNA binding site 557722015081 FCD domain; Region: FCD; cl11656 557722015082 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 557722015083 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 557722015084 putative NAD(P) binding site [chemical binding]; other site 557722015085 homodimer interface [polypeptide binding]; other site 557722015086 homotetramer interface [polypeptide binding]; other site 557722015087 active site 557722015088 ornithine cyclodeaminase; Validated; Region: PRK06141 557722015089 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015090 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 557722015091 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 557722015092 Walker A/P-loop; other site 557722015093 ATP binding site [chemical binding]; other site 557722015094 Q-loop/lid; other site 557722015095 ABC transporter signature motif; other site 557722015096 Walker B; other site 557722015097 D-loop; other site 557722015098 H-loop/switch region; other site 557722015099 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 557722015100 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 557722015101 Walker A/P-loop; other site 557722015102 ATP binding site [chemical binding]; other site 557722015103 Q-loop/lid; other site 557722015104 ABC transporter signature motif; other site 557722015105 Walker B; other site 557722015106 D-loop; other site 557722015107 H-loop/switch region; other site 557722015108 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 557722015109 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 557722015110 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 557722015111 TM-ABC transporter signature motif; other site 557722015112 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 557722015113 TM-ABC transporter signature motif; other site 557722015114 leucine ABC transporter subunit substrate-binding protein LivK; Provisional; Region: PRK15404 557722015115 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 557722015116 dimerization interface [polypeptide binding]; other site 557722015117 ligand binding site [chemical binding]; other site 557722015118 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722015119 Helix-turn-helix domains; Region: HTH; cl00088 557722015120 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722015121 dimerization interface [polypeptide binding]; other site 557722015122 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557722015123 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722015124 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722015125 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722015126 dimer interface [polypeptide binding]; other site 557722015127 putative CheW interface [polypeptide binding]; other site 557722015128 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 557722015129 nudix motif; other site 557722015130 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 557722015131 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722015132 active site 557722015133 nucleotide binding site [chemical binding]; other site 557722015134 HIGH motif; other site 557722015135 KMSKS motif; other site 557722015136 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 557722015137 Isochorismatase family; Region: Isochorismatase; pfam00857 557722015138 catalytic triad [active] 557722015139 metal binding site [ion binding]; metal-binding site 557722015140 conserved cis-peptide bond; other site 557722015141 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 557722015142 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 557722015143 active site 557722015144 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 557722015145 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 557722015146 homodimer interface [polypeptide binding]; other site 557722015147 NAD binding pocket [chemical binding]; other site 557722015148 ATP binding pocket [chemical binding]; other site 557722015149 Mg binding site [ion binding]; other site 557722015150 active-site loop [active] 557722015151 Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: fatty_acyltransferase_like; cd01846 557722015152 active site 557722015153 catalytic triad [active] 557722015154 oxyanion hole [active] 557722015155 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 557722015156 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 557722015157 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722015158 putative peptidoglycan binding site; other site 557722015159 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 557722015160 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722015161 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 557722015162 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 557722015163 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 557722015164 Uncharacterized conserved protein [Function unknown]; Region: COG2308 557722015165 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 557722015166 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; cl00980 557722015167 hypothetical protein; Provisional; Region: PRK01254 557722015168 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 557722015169 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 557722015170 alanine racemase; Reviewed; Region: alr; PRK00053 557722015171 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 557722015172 active site 557722015173 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722015174 substrate binding site [chemical binding]; other site 557722015175 catalytic residues [active] 557722015176 dimer interface [polypeptide binding]; other site 557722015177 replicative DNA helicase; Provisional; Region: PRK05748 557722015178 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 557722015179 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 557722015180 Walker A motif; other site 557722015181 ATP binding site [chemical binding]; other site 557722015182 Walker B motif; other site 557722015183 DNA binding loops [nucleotide binding] 557722015184 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 557722015185 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 557722015186 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 557722015187 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 557722015188 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 557722015189 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 557722015190 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 557722015191 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557722015192 exoribonuclease R; Provisional; Region: PRK11642 557722015193 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557722015194 RNB domain; Region: RNB; pfam00773 557722015195 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 557722015196 RNA binding site [nucleotide binding]; other site 557722015197 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 557722015198 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 557722015199 GDP-binding site [chemical binding]; other site 557722015200 ACT binding site; other site 557722015201 IMP binding site; other site 557722015202 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 557722015203 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 557722015204 dimer interface [polypeptide binding]; other site 557722015205 motif 1; other site 557722015206 active site 557722015207 motif 2; other site 557722015208 motif 3; other site 557722015209 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 557722015210 FtsH protease regulator HflC; Provisional; Region: PRK11029 557722015211 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 557722015212 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 557722015213 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 557722015214 HflK protein; Region: hflK; TIGR01933 557722015215 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 557722015216 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 557722015217 HflX GTPase family; Region: HflX; cd01878 557722015218 G1 box; other site 557722015219 GTP/Mg2+ binding site [chemical binding]; other site 557722015220 Switch I region; other site 557722015221 G2 box; other site 557722015222 G3 box; other site 557722015223 Switch II region; other site 557722015224 G4 box; other site 557722015225 G5 box; other site 557722015226 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 557722015227 Sm1 motif; other site 557722015228 intra - hexamer interaction site; other site 557722015229 inter - hexamer interaction site [polypeptide binding]; other site 557722015230 nucleotide binding pocket [chemical binding]; other site 557722015231 Sm2 motif; other site 557722015232 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722015233 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 557722015234 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 557722015235 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722015236 ATP binding site [chemical binding]; other site 557722015237 Mg2+ binding site [ion binding]; other site 557722015238 G-X-G motif; other site 557722015239 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 557722015240 ATP binding site [chemical binding]; other site 557722015241 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 557722015242 AMIN domain; Region: AMIN; pfam11741 557722015243 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 557722015244 active site 557722015245 metal binding site [ion binding]; metal-binding site 557722015246 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 557722015247 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 557722015248 putative carbohydrate kinase; Provisional; Region: PRK10565 557722015249 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 557722015250 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 557722015251 putative substrate binding site [chemical binding]; other site 557722015252 putative ATP binding site [chemical binding]; other site 557722015253 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 557722015254 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 557722015255 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 557722015256 putative active site [active] 557722015257 putative substrate binding site [chemical binding]; other site 557722015258 catalytic site [active] 557722015259 dimer interface [polypeptide binding]; other site 557722015260 GTPase RsgA; Reviewed; Region: PRK12288 557722015261 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 557722015262 RNA binding site [nucleotide binding]; other site 557722015263 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 557722015264 GTPase/Zn-binding domain interface [polypeptide binding]; other site 557722015265 GTP/Mg2+ binding site [chemical binding]; other site 557722015266 G4 box; other site 557722015267 G5 box; other site 557722015268 G1 box; other site 557722015269 Switch I region; other site 557722015270 G2 box; other site 557722015271 G3 box; other site 557722015272 Switch II region; other site 557722015273 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 557722015274 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 557722015275 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557722015276 ligand binding site [chemical binding]; other site 557722015277 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 557722015278 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 557722015279 HDOD domain; Region: HDOD; pfam08668 557722015280 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 557722015281 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 557722015282 active site residue [active] 557722015283 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 557722015284 active site residue [active] 557722015285 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 557722015286 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557722015287 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl09944 557722015288 active site 557722015289 phosphorylation site [posttranslational modification] 557722015290 dimerization interface [polypeptide binding]; other site 557722015291 PAS fold; Region: PAS; pfam00989 557722015292 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722015293 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722015294 metal binding site [ion binding]; metal-binding site 557722015295 active site 557722015296 I-site; other site 557722015297 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722015298 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_1; cd04870 557722015299 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB); Region: ACT_PSP_2; cd04871 557722015300 phosphoserine phosphatase SerB; Region: serB; TIGR00338 557722015301 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722015302 motif II; other site 557722015303 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 557722015304 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 557722015305 metal binding site [ion binding]; metal-binding site 557722015306 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 557722015307 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 557722015308 Protein of unknown function (DUF330); Region: DUF330; cl01135 557722015309 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 557722015310 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 557722015311 CAP-like domain; other site 557722015312 active site 557722015313 primary dimer interface [polypeptide binding]; other site 557722015314 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 557722015315 catalytic motif [active] 557722015316 Catalytic residue [active] 557722015317 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 557722015318 SdiA-regulated; Region: SdiA-regulated; cd09971 557722015319 putative active site [active] 557722015320 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 557722015321 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722015322 ATP binding site [chemical binding]; other site 557722015323 Mg2+ binding site [ion binding]; other site 557722015324 G-X-G motif; other site 557722015325 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 557722015326 anchoring element; other site 557722015327 dimer interface [polypeptide binding]; other site 557722015328 ATP binding site [chemical binding]; other site 557722015329 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 557722015330 active site 557722015331 metal binding site [ion binding]; metal-binding site 557722015332 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 557722015333 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 557722015334 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 557722015335 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557722015336 active site 557722015337 metal binding site [ion binding]; metal-binding site 557722015338 hexamer interface [polypeptide binding]; other site 557722015339 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 557722015340 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 557722015341 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 557722015342 dimer interface [polypeptide binding]; other site 557722015343 ADP-ribose binding site [chemical binding]; other site 557722015344 active site 557722015345 nudix motif; other site 557722015346 metal binding site [ion binding]; metal-binding site 557722015347 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 557722015348 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 557722015349 ThiC-associated domain; Region: ThiC-associated; pfam13667 557722015350 ThiC family; Region: ThiC; cl08031 557722015351 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 557722015352 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 557722015353 aspartate aminotransferase; Provisional; Region: PRK05764 557722015354 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722015355 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722015356 homodimer interface [polypeptide binding]; other site 557722015357 catalytic residue [active] 557722015358 hypothetical protein; Provisional; Region: PRK07524 557722015359 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557722015360 PYR/PP interface [polypeptide binding]; other site 557722015361 dimer interface [polypeptide binding]; other site 557722015362 TPP binding site [chemical binding]; other site 557722015363 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722015364 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 557722015365 TPP-binding site [chemical binding]; other site 557722015366 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 557722015367 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015368 CoA-ligase; Region: Ligase_CoA; cl02894 557722015369 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722015370 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722015371 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722015372 active site 557722015373 enoyl-CoA hydratase; Provisional; Region: PRK06688 557722015374 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 557722015375 substrate binding site [chemical binding]; other site 557722015376 oxyanion hole (OAH) forming residues; other site 557722015377 trimer interface [polypeptide binding]; other site 557722015378 Amino acid transporters [Amino acid transport and metabolism]; Region: LysP; COG0833 557722015379 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 557722015380 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722015381 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722015382 dimer interface [polypeptide binding]; other site 557722015383 phosphorylation site [posttranslational modification] 557722015384 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722015385 ATP binding site [chemical binding]; other site 557722015386 Mg2+ binding site [ion binding]; other site 557722015387 G-X-G motif; other site 557722015388 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722015389 Response regulator receiver domain; Region: Response_reg; pfam00072 557722015390 active site 557722015391 phosphorylation site [posttranslational modification] 557722015392 intermolecular recognition site; other site 557722015393 dimerization interface [polypeptide binding]; other site 557722015394 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 557722015395 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722015396 active site 557722015397 phosphorylation site [posttranslational modification] 557722015398 intermolecular recognition site; other site 557722015399 dimerization interface [polypeptide binding]; other site 557722015400 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722015401 DNA binding site [nucleotide binding] 557722015402 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 557722015403 Helix-turn-helix domains; Region: HTH; cl00088 557722015404 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 557722015405 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557722015406 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722015407 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 557722015408 Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_3_FMN; cd04734 557722015409 putative active site [active] 557722015410 putative FMN binding site [chemical binding]; other site 557722015411 putative substrate binding site [chemical binding]; other site 557722015412 putative catalytic residue [active] 557722015413 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 557722015414 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722015415 non-specific DNA binding site [nucleotide binding]; other site 557722015416 salt bridge; other site 557722015417 sequence-specific DNA binding site [nucleotide binding]; other site 557722015418 Cupin domain; Region: Cupin_2; cl09118 557722015419 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 557722015420 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 557722015421 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722015422 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722015423 Helix-turn-helix domains; Region: HTH; cl00088 557722015424 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722015425 dimerization interface [polypeptide binding]; other site 557722015426 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557722015427 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 557722015428 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015429 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 557722015430 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 557722015431 active site 557722015432 catalytic tetrad [active] 557722015433 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722015434 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722015435 active site 557722015436 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557722015437 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722015438 active site 557722015439 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557722015440 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 557722015441 dimer interface [polypeptide binding]; other site 557722015442 active site 557722015443 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557722015444 Ligand Binding Site [chemical binding]; other site 557722015445 Molecular Tunnel; other site 557722015446 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 557722015447 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 557722015448 putative ribose interaction site [chemical binding]; other site 557722015449 putative ADP binding site [chemical binding]; other site 557722015450 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557722015451 active site 557722015452 nucleotide binding site [chemical binding]; other site 557722015453 HIGH motif; other site 557722015454 KMSKS motif; other site 557722015455 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 557722015456 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 557722015457 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 557722015458 Walker A/P-loop; other site 557722015459 ATP binding site [chemical binding]; other site 557722015460 Q-loop/lid; other site 557722015461 ABC transporter signature motif; other site 557722015462 Walker B; other site 557722015463 D-loop; other site 557722015464 H-loop/switch region; other site 557722015465 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cd05120 557722015466 active site 557722015467 substrate binding site [chemical binding]; other site 557722015468 ATP binding site [chemical binding]; other site 557722015469 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 557722015470 O-Antigen ligase; Region: Wzy_C; cl04850 557722015471 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557722015472 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 557722015473 active site 557722015474 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722015475 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 557722015476 Mig-14; Region: Mig-14; pfam07395 557722015477 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722015478 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 557722015479 putative ADP-binding pocket [chemical binding]; other site 557722015480 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 557722015481 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 557722015482 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cd05120 557722015483 active site 557722015484 ATP binding site [chemical binding]; other site 557722015485 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722015486 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722015487 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722015488 ATP binding site [chemical binding]; other site 557722015489 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722015490 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722015491 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 557722015492 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 557722015493 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 557722015494 putative active site [active] 557722015495 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 557722015496 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 557722015497 putative active site [active] 557722015498 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 557722015499 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 557722015500 homodimer interface [polypeptide binding]; other site 557722015501 substrate-cofactor binding pocket; other site 557722015502 catalytic residue [active] 557722015503 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 557722015504 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557722015505 metal binding triad; other site 557722015506 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557722015507 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557722015508 metal binding triad; other site 557722015509 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557722015510 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 557722015511 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 557722015512 dimer interface [polypeptide binding]; other site 557722015513 TPP-binding site [chemical binding]; other site 557722015514 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 557722015515 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_long; TIGR01348 557722015516 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722015517 E3 interaction surface; other site 557722015518 lipoyl attachment site [posttranslational modification]; other site 557722015519 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 557722015520 E3 interaction surface; other site 557722015521 lipoyl attachment site [posttranslational modification]; other site 557722015522 e3 binding domain; Region: E3_binding; pfam02817 557722015523 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 557722015524 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 557722015525 GAF domain; Region: GAF; cl15785 557722015526 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722015527 PAS domain; Region: PAS_9; pfam13426 557722015528 putative active site [active] 557722015529 heme pocket [chemical binding]; other site 557722015530 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722015531 metal binding site [ion binding]; metal-binding site 557722015532 active site 557722015533 I-site; other site 557722015534 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722015535 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 557722015536 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 557722015537 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722015538 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722015539 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722015540 active site 557722015541 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722015542 NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain [Inorganic ion transport and metabolism]; Region: COG3263 557722015543 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722015544 Transporter associated domain; Region: CorC_HlyC; cl08393 557722015545 hypothetical protein; Provisional; Region: PRK11281 557722015546 Vegetative insecticide protein 3A N terminal; Region: Vip3A_N; pfam12495 557722015547 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 557722015548 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722015549 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 557722015550 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 557722015551 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 557722015552 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 557722015553 homodimer interface [polypeptide binding]; other site 557722015554 substrate-cofactor binding pocket; other site 557722015555 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722015556 catalytic residue [active] 557722015557 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722015558 CoenzymeA binding site [chemical binding]; other site 557722015559 subunit interaction site [polypeptide binding]; other site 557722015560 PHB binding site; other site 557722015561 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722015562 Ligand Binding Site [chemical binding]; other site 557722015563 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 557722015564 Ligand Binding Site [chemical binding]; other site 557722015565 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 557722015566 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722015567 P-loop; other site 557722015568 Magnesium ion binding site [ion binding]; other site 557722015569 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722015570 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 557722015571 Helix-turn-helix domains; Region: HTH; cl00088 557722015572 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 557722015573 dimerization interface [polypeptide binding]; other site 557722015574 substrate binding pocket [chemical binding]; other site 557722015575 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722015576 putative substrate translocation pore; other site 557722015577 short chain dehydrogenase; Provisional; Region: PRK06197 557722015578 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015579 NAD(P) binding site [chemical binding]; other site 557722015580 active site 557722015581 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722015582 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722015583 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 557722015584 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 557722015585 substrate binding site [chemical binding]; other site 557722015586 active site 557722015587 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 557722015588 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 557722015589 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015590 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722015591 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 557722015592 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 557722015593 active site 557722015594 dimer interface [polypeptide binding]; other site 557722015595 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 557722015596 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 557722015597 active site 557722015598 FMN binding site [chemical binding]; other site 557722015599 substrate binding site [chemical binding]; other site 557722015600 3Fe-4S cluster binding site [ion binding]; other site 557722015601 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 557722015602 domain interface; other site 557722015603 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 557722015604 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722015605 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 557722015606 Sporulation related domain; Region: SPOR; cl10051 557722015607 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 557722015608 active site 557722015609 dimer interface [polypeptide binding]; other site 557722015610 metal binding site [ion binding]; metal-binding site 557722015611 shikimate kinase; Reviewed; Region: aroK; PRK00131 557722015612 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 557722015613 ADP binding site [chemical binding]; other site 557722015614 magnesium binding site [ion binding]; other site 557722015615 putative shikimate binding site; other site 557722015616 AMIN domain; Region: AMIN; pfam11741 557722015617 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 557722015618 Secretin and TonB N terminus short domain; Region: STN; cl06624 557722015619 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 557722015620 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557722015621 Pilus assembly protein, PilP; Region: PilP; cl01235 557722015622 Pilus assembly protein, PilO; Region: PilO; cl01234 557722015623 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 557722015624 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 557722015625 Competence protein A; Region: Competence_A; pfam11104 557722015626 Cell division protein FtsA; Region: FtsA; cl11496 557722015627 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 557722015628 Transglycosylase; Region: Transgly; cl07896 557722015629 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722015630 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 557722015631 Malic enzyme, N-terminal domain; Region: malic; pfam00390 557722015632 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 557722015633 putative NAD(P) binding site [chemical binding]; other site 557722015634 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 557722015635 Peptidase family M48; Region: Peptidase_M48; cl12018 557722015636 Staphylococcal nuclease homologues; Region: SNc; smart00318 557722015637 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 557722015638 Catalytic site; other site 557722015639 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 557722015640 primosome assembly protein PriA; Validated; Region: PRK05580 557722015641 primosome assembly protein PriA; Validated; Region: PRK05580 557722015642 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722015643 ATP binding site [chemical binding]; other site 557722015644 putative Mg++ binding site [ion binding]; other site 557722015645 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722015646 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 557722015647 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 557722015648 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 557722015649 active site 557722015650 HIGH motif; other site 557722015651 KMSK motif region; other site 557722015652 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 557722015653 tRNA binding surface [nucleotide binding]; other site 557722015654 anticodon binding site; other site 557722015655 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 557722015656 Sporulation related domain; Region: SPOR; cl10051 557722015657 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 557722015658 active site 557722015659 HslU subunit interaction site [polypeptide binding]; other site 557722015660 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 557722015661 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722015662 Walker A motif; other site 557722015663 ATP binding site [chemical binding]; other site 557722015664 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722015665 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 557722015666 Protein of unknown function (DUF971); Region: DUF971; cl01414 557722015667 poly(R)-hydroxyalkanoic acid synthase, class II; Region: PHA_synth_II; TIGR01839 557722015668 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 557722015669 poly(3-hydroxyalkanoate) depolymerase; Region: PHA_depoly_arom; TIGR02240 557722015670 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722015671 poly(R)-hydroxyalkanoic acid synthase, class II; Region: PHA_synth_II; TIGR01839 557722015672 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 557722015673 Helix-turn-helix domains; Region: HTH; cl00088 557722015674 Bacterial transcriptional repressor; Region: TetR; pfam13972 557722015675 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; cl07863 557722015676 Poly(hydroxyalcanoate) granule associated protein (phasin); Region: Phasin; cl07863 557722015677 Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn); Region: PHA_gran_rgn; cl09865 557722015678 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 557722015679 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722015680 S-adenosylmethionine binding site [chemical binding]; other site 557722015681 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 557722015682 SCP-2 sterol transfer family; Region: SCP2; cl01225 557722015683 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 557722015684 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 557722015685 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 557722015686 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 557722015687 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 557722015688 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 557722015689 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 557722015690 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 557722015691 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557722015692 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557722015693 dimer interface [polypeptide binding]; other site 557722015694 putative CheW interface [polypeptide binding]; other site 557722015695 Uncharacterized protein family (UPF0158); Region: UPF0158; pfam03682 557722015696 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557722015697 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722015698 Walker A/P-loop; other site 557722015699 ATP binding site [chemical binding]; other site 557722015700 Q-loop/lid; other site 557722015701 ABC transporter signature motif; other site 557722015702 Walker B; other site 557722015703 D-loop; other site 557722015704 H-loop/switch region; other site 557722015705 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722015706 dimer interface [polypeptide binding]; other site 557722015707 conserved gate region; other site 557722015708 putative PBP binding loops; other site 557722015709 ABC-ATPase subunit interface; other site 557722015710 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722015711 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722015712 substrate binding pocket [chemical binding]; other site 557722015713 membrane-bound complex binding site; other site 557722015714 hinge residues; other site 557722015715 Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: MdoH; COG2943 557722015716 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 557722015717 Ligand binding site; other site 557722015718 DXD motif; other site 557722015719 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 557722015720 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 557722015721 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 557722015722 putative active site [active] 557722015723 dimerization interface [polypeptide binding]; other site 557722015724 putative tRNAtyr binding site [nucleotide binding]; other site 557722015725 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 557722015726 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722015727 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722015728 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 557722015729 nudix motif; other site 557722015730 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 557722015731 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722015732 substrate binding pocket [chemical binding]; other site 557722015733 membrane-bound complex binding site; other site 557722015734 hinge residues; other site 557722015735 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 557722015736 homotrimer interaction site [polypeptide binding]; other site 557722015737 putative active site [active] 557722015738 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 557722015739 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015740 Helix-turn-helix domains; Region: HTH; cl00088 557722015741 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722015742 dimerization interface [polypeptide binding]; other site 557722015743 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722015744 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722015745 Sel1 repeat; Region: Sel1; cl02723 557722015746 Sel1 repeat; Region: Sel1; cl02723 557722015747 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 557722015748 Sel1 repeat; Region: Sel1; cl02723 557722015749 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 557722015750 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 557722015751 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 557722015752 putative active site [active] 557722015753 catalytic site [active] 557722015754 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 557722015755 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 557722015756 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 557722015757 putative active site [active] 557722015758 catalytic site [active] 557722015759 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722015760 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722015761 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722015762 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 557722015763 N-formylglutamate amidohydrolase; Region: FGase; cl01522 557722015764 imidazolonepropionase; Validated; Region: PRK09356 557722015765 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 557722015766 active site 557722015767 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 557722015768 active sites [active] 557722015769 tetramer interface [polypeptide binding]; other site 557722015770 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557722015771 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 557722015772 Walker A/P-loop; other site 557722015773 ATP binding site [chemical binding]; other site 557722015774 Q-loop/lid; other site 557722015775 ABC transporter signature motif; other site 557722015776 Walker B; other site 557722015777 D-loop; other site 557722015778 H-loop/switch region; other site 557722015779 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722015780 dimer interface [polypeptide binding]; other site 557722015781 conserved gate region; other site 557722015782 putative PBP binding loops; other site 557722015783 ABC-ATPase subunit interface; other site 557722015784 NMT1-like family; Region: NMT1_2; cl15260 557722015785 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 557722015786 putative proline-specific permease; Provisional; Region: proY; PRK10580 557722015787 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 557722015788 active sites [active] 557722015789 tetramer interface [polypeptide binding]; other site 557722015790 Sodium:solute symporter family; Region: SSF; cl00456 557722015791 urocanate hydratase; Provisional; Region: PRK05414 557722015792 NMT1-like family; Region: NMT1_2; cl15260 557722015793 Fatty acid desaturase [Lipid metabolism]; Region: DesA; COG3239 557722015794 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 557722015795 putative di-iron ligands [ion binding]; other site 557722015796 NMT1-like family; Region: NMT1_2; cl15260 557722015797 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 557722015798 HutD; Region: HutD; cl01532 557722015799 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 557722015800 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722015801 DNA-binding site [nucleotide binding]; DNA binding site 557722015802 UTRA domain; Region: UTRA; cl01230 557722015803 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 557722015804 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_E; cd01313 557722015805 active site 557722015806 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 557722015807 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 557722015808 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 557722015809 fructose-1,6-bisphosphatase family protein; Region: PLN02628 557722015810 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 557722015811 AMP binding site [chemical binding]; other site 557722015812 metal binding site [ion binding]; metal-binding site 557722015813 active site 557722015814 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 557722015815 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557722015816 dimer interface [polypeptide binding]; other site 557722015817 active site 557722015818 metal binding site [ion binding]; metal-binding site 557722015819 glutathione binding site [chemical binding]; other site 557722015820 Phospholipase/lecithinase/hemolysin [Lipid metabolism / General function prediction only]; Region: COG3240 557722015821 Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: Triacylglycerol_lipase_like; cd01847 557722015822 active site 557722015823 catalytic triad [active] 557722015824 oxyanion hole [active] 557722015825 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 557722015826 Protein of unknown function (DUF3999); Region: DUF3999; pfam13163 557722015827 Protein of unknown function (DUF3999); Region: DUF3999; pfam13163 557722015828 Predicted membrane protein [Function unknown]; Region: COG5373 557722015829 Predicted membrane protein [Function unknown]; Region: COG5373 557722015830 Predicted membrane protein [Function unknown]; Region: COG5373 557722015831 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015832 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg6; cd04781 557722015833 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 557722015834 DNA binding residues [nucleotide binding] 557722015835 putative dimer interface [polypeptide binding]; other site 557722015836 putative metal binding residues [ion binding]; other site 557722015837 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 557722015838 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 557722015839 G1 box; other site 557722015840 putative GEF interaction site [polypeptide binding]; other site 557722015841 GTP/Mg2+ binding site [chemical binding]; other site 557722015842 Switch I region; other site 557722015843 G2 box; other site 557722015844 G3 box; other site 557722015845 Switch II region; other site 557722015846 G4 box; other site 557722015847 G5 box; other site 557722015848 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 557722015849 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 557722015850 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 557722015851 THUMP domain; Region: THUMP; cl12076 557722015852 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 557722015853 Ligand Binding Site [chemical binding]; other site 557722015854 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 557722015855 glutamine synthetase; Provisional; Region: glnA; PRK09469 557722015856 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 557722015857 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722015858 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 557722015859 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722015860 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557722015861 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557722015862 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 557722015863 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722015864 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722015865 dimer interface [polypeptide binding]; other site 557722015866 phosphorylation site [posttranslational modification] 557722015867 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722015868 ATP binding site [chemical binding]; other site 557722015869 Mg2+ binding site [ion binding]; other site 557722015870 G-X-G motif; other site 557722015871 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 557722015872 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722015873 active site 557722015874 phosphorylation site [posttranslational modification] 557722015875 intermolecular recognition site; other site 557722015876 dimerization interface [polypeptide binding]; other site 557722015877 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722015878 Walker A motif; other site 557722015879 ATP binding site [chemical binding]; other site 557722015880 Walker B motif; other site 557722015881 arginine finger; other site 557722015882 Helix-turn-helix domains; Region: HTH; cl00088 557722015883 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 557722015884 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 557722015885 SecA binding site; other site 557722015886 Preprotein binding site; other site 557722015887 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 557722015888 GSH binding site [chemical binding]; other site 557722015889 catalytic residues [active] 557722015890 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 557722015891 active site residue [active] 557722015892 Sulfatase; Region: Sulfatase; cl10460 557722015893 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 557722015894 CAAX protease self-immunity; Region: Abi; cl00558 557722015895 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 557722015896 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 557722015897 C-terminal peptidase (prc); Region: prc; TIGR00225 557722015898 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 557722015899 protein binding site [polypeptide binding]; other site 557722015900 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 557722015901 Catalytic dyad [active] 557722015902 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 557722015903 NodB motif; other site 557722015904 putative active site [active] 557722015905 putative catalytic site [active] 557722015906 Zn binding site [ion binding]; other site 557722015907 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 557722015908 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722015909 substrate binding pocket [chemical binding]; other site 557722015910 membrane-bound complex binding site; other site 557722015911 hinge residues; other site 557722015912 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722015913 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722015914 substrate binding pocket [chemical binding]; other site 557722015915 membrane-bound complex binding site; other site 557722015916 hinge residues; other site 557722015917 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722015918 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722015919 substrate binding pocket [chemical binding]; other site 557722015920 membrane-bound complex binding site; other site 557722015921 hinge residues; other site 557722015922 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 557722015923 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 557722015924 substrate binding site [chemical binding]; other site 557722015925 glutamase interaction surface [polypeptide binding]; other site 557722015926 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 557722015927 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 557722015928 catalytic residues [active] 557722015929 Uncharacterized conserved protein (DUF2164); Region: DUF2164; cl02278 557722015930 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 557722015931 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 557722015932 putative active site [active] 557722015933 oxyanion strand; other site 557722015934 catalytic triad [active] 557722015935 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 557722015936 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 557722015937 putative active site pocket [active] 557722015938 4-fold oligomerization interface [polypeptide binding]; other site 557722015939 metal binding residues [ion binding]; metal-binding site 557722015940 3-fold/trimer interface [polypeptide binding]; other site 557722015941 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722015942 Predicted dehydrogenase [General function prediction only]; Region: COG0579 557722015943 AsmA family; Region: AsmA; pfam05170 557722015944 AsmA-like C-terminal region; Region: AsmA_2; cl15864 557722015945 AsmA-like C-terminal region; Region: AsmA_2; cl15864 557722015946 adenine DNA glycosylase; Provisional; Region: PRK10880 557722015947 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557722015948 minor groove reading motif; other site 557722015949 helix-hairpin-helix signature motif; other site 557722015950 substrate binding pocket [chemical binding]; other site 557722015951 active site 557722015952 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 557722015953 DNA binding and oxoG recognition site [nucleotide binding] 557722015954 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 557722015955 putative oxidoreductase; Provisional; Region: PRK11579 557722015956 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015957 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 557722015958 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722015959 classical (c) SDRs; Region: SDR_c; cd05233 557722015960 NAD(P) binding site [chemical binding]; other site 557722015961 active site 557722015962 Protein of unknown function (DUF502); Region: DUF502; cl01107 557722015963 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 557722015964 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 557722015965 Walker A/P-loop; other site 557722015966 ATP binding site [chemical binding]; other site 557722015967 Q-loop/lid; other site 557722015968 ABC transporter signature motif; other site 557722015969 Walker B; other site 557722015970 D-loop; other site 557722015971 H-loop/switch region; other site 557722015972 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722015973 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722015974 substrate binding pocket [chemical binding]; other site 557722015975 membrane-bound complex binding site; other site 557722015976 hinge residues; other site 557722015977 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722015978 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722015979 dimer interface [polypeptide binding]; other site 557722015980 conserved gate region; other site 557722015981 putative PBP binding loops; other site 557722015982 ABC-ATPase subunit interface; other site 557722015983 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557722015984 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722015985 dimer interface [polypeptide binding]; other site 557722015986 conserved gate region; other site 557722015987 putative PBP binding loops; other site 557722015988 ABC-ATPase subunit interface; other site 557722015989 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722015990 Helix-turn-helix domains; Region: HTH; cl00088 557722015991 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557722015992 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557722015993 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 557722015994 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722015995 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722015996 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557722015997 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722015998 putative substrate translocation pore; other site 557722015999 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016000 potential protein location (hypothetical protein PLES_55521 [Pseudomonas aeruginosa LESB58]) that overlaps RNA (tRNA-T) 557722016001 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 557722016002 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 557722016003 NAD binding site [chemical binding]; other site 557722016004 substrate binding site [chemical binding]; other site 557722016005 homodimer interface [polypeptide binding]; other site 557722016006 active site 557722016007 dTDP-4-dehydrorhamnose reductase; Region: rmlD; TIGR01214 557722016008 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 557722016009 NADP binding site [chemical binding]; other site 557722016010 active site 557722016011 putative substrate binding site [chemical binding]; other site 557722016012 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 557722016013 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 557722016014 substrate binding site; other site 557722016015 tetramer interface; other site 557722016016 Cupin domain; Region: Cupin_2; cl09118 557722016017 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 557722016018 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722016019 dimer interface [polypeptide binding]; other site 557722016020 phosphorylation site [posttranslational modification] 557722016021 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722016022 ATP binding site [chemical binding]; other site 557722016023 Mg2+ binding site [ion binding]; other site 557722016024 G-X-G motif; other site 557722016025 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722016026 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722016027 active site 557722016028 phosphorylation site [posttranslational modification] 557722016029 intermolecular recognition site; other site 557722016030 dimerization interface [polypeptide binding]; other site 557722016031 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722016032 Walker A motif; other site 557722016033 ATP binding site [chemical binding]; other site 557722016034 Walker B motif; other site 557722016035 arginine finger; other site 557722016036 Helix-turn-helix domains; Region: HTH; cl00088 557722016037 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 557722016038 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 557722016039 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 557722016040 DctM-like transporters; Region: DctM; pfam06808 557722016041 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 557722016042 arginine/ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557722016043 Amidinotransferase; Region: Amidinotransf; cl12043 557722016044 ornithine carbamoyltransferase; Validated; Region: PRK02102 557722016045 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557722016046 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016047 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 557722016048 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 557722016049 putative substrate binding site [chemical binding]; other site 557722016050 nucleotide binding site [chemical binding]; other site 557722016051 nucleotide binding site [chemical binding]; other site 557722016052 homodimer interface [polypeptide binding]; other site 557722016053 'elongating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type I and II and polyketide synthases.They are characterized by the utlization of acyl carrier protein (ACP) thioesters as...; Region: elong_cond_enzymes; cd00828 557722016054 active site 557722016055 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 557722016056 active site 557722016057 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 557722016058 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 557722016059 dimer interface [polypeptide binding]; other site 557722016060 ADP-ribose binding site [chemical binding]; other site 557722016061 active site 557722016062 nudix motif; other site 557722016063 metal binding site [ion binding]; metal-binding site 557722016064 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 557722016065 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722016066 motif II; other site 557722016067 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 557722016068 BON domain; Region: BON; cl02771 557722016069 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 557722016070 putative peptidoglycan binding site; other site 557722016071 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722016072 Helix-turn-helix domains; Region: HTH; cl00088 557722016073 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722016074 dimerization interface [polypeptide binding]; other site 557722016075 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 557722016076 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 557722016077 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 557722016078 putative molybdopterin cofactor binding site [chemical binding]; other site 557722016079 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 557722016080 putative molybdopterin cofactor binding site; other site 557722016081 Global regulator protein family; Region: CsrA; cl00670 557722016082 Chorismate mutase type II; Region: CM_2; cl00693 557722016083 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722016084 active site 557722016085 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 557722016086 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 557722016087 active site 557722016088 NAD binding site [chemical binding]; other site 557722016089 metal binding site [ion binding]; metal-binding site 557722016090 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557722016091 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557722016092 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557722016093 active site 557722016094 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557722016095 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 557722016096 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016097 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722016098 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722016099 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722016100 Helix-turn-helix domains; Region: HTH; cl00088 557722016101 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722016102 dimerization interface [polypeptide binding]; other site 557722016103 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 557722016104 dimer interface [polypeptide binding]; other site 557722016105 FMN binding site [chemical binding]; other site 557722016106 Fimbrial protein; Region: Fimbrial; cl01416 557722016107 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 557722016108 active site 557722016109 substrate-binding site [chemical binding]; other site 557722016110 metal-binding site [ion binding] 557722016111 ATP binding site [chemical binding]; other site 557722016112 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 557722016113 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 557722016114 dimerization interface [polypeptide binding]; other site 557722016115 domain crossover interface; other site 557722016116 redox-dependent activation switch; other site 557722016117 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 557722016118 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 557722016119 RNA binding surface [nucleotide binding]; other site 557722016120 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 557722016121 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 557722016122 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722016123 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 557722016124 dimer interface [polypeptide binding]; other site 557722016125 catalytic triad [active] 557722016126 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 557722016127 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 557722016128 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722016129 ATP binding site [chemical binding]; other site 557722016130 Mg2+ binding site [ion binding]; other site 557722016131 G-X-G motif; other site 557722016132 osmolarity response regulator; Provisional; Region: ompR; PRK09468 557722016133 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722016134 active site 557722016135 phosphorylation site [posttranslational modification] 557722016136 intermolecular recognition site; other site 557722016137 dimerization interface [polypeptide binding]; other site 557722016138 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722016139 DNA binding site [nucleotide binding] 557722016140 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 557722016141 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 557722016142 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 557722016143 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 557722016144 RNA binding site [nucleotide binding]; other site 557722016145 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722016146 CoenzymeA binding site [chemical binding]; other site 557722016147 subunit interaction site [polypeptide binding]; other site 557722016148 PHB binding site; other site 557722016149 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl15791 557722016150 N-acetylglutamate synthase; Validated; Region: PRK05279 557722016151 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 557722016152 putative feedback inhibition sensing region; other site 557722016153 putative nucleotide binding site [chemical binding]; other site 557722016154 putative substrate binding site [chemical binding]; other site 557722016155 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557722016156 Coenzyme A binding pocket [chemical binding]; other site 557722016157 MarC family integral membrane protein; Region: MarC; cl00919 557722016158 acetylornithine deacetylase; Provisional; Region: PRK05111 557722016159 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 557722016160 metal binding site [ion binding]; metal-binding site 557722016161 putative dimer interface [polypeptide binding]; other site 557722016162 Phosphate transporter family; Region: PHO4; cl00396 557722016163 Phosphate transporter family; Region: PHO4; cl00396 557722016164 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 557722016165 Uncharacterized conserved protein [Function unknown]; Region: COG3025 557722016166 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 557722016167 putative active site [active] 557722016168 putative metal binding residues [ion binding]; other site 557722016169 signature motif; other site 557722016170 putative triphosphate binding site [ion binding]; other site 557722016171 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 557722016172 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 557722016173 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 557722016174 Walker A motif; other site 557722016175 ATP binding site [chemical binding]; other site 557722016176 Walker B motif; other site 557722016177 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 557722016178 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 557722016179 glycine dehydrogenase; Provisional; Region: PRK12566 557722016180 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 557722016181 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557722016182 catalytic residue [active] 557722016183 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 557722016184 tetramer interface [polypeptide binding]; other site 557722016185 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722016186 catalytic residue [active] 557722016187 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 557722016188 lipoyl attachment site [posttranslational modification]; other site 557722016189 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 557722016190 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 557722016191 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 557722016192 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722016193 dimer interface [polypeptide binding]; other site 557722016194 conserved gate region; other site 557722016195 putative PBP binding loops; other site 557722016196 ABC-ATPase subunit interface; other site 557722016197 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722016198 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 557722016199 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 557722016200 Helix-turn-helix domains; Region: HTH; cl00088 557722016201 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 557722016202 dimerization interface [polypeptide binding]; other site 557722016203 substrate binding pocket [chemical binding]; other site 557722016204 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016205 putative substrate translocation pore; other site 557722016206 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557722016207 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK05714 557722016208 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016209 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722016210 CoenzymeA binding site [chemical binding]; other site 557722016211 subunit interaction site [polypeptide binding]; other site 557722016212 PHB binding site; other site 557722016213 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016214 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 557722016215 proline aminopeptidase P II; Provisional; Region: PRK10879 557722016216 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 557722016217 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 557722016218 active site 557722016219 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 557722016220 TIGR02449 family protein; Region: TIGR02449 557722016221 Cell division protein ZapA; Region: ZapA; cl01146 557722016222 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 557722016223 EVE domain; Region: EVE; cl00728 557722016224 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 557722016225 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722016226 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 557722016227 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016228 Walker A/P-loop; other site 557722016229 ATP binding site [chemical binding]; other site 557722016230 Q-loop/lid; other site 557722016231 ABC transporter signature motif; other site 557722016232 Walker B; other site 557722016233 D-loop; other site 557722016234 H-loop/switch region; other site 557722016235 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016236 Walker A/P-loop; other site 557722016237 ATP binding site [chemical binding]; other site 557722016238 Q-loop/lid; other site 557722016239 ABC transporter signature motif; other site 557722016240 Walker B; other site 557722016241 D-loop; other site 557722016242 H-loop/switch region; other site 557722016243 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 557722016244 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722016245 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557722016246 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722016247 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 557722016248 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 557722016249 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 557722016250 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 557722016251 NAD(P) binding site [chemical binding]; other site 557722016252 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 557722016253 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016254 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016255 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 557722016256 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722016257 catalytic loop [active] 557722016258 iron binding site [ion binding]; other site 557722016259 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 557722016260 FAD binding pocket [chemical binding]; other site 557722016261 FAD binding motif [chemical binding]; other site 557722016262 phosphate binding motif [ion binding]; other site 557722016263 beta-alpha-beta structure motif; other site 557722016264 NAD binding pocket [chemical binding]; other site 557722016265 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 557722016266 OpgC protein; Region: OpgC_C; cl00792 557722016267 Acyltransferase family; Region: Acyl_transf_3; pfam01757 557722016268 transcription termination factor Rho; Provisional; Region: rho; PRK09376 557722016269 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 557722016270 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 557722016271 RNA binding site [nucleotide binding]; other site 557722016272 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 557722016273 multimer interface [polypeptide binding]; other site 557722016274 Walker A motif; other site 557722016275 ATP binding site [chemical binding]; other site 557722016276 Walker B motif; other site 557722016277 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 557722016278 catalytic residues [active] 557722016279 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 557722016280 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 557722016281 polyphosphate kinase; Provisional; Region: PRK05443 557722016282 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 557722016283 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 557722016284 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 557722016285 putative domain interface [polypeptide binding]; other site 557722016286 putative active site [active] 557722016287 catalytic site [active] 557722016288 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 557722016289 putative domain interface [polypeptide binding]; other site 557722016290 putative active site [active] 557722016291 catalytic site [active] 557722016292 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 557722016293 dimer interface [polypeptide binding]; other site 557722016294 active site 557722016295 aspartate-rich active site metal binding site; other site 557722016296 allosteric magnesium binding site [ion binding]; other site 557722016297 Schiff base residues; other site 557722016298 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557722016299 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 557722016300 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 557722016301 conserved cys residue [active] 557722016302 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 557722016303 CoenzymeA binding site [chemical binding]; other site 557722016304 subunit interaction site [polypeptide binding]; other site 557722016305 PHB binding site; other site 557722016306 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 557722016307 Cytochrome c; Region: Cytochrom_C; cl11414 557722016308 Iron permease FTR1 family; Region: FTR1; cl00475 557722016309 LysE type translocator; Region: LysE; cl00565 557722016310 Integral membrane protein TerC family; Region: TerC; cl10468 557722016311 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557722016312 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 557722016313 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016314 Walker A/P-loop; other site 557722016315 ATP binding site [chemical binding]; other site 557722016316 Q-loop/lid; other site 557722016317 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722016318 ABC transporter signature motif; other site 557722016319 Walker B; other site 557722016320 D-loop; other site 557722016321 ABC transporter; Region: ABC_tran_2; pfam12848 557722016322 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 557722016323 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 557722016324 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 557722016325 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 557722016326 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 557722016327 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 557722016328 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 557722016329 HemY protein N-terminus; Region: HemY_N; pfam07219 557722016330 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 557722016331 binding surface 557722016332 TPR motif; other site 557722016333 HemX; Region: HemX; pfam04375 557722016334 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 557722016335 uroporphyrinogen-III synthase; Validated; Region: PRK05752 557722016336 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 557722016337 active site 557722016338 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 557722016339 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 557722016340 domain interfaces; other site 557722016341 active site 557722016342 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 557722016343 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722016344 active site 557722016345 phosphorylation site [posttranslational modification] 557722016346 intermolecular recognition site; other site 557722016347 dimerization interface [polypeptide binding]; other site 557722016348 LytTr DNA-binding domain; Region: LytTR; cl04498 557722016349 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 557722016350 Histidine kinase; Region: His_kinase; pfam06580 557722016351 argininosuccinate lyase; Provisional; Region: PRK00855 557722016352 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 557722016353 active sites [active] 557722016354 tetramer interface [polypeptide binding]; other site 557722016355 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 557722016356 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557722016357 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 557722016358 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 557722016359 Protein of unknown function (DUF796); Region: DUF796; cl01226 557722016360 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 557722016361 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 557722016362 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 557722016363 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 557722016364 substrate binding pocket [chemical binding]; other site 557722016365 membrane-bound complex binding site; other site 557722016366 hinge residues; other site 557722016367 Phosphate-starvation-inducible E; Region: PsiE; cl01264 557722016368 Adenylate cyclase [Nucleotide transport and metabolism]; Region: CyaA; COG3072 557722016369 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 557722016370 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 557722016371 adenylate cyclase; Provisional; Region: cyaA; PRK09450 557722016372 Uncharacterized conserved protein [Function unknown]; Region: COG4278 557722016373 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 557722016374 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557722016375 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 557722016376 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 557722016377 putative iron binding site [ion binding]; other site 557722016378 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 557722016379 diaminopimelate decarboxylase; Region: lysA; TIGR01048 557722016380 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 557722016381 active site 557722016382 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722016383 substrate binding site [chemical binding]; other site 557722016384 catalytic residues [active] 557722016385 dimer interface [polypeptide binding]; other site 557722016386 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 557722016387 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722016388 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 557722016389 GAF domain; Region: GAF; cl15785 557722016390 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 557722016391 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 557722016392 DNA binding site [nucleotide binding] 557722016393 Int/Topo IB signature motif; other site 557722016394 active site 557722016395 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 557722016396 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 557722016397 motif II; other site 557722016398 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722016399 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722016400 DNA-binding site [nucleotide binding]; DNA binding site 557722016401 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722016402 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722016403 homodimer interface [polypeptide binding]; other site 557722016404 catalytic residue [active] 557722016405 Fimbrial protein; Region: Fimbrial; cl01416 557722016406 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 557722016407 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 557722016408 Nitrogen regulatory protein P-II; Region: P-II; cl00412 557722016409 Nitrogen regulatory protein P-II; Region: P-II; smart00938 557722016410 Membrane fusogenic activity; Region: BMFP; cl01115 557722016411 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 557722016412 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 557722016413 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016414 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 557722016415 BCCT family transporter; Region: BCCT; cl00569 557722016416 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722016417 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557722016418 Helix-turn-helix domains; Region: HTH; cl00088 557722016419 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 557722016420 dimerization interface [polypeptide binding]; other site 557722016421 substrate binding pocket [chemical binding]; other site 557722016422 multidrug efflux protein NorA; Provisional; Region: PRK00187 557722016423 MatE; Region: MatE; cl10513 557722016424 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 557722016425 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 557722016426 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 557722016427 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016428 Family description; Region: UvrD_C_2; cl15862 557722016429 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 557722016430 pyruvate oxidase; Region: pyruv_oxi_spxB; TIGR02720 557722016431 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 557722016432 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 557722016433 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 557722016434 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722016435 active site 557722016436 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 557722016437 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722016438 Cytochrome c; Region: Cytochrom_C; cl11414 557722016439 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 557722016440 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 557722016441 non-specific DNA binding site [nucleotide binding]; other site 557722016442 salt bridge; other site 557722016443 sequence-specific DNA binding site [nucleotide binding]; other site 557722016444 Cupin domain; Region: Cupin_2; cl09118 557722016445 alanine racemase; Reviewed; Region: dadX; PRK03646 557722016446 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 557722016447 active site 557722016448 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722016449 substrate binding site [chemical binding]; other site 557722016450 catalytic residues [active] 557722016451 dimer interface [polypeptide binding]; other site 557722016452 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 557722016453 homotrimer interaction site [polypeptide binding]; other site 557722016454 putative active site [active] 557722016455 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 557722016456 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016457 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 557722016458 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 557722016459 Dicarboxylate transport; Region: DctA-YdbH; cl14674 557722016460 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557722016461 Helix-turn-helix domains; Region: HTH; cl00088 557722016462 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016463 FAD dependent oxidoreductase; Region: DAO; pfam01266 557722016464 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 557722016465 PLD-like domain; Region: PLDc_2; pfam13091 557722016466 putative active site [active] 557722016467 catalytic site [active] 557722016468 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 557722016469 putative active site [active] 557722016470 catalytic site [active] 557722016471 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016472 putative substrate translocation pore; other site 557722016473 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 557722016474 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 557722016475 NAD(P) binding site [chemical binding]; other site 557722016476 catalytic residues [active] 557722016477 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 557722016478 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722016479 inhibitor-cofactor binding pocket; inhibition site 557722016480 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722016481 catalytic residue [active] 557722016482 Cupin domain; Region: Cupin_2; cl09118 557722016483 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 557722016484 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 557722016485 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557722016486 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557722016487 peptide binding site [polypeptide binding]; other site 557722016488 hypothetical protein; Reviewed; Region: PRK00024 557722016489 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 557722016490 MPN+ (JAMM) motif; other site 557722016491 Zinc-binding site [ion binding]; other site 557722016492 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 557722016493 Flavoprotein; Region: Flavoprotein; cl08021 557722016494 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 557722016495 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 557722016496 trimer interface [polypeptide binding]; other site 557722016497 active site 557722016498 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 557722016499 phosphoglucosamine mutase; Region: Arch_GlmM; TIGR03990 557722016500 active site 557722016501 substrate binding site [chemical binding]; other site 557722016502 metal binding site [ion binding]; metal-binding site 557722016503 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 557722016504 feedback inhibition sensing region; other site 557722016505 homohexameric interface [polypeptide binding]; other site 557722016506 nucleotide binding site [chemical binding]; other site 557722016507 N-acetyl-L-glutamate binding site [chemical binding]; other site 557722016508 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 557722016509 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722016510 SurA N-terminal domain; Region: SurA_N_3; cl07813 557722016511 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722016512 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557722016513 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 557722016514 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3; Region: PLPDE_III_DSD_D-TA_like_3; cd06814 557722016515 dimer interface [polypeptide binding]; other site 557722016516 active site 557722016517 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557722016518 substrate binding site [chemical binding]; other site 557722016519 catalytic residue [active] 557722016520 FAD-linked oxidoreductase; Region: bact_FAD_ox; TIGR01679 557722016521 FAD binding domain; Region: FAD_binding_4; pfam01565 557722016522 D-arabinono-1,4-lactone oxidase; Region: ALO; cl04370 557722016523 Cytochrome c; Region: Cytochrom_C; cl11414 557722016524 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722016525 active site 557722016526 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 557722016527 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557722016528 active site 557722016529 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 557722016530 putative active site [active] 557722016531 putative DNA binding site [nucleotide binding]; other site 557722016532 putative phosphate binding site [ion binding]; other site 557722016533 putative catalytic site [active] 557722016534 metal binding site A [ion binding]; metal-binding site 557722016535 putative AP binding site [nucleotide binding]; other site 557722016536 putative metal binding site B [ion binding]; other site 557722016537 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296; cl15800 557722016538 ribonuclease PH; Reviewed; Region: rph; PRK00173 557722016539 Ribonuclease PH; Region: RNase_PH_bact; cd11362 557722016540 hexamer interface [polypeptide binding]; other site 557722016541 active site 557722016542 hypothetical protein; Provisional; Region: PRK11820 557722016543 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 557722016544 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 557722016545 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 557722016546 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 557722016547 catalytic site [active] 557722016548 G-X2-G-X-G-K; other site 557722016549 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 557722016550 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 557722016551 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 557722016552 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 557722016553 synthetase active site [active] 557722016554 NTP binding site [chemical binding]; other site 557722016555 metal binding site [ion binding]; metal-binding site 557722016556 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 557722016557 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 557722016558 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 557722016559 homotrimer interaction site [polypeptide binding]; other site 557722016560 putative active site [active] 557722016561 LysE type translocator; Region: LysE; cl00565 557722016562 Cupin domain; Region: Cupin_2; cl09118 557722016563 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557722016564 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722016565 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557722016566 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 557722016567 putative NAD(P) binding site [chemical binding]; other site 557722016568 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 557722016569 Helix-turn-helix domains; Region: HTH; cl00088 557722016570 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 557722016571 dimerization interface [polypeptide binding]; other site 557722016572 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 557722016573 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 557722016574 ssDNA binding site; other site 557722016575 generic binding surface II; other site 557722016576 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 557722016577 ATP binding site [chemical binding]; other site 557722016578 putative Mg++ binding site [ion binding]; other site 557722016579 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 557722016580 nucleotide binding region [chemical binding]; other site 557722016581 ATP-binding site [chemical binding]; other site 557722016582 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 557722016583 putative deacylase active site [active] 557722016584 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 557722016585 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 557722016586 IHF dimer interface [polypeptide binding]; other site 557722016587 IHF - DNA interface [nucleotide binding]; other site 557722016588 NADH:flavorubredoxin oxidoreductase; Provisional; Region: PRK04965 557722016589 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557722016590 Rubredoxin [Energy production and conversion]; Region: COG1773 557722016591 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 557722016592 iron binding site [ion binding]; other site 557722016593 Rubredoxin [Energy production and conversion]; Region: COG1773 557722016594 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 557722016595 iron binding site [ion binding]; other site 557722016596 Domain of unknown function (DUF336); Region: DUF336; cl01249 557722016597 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 557722016598 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 557722016599 Cysteine-rich domain; Region: CCG; pfam02754 557722016600 Cysteine-rich domain; Region: CCG; pfam02754 557722016601 FAD binding domain; Region: FAD_binding_4; pfam01565 557722016602 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 557722016603 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 557722016604 FAD binding domain; Region: FAD_binding_4; pfam01565 557722016605 DNA-binding transcriptional regulator GlcC; Provisional; Region: PRK09990 557722016606 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722016607 DNA-binding site [nucleotide binding]; DNA binding site 557722016608 FCD domain; Region: FCD; cl11656 557722016609 UTRA domain; Region: UTRA; cl01230 557722016610 UbiA prenyltransferase family; Region: UbiA; cl00337 557722016611 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4315 557722016612 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 557722016613 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 557722016614 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 557722016615 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722016616 active site 557722016617 phosphorylation site [posttranslational modification] 557722016618 intermolecular recognition site; other site 557722016619 dimerization interface [polypeptide binding]; other site 557722016620 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 557722016621 DNA binding site [nucleotide binding] 557722016622 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 557722016623 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557722016624 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722016625 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722016626 dimer interface [polypeptide binding]; other site 557722016627 phosphorylation site [posttranslational modification] 557722016628 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722016629 ATP binding site [chemical binding]; other site 557722016630 Mg2+ binding site [ion binding]; other site 557722016631 G-X-G motif; other site 557722016632 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 557722016633 Domain of unknown function DUF21; Region: DUF21; pfam01595 557722016634 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 557722016635 Transporter associated domain; Region: CorC_HlyC; cl08393 557722016636 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557722016637 Peptidase family M23; Region: Peptidase_M23; pfam01551 557722016638 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722016639 Response regulator receiver domain; Region: Response_reg; pfam00072 557722016640 active site 557722016641 phosphorylation site [posttranslational modification] 557722016642 intermolecular recognition site; other site 557722016643 dimerization interface [polypeptide binding]; other site 557722016644 transcriptional regulator PhoU; Provisional; Region: PRK11115 557722016645 PhoU domain; Region: PhoU; pfam01895 557722016646 PhoU domain; Region: PhoU; pfam01895 557722016647 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 557722016648 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 557722016649 Walker A/P-loop; other site 557722016650 ATP binding site [chemical binding]; other site 557722016651 Q-loop/lid; other site 557722016652 ABC transporter signature motif; other site 557722016653 Walker B; other site 557722016654 D-loop; other site 557722016655 H-loop/switch region; other site 557722016656 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 557722016657 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722016658 dimer interface [polypeptide binding]; other site 557722016659 conserved gate region; other site 557722016660 putative PBP binding loops; other site 557722016661 ABC-ATPase subunit interface; other site 557722016662 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 557722016663 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722016664 ABC-ATPase subunit interface; other site 557722016665 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 557722016666 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016667 metabolite-proton symporter; Region: 2A0106; TIGR00883 557722016668 putative substrate translocation pore; other site 557722016669 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 557722016670 choline dehydrogenase; Validated; Region: PRK02106 557722016671 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557722016672 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557722016673 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 557722016674 tetrameric interface [polypeptide binding]; other site 557722016675 NAD binding site [chemical binding]; other site 557722016676 catalytic residues [active] 557722016677 transcriptional regulator BetI; Validated; Region: PRK00767 557722016678 Helix-turn-helix domains; Region: HTH; cl00088 557722016679 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 557722016680 BCCT family transporter; Region: BCCT; cl00569 557722016681 choline ABC transporter, ATP-binding protein; Region: ABC_choXWV_ATP; TIGR03415 557722016682 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016683 Walker A/P-loop; other site 557722016684 ATP binding site [chemical binding]; other site 557722016685 Q-loop/lid; other site 557722016686 ABC transporter signature motif; other site 557722016687 Walker B; other site 557722016688 D-loop; other site 557722016689 H-loop/switch region; other site 557722016690 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722016691 dimer interface [polypeptide binding]; other site 557722016692 conserved gate region; other site 557722016693 putative PBP binding loops; other site 557722016694 ABC-ATPase subunit interface; other site 557722016695 NMT1-like family; Region: NMT1_2; cl15260 557722016696 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 557722016697 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 557722016698 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 557722016699 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 557722016700 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 557722016701 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 557722016702 conserved cys residue [active] 557722016703 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722016704 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 557722016705 Helix-turn-helix domains; Region: HTH; cl00088 557722016706 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 557722016707 putative dimerization interface [polypeptide binding]; other site 557722016708 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 557722016709 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 557722016710 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 557722016711 active site 557722016712 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07066 557722016713 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016714 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557722016715 Prokaryotic protein of unknown function (DUF849); Region: DUF849; cl15827 557722016716 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 557722016717 NMT1-like family; Region: NMT1_2; cl15260 557722016718 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 557722016719 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 557722016720 conserved cys residue [active] 557722016721 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557722016722 acetylornithine deacetylase (ArgE); Region: AcOrn-deacetyl; TIGR01892 557722016723 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 557722016724 metal binding site [ion binding]; metal-binding site 557722016725 putative dimer interface [polypeptide binding]; other site 557722016726 Family of unknown function (DUF1028); Region: DUF1028; pfam06267 557722016727 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 557722016728 homotrimer interaction site [polypeptide binding]; other site 557722016729 putative active site [active] 557722016730 flavin-dependent oxidoreductase, MSMEG_0569 family; Region: MSMEG_0569_nitr; TIGR04046 557722016731 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016732 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 557722016733 Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Region: PLDc_PaCLS_like_1; cd09155 557722016734 putative active site [active] 557722016735 catalytic site [active] 557722016736 Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins; Region: PLDc_PaCLS_like_2; cd09161 557722016737 putative active site [active] 557722016738 catalytic site [active] 557722016739 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 557722016740 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 557722016741 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 557722016742 active site 557722016743 dimer interface [polypeptide binding]; other site 557722016744 Heme NO binding; Region: HNOB; cl15268 557722016745 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 557722016746 Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_3_FMN; cd04734 557722016747 putative active site [active] 557722016748 putative FMN binding site [chemical binding]; other site 557722016749 putative substrate binding site [chemical binding]; other site 557722016750 putative catalytic residue [active] 557722016751 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016752 Domain of unknown function (DUF3483); Region: DUF3483; pfam11982 557722016753 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 557722016754 Cysteine-rich domain; Region: CCG; pfam02754 557722016755 Cysteine-rich domain; Region: CCG; pfam02754 557722016756 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 557722016757 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 557722016758 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 557722016759 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 557722016760 Ligand Binding Site [chemical binding]; other site 557722016761 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 557722016762 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 557722016763 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 557722016764 Cell division protein ZapA; Region: ZapA; cl01146 557722016765 Short repeat of unknown function (DUF308); Region: DUF308; cl15828 557722016766 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 557722016767 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 557722016768 [2Fe-2S] cluster binding site [ion binding]; other site 557722016769 C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_GbcA-like; cd08884 557722016770 putative alpha subunit interface [polypeptide binding]; other site 557722016771 putative active site [active] 557722016772 putative substrate binding site [chemical binding]; other site 557722016773 Fe binding site [ion binding]; other site 557722016774 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 557722016775 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 557722016776 FAD binding pocket [chemical binding]; other site 557722016777 FAD binding motif [chemical binding]; other site 557722016778 phosphate binding motif [ion binding]; other site 557722016779 beta-alpha-beta structure motif; other site 557722016780 NAD binding pocket [chemical binding]; other site 557722016781 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 557722016782 catalytic loop [active] 557722016783 iron binding site [ion binding]; other site 557722016784 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 557722016785 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 557722016786 tetramer interface [polypeptide binding]; other site 557722016787 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722016788 catalytic residue [active] 557722016789 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 557722016790 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 557722016791 dimer interface [polypeptide binding]; other site 557722016792 glycine-pyridoxal phosphate binding site [chemical binding]; other site 557722016793 active site 557722016794 folate binding site [chemical binding]; other site 557722016795 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 557722016796 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016797 Sarcosine oxidase, delta subunit family; Region: SoxD; cl01767 557722016798 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 557722016799 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 557722016800 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 557722016801 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 557722016802 formyltetrahydrofolate deformylase; Reviewed; Region: PRK13011 557722016803 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 557722016804 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 557722016805 putative active site [active] 557722016806 putative substrate binding site [chemical binding]; other site 557722016807 putative cosubstrate binding site; other site 557722016808 catalytic site [active] 557722016809 formaldehyde dehydrogenase, glutathione-independent; Region: fdhA_non_GSH; TIGR02819 557722016810 Pseudomonas putida aldehyde-dismutating formaldehyde dehydrogenase (PFDH); Region: PFDH_like; cd08282 557722016811 NAD binding site [chemical binding]; other site 557722016812 catalytic Zn binding site [ion binding]; other site 557722016813 structural Zn binding site [ion binding]; other site 557722016814 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 557722016815 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 557722016816 active site 557722016817 phosphate binding residues; other site 557722016818 catalytic residues [active] 557722016819 Protein of unknown function (DUF3299); Region: DUF3299; cl01387 557722016820 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 557722016821 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722016822 AIR carboxylase; Region: AIRC; cl00310 557722016823 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 557722016824 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 557722016825 NAD binding site [chemical binding]; other site 557722016826 substrate binding site [chemical binding]; other site 557722016827 catalytic Zn binding site [ion binding]; other site 557722016828 tetramer interface [polypeptide binding]; other site 557722016829 structural Zn binding site [ion binding]; other site 557722016830 cell density-dependent motility repressor; Provisional; Region: PRK10082 557722016831 Helix-turn-helix domains; Region: HTH; cl00088 557722016832 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 557722016833 dimerization interface [polypeptide binding]; other site 557722016834 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 557722016835 Aspartase; Region: Aspartase; cd01357 557722016836 active sites [active] 557722016837 tetramer interface [polypeptide binding]; other site 557722016838 putative inner membrane protein; Provisional; Region: PRK11099 557722016839 Sulphur transport; Region: Sulf_transp; cl01018 557722016840 putative inner membrane protein; Provisional; Region: PRK11099 557722016841 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 557722016842 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722016843 DNA-binding site [nucleotide binding]; DNA binding site 557722016844 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 557722016845 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722016846 homodimer interface [polypeptide binding]; other site 557722016847 catalytic residue [active] 557722016848 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722016849 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557722016850 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722016851 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 557722016852 aromatic amino acid transport protein; Region: araaP; TIGR00837 557722016853 pyruvate carboxylase subunit B; Validated; Region: PRK09282 557722016854 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 557722016855 active site 557722016856 catalytic residues [active] 557722016857 metal binding site [ion binding]; metal-binding site 557722016858 homodimer binding site [polypeptide binding]; other site 557722016859 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 557722016860 carboxyltransferase (CT) interaction site; other site 557722016861 biotinylation site [posttranslational modification]; other site 557722016862 pyruvate carboxylase subunit A; Validated; Region: PRK07178 557722016863 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557722016864 ATP-grasp domain; Region: ATP-grasp_4; cl03087 557722016865 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 557722016866 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557722016867 Helix-turn-helix domains; Region: HTH; cl00088 557722016868 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 557722016869 putative dimerization interface [polypeptide binding]; other site 557722016870 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 557722016871 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 557722016872 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 557722016873 putative active site [active] 557722016874 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 557722016875 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 557722016876 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 557722016877 putative protease; Provisional; Region: PRK15452 557722016878 Peptidase family U32; Region: Peptidase_U32; cl03113 557722016879 PAS fold; Region: PAS_3; pfam08447 557722016880 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 557722016881 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 557722016882 PAS domain; Region: PAS_9; pfam13426 557722016883 putative active site [active] 557722016884 heme pocket [chemical binding]; other site 557722016885 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557722016886 metal binding site [ion binding]; metal-binding site 557722016887 active site 557722016888 I-site; other site 557722016889 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 557722016890 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 557722016891 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722016892 Family description; Region: UvrD_C_2; cl15862 557722016893 EamA-like transporter family; Region: EamA; cl01037 557722016894 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 557722016895 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 557722016896 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722016897 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 557722016898 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557722016899 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_4; cd03795 557722016900 putative ADP-binding pocket [chemical binding]; other site 557722016901 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 557722016902 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 557722016903 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 557722016904 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 557722016905 Walker A/P-loop; other site 557722016906 ATP binding site [chemical binding]; other site 557722016907 Q-loop/lid; other site 557722016908 ABC transporter signature motif; other site 557722016909 Walker B; other site 557722016910 D-loop; other site 557722016911 H-loop/switch region; other site 557722016912 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 557722016913 putative carbohydrate binding site [chemical binding]; other site 557722016914 ABC-2 type transporter; Region: ABC2_membrane; cl11417 557722016915 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 557722016916 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 557722016917 Substrate binding site; other site 557722016918 Cupin domain; Region: Cupin_2; cl09118 557722016919 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016920 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 557722016921 NAD(P) binding site [chemical binding]; other site 557722016922 active site 557722016923 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722016924 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 557722016925 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cd01635 557722016926 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557722016927 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016928 OpgC protein; Region: OpgC_C; cl00792 557722016929 OpgC protein; Region: OpgC_C; cl00792 557722016930 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722016931 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 557722016932 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 557722016933 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 557722016934 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 557722016935 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 557722016936 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 557722016937 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 557722016938 Membrane transport protein; Region: Mem_trans; cl09117 557722016939 Protein of unknown function (DUF2388); Region: DUF2388; cl09731 557722016940 Citrate transporter; Region: CitMHS; pfam03600 557722016941 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 557722016942 transmembrane helices; other site 557722016943 Integral membrane protein TerC family; Region: TerC; cl10468 557722016944 RF-1 domain; Region: RF-1; cl02875 557722016945 hypothetical protein; Reviewed; Region: PRK09588 557722016946 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl15780 557722016947 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl15306 557722016948 substrate binding pocket [chemical binding]; other site 557722016949 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557722016950 membrane-bound complex binding site; other site 557722016951 hinge residues; other site 557722016952 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 557722016953 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 557722016954 PhoU domain; Region: PhoU; pfam01895 557722016955 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 557722016956 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 557722016957 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557722016958 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 557722016959 citrate-proton symporter; Provisional; Region: PRK15075 557722016960 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722016961 putative substrate translocation pore; other site 557722016962 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 557722016963 Nucleoside recognition; Region: Gate; cl00486 557722016964 Nucleoside recognition; Region: Gate; cl00486 557722016965 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 557722016966 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557722016967 Inhibitor of vertebrate lysozyme (Ivy); Region: Ivy; cl07428 557722016968 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722016969 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722016970 active site 557722016971 phosphorylation site [posttranslational modification] 557722016972 intermolecular recognition site; other site 557722016973 dimerization interface [polypeptide binding]; other site 557722016974 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722016975 Walker A motif; other site 557722016976 ATP binding site [chemical binding]; other site 557722016977 Walker B motif; other site 557722016978 arginine finger; other site 557722016979 Helix-turn-helix domains; Region: HTH; cl00088 557722016980 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 557722016981 dimerization interface [polypeptide binding]; other site 557722016982 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557722016983 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 557722016984 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722016985 dimer interface [polypeptide binding]; other site 557722016986 phosphorylation site [posttranslational modification] 557722016987 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722016988 ATP binding site [chemical binding]; other site 557722016989 Mg2+ binding site [ion binding]; other site 557722016990 G-X-G motif; other site 557722016991 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 557722016992 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 557722016993 amidase catalytic site [active] 557722016994 Zn binding residues [ion binding]; other site 557722016995 substrate binding site [chemical binding]; other site 557722016996 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 557722016997 MarC family integral membrane protein; Region: MarC; cl00919 557722016998 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 557722016999 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 557722017000 putative catalytic site [active] 557722017001 putative metal binding site [ion binding]; other site 557722017002 putative phosphate binding site [ion binding]; other site 557722017003 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 557722017004 putative catalytic site [active] 557722017005 putative phosphate binding site [ion binding]; other site 557722017006 putative metal binding site [ion binding]; other site 557722017007 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 557722017008 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 557722017009 catalytic residues [active] 557722017010 hinge region; other site 557722017011 alpha helical domain; other site 557722017012 Cytochrome c; Region: Cytochrom_C; cl11414 557722017013 Cytochrome c; Region: Cytochrom_C; cl11414 557722017014 Cytochrome c; Region: Cytochrom_C; cl11414 557722017015 Predicted GTPase [General function prediction only]; Region: COG0218 557722017016 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 557722017017 G1 box; other site 557722017018 GTP/Mg2+ binding site [chemical binding]; other site 557722017019 Switch I region; other site 557722017020 G2 box; other site 557722017021 G3 box; other site 557722017022 Switch II region; other site 557722017023 G4 box; other site 557722017024 G5 box; other site 557722017025 DNA polymerase I; Provisional; Region: PRK05755 557722017026 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 557722017027 active site 557722017028 metal binding site 1 [ion binding]; metal-binding site 557722017029 putative 5' ssDNA interaction site; other site 557722017030 metal binding site 3; metal-binding site 557722017031 metal binding site 2 [ion binding]; metal-binding site 557722017032 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 557722017033 putative DNA binding site [nucleotide binding]; other site 557722017034 putative metal binding site [ion binding]; other site 557722017035 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 557722017036 active site 557722017037 catalytic site [active] 557722017038 substrate binding site [chemical binding]; other site 557722017039 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 557722017040 active site 557722017041 DNA binding site [nucleotide binding] 557722017042 catalytic site [active] 557722017043 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 557722017044 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 557722017045 Phosphotransferase enzyme family; Region: APH; pfam01636 557722017046 putative active site [active] 557722017047 putative substrate binding site [chemical binding]; other site 557722017048 ATP binding site [chemical binding]; other site 557722017049 TSCPD domain; Region: TSCPD; cl14834 557722017050 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 557722017051 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 557722017052 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 557722017053 active site 557722017054 dimer interface [polypeptide binding]; other site 557722017055 effector binding site; other site 557722017056 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 557722017057 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 557722017058 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 557722017059 metal binding site [ion binding]; metal-binding site 557722017060 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 557722017061 metal binding site 2 [ion binding]; metal-binding site 557722017062 putative DNA binding helix; other site 557722017063 metal binding site 1 [ion binding]; metal-binding site 557722017064 dimer interface [polypeptide binding]; other site 557722017065 structural Zn2+ binding site [ion binding]; other site 557722017066 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 557722017067 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 557722017068 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 557722017069 dimer interface [polypeptide binding]; other site 557722017070 putative PBP binding regions; other site 557722017071 ABC-ATPase subunit interface; other site 557722017072 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 557722017073 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 557722017074 Walker A/P-loop; other site 557722017075 ATP binding site [chemical binding]; other site 557722017076 Q-loop/lid; other site 557722017077 ABC transporter signature motif; other site 557722017078 Walker B; other site 557722017079 D-loop; other site 557722017080 H-loop/switch region; other site 557722017081 NIL domain; Region: NIL; cl09633 557722017082 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 557722017083 dimer interface [polypeptide binding]; other site 557722017084 conserved gate region; other site 557722017085 ABC-ATPase subunit interface; other site 557722017086 NMT1-like family; Region: NMT1_2; cl15260 557722017087 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 557722017088 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 557722017089 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 557722017090 putative active site [active] 557722017091 Isochorismatase family; Region: Isochorismatase; pfam00857 557722017092 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 557722017093 catalytic triad [active] 557722017094 conserved cis-peptide bond; other site 557722017095 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722017096 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722017097 N-formylglutamate amidohydrolase; Region: FGase; cl01522 557722017098 amino acid transporter; Region: 2A0306; TIGR00909 557722017099 Spore germination protein; Region: Spore_permease; cl15802 557722017100 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557722017101 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 557722017102 active site 557722017103 phosphorylation site [posttranslational modification] 557722017104 intermolecular recognition site; other site 557722017105 dimerization interface [polypeptide binding]; other site 557722017106 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 557722017107 Walker A motif; other site 557722017108 ATP binding site [chemical binding]; other site 557722017109 Walker B motif; other site 557722017110 arginine finger; other site 557722017111 Helix-turn-helix domains; Region: HTH; cl00088 557722017112 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 557722017113 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 557722017114 dimer interface [polypeptide binding]; other site 557722017115 phosphorylation site [posttranslational modification] 557722017116 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 557722017117 ATP binding site [chemical binding]; other site 557722017118 Mg2+ binding site [ion binding]; other site 557722017119 G-X-G motif; other site 557722017120 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557722017121 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 557722017122 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722017123 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 557722017124 pyridoxamine kinase; Validated; Region: PRK05756 557722017125 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 557722017126 pyridoxal binding site [chemical binding]; other site 557722017127 dimer interface [polypeptide binding]; other site 557722017128 ATP binding site [chemical binding]; other site 557722017129 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557722017130 putative cation:proton antiport protein; Provisional; Region: PRK10669 557722017131 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557722017132 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722017133 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 557722017134 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722017135 classical (c) SDRs; Region: SDR_c; cd05233 557722017136 NAD(P) binding site [chemical binding]; other site 557722017137 active site 557722017138 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557722017139 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557722017140 aminotransferase; Validated; Region: PRK07046 557722017141 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 557722017142 inhibitor-cofactor binding pocket; inhibition site 557722017143 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557722017144 catalytic residue [active] 557722017145 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557722017146 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722017147 NAD(P) binding site [chemical binding]; other site 557722017148 active site 557722017149 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557722017150 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557722017151 DNA-binding site [nucleotide binding]; DNA binding site 557722017152 FCD domain; Region: FCD; cl11656 557722017153 Bacterial protein of unknown function (DUF903); Region: DUF903; pfam06004 557722017154 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 557722017155 Tim44-like domain; Region: Tim44; cl09208 557722017156 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 557722017157 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 557722017158 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 557722017159 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722017160 putative substrate translocation pore; other site 557722017161 Gram-negative bacterial tonB protein; Region: TonB; cl10048 557722017162 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722017163 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 557722017164 Protein of unknown function (DUF1826); Region: DUF1826; pfam08856 557722017165 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 557722017166 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 557722017167 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 557722017168 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557722017169 AMIN domain; Region: AMIN; pfam11741 557722017170 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 557722017171 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 557722017172 active site 557722017173 metal binding site [ion binding]; metal-binding site 557722017174 Type I GTP cyclohydrolase folE2; Region: GCHY-1; cl00642 557722017175 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 557722017176 Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed...; Region: LbH_gamma_CA; cd00710 557722017177 trimer interface [polypeptide binding]; other site 557722017178 active site 557722017179 dihydroorotase; Reviewed; Region: PRK09236 557722017180 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 557722017181 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 557722017182 active site 557722017183 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 557722017184 Domain of unknown function (DUF1850); Region: DUF1850; cl01950 557722017185 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 557722017186 DctM-like transporters; Region: DctM; pfam06808 557722017187 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 557722017188 NMT1-like family; Region: NMT1_2; cl15260 557722017189 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 557722017190 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 557722017191 S-adenosylmethionine binding site [chemical binding]; other site 557722017192 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 557722017193 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557722017194 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 557722017195 putative substrate translocation pore; other site 557722017196 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 557722017197 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 557722017198 glutaminase active site [active] 557722017199 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 557722017200 dimer interface [polypeptide binding]; other site 557722017201 active site 557722017202 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 557722017203 dimer interface [polypeptide binding]; other site 557722017204 active site 557722017205 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 557722017206 Helix-turn-helix domains; Region: HTH; cl00088 557722017207 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 557722017208 Peptidase family M23; Region: Peptidase_M23; pfam01551 557722017209 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 557722017210 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 557722017211 Substrate binding site; other site 557722017212 Mg++ binding site; other site 557722017213 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 557722017214 active site 557722017215 substrate binding site [chemical binding]; other site 557722017216 CoA binding site [chemical binding]; other site 557722017217 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 557722017218 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 557722017219 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 557722017220 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 557722017221 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 557722017222 alpha subunit interaction interface [polypeptide binding]; other site 557722017223 Walker A motif; other site 557722017224 ATP binding site [chemical binding]; other site 557722017225 Walker B motif; other site 557722017226 inhibitor binding site; inhibition site 557722017227 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 557722017228 ATP synthase; Region: ATP-synt; cl00365 557722017229 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 557722017230 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 557722017231 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 557722017232 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 557722017233 beta subunit interaction interface [polypeptide binding]; other site 557722017234 Walker A motif; other site 557722017235 ATP binding site [chemical binding]; other site 557722017236 Walker B motif; other site 557722017237 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 557722017238 Plant ATP synthase F0; Region: YMF19; cl07975 557722017239 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 557722017240 Plant ATP synthase F0; Region: YMF19; cl07975 557722017241 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 557722017242 ATP synthase subunit C; Region: ATP-synt_C; cl00466 557722017243 ATP synthase A chain; Region: ATP-synt_A; cl00413 557722017244 ATP synthase I chain; Region: ATP_synt_I; cl09170 557722017245 ParB-like partition proteins; Region: parB_part; TIGR00180 557722017246 ParB-like nuclease domain; Region: ParBc; cl02129 557722017247 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 557722017248 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722017249 P-loop; other site 557722017250 Magnesium ion binding site [ion binding]; other site 557722017251 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 557722017252 Magnesium ion binding site [ion binding]; other site 557722017253 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 557722017254 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 557722017255 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557722017256 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 557722017257 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 557722017258 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 557722017259 trmE is a tRNA modification GTPase; Region: trmE; cd04164 557722017260 G1 box; other site 557722017261 GTP/Mg2+ binding site [chemical binding]; other site 557722017262 Switch I region; other site 557722017263 G2 box; other site 557722017264 Switch II region; other site 557722017265 G3 box; other site 557722017266 G4 box; other site 557722017267 G5 box; other site 557722017268 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 557722017269 membrane protein insertase; Provisional; Region: PRK01318 557722017270 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 557722017271 Ribonuclease P; Region: Ribonuclease_P; cl00457