-- dump date 20120504_161621 -- class Genbank::misc_feature -- table misc_feature_note -- id note 319224000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 319224000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 319224000003 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 319224000004 Walker A motif; other site 319224000005 ATP binding site [chemical binding]; other site 319224000006 Walker B motif; other site 319224000007 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000008 arginine finger; other site 319224000009 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 319224000010 DnaA box-binding interface [nucleotide binding]; other site 319224000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 319224000012 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 319224000013 putative DNA binding surface [nucleotide binding]; other site 319224000014 dimer interface [polypeptide binding]; other site 319224000015 beta-clamp/clamp loader binding surface; other site 319224000016 beta-clamp/translesion DNA polymerase binding surface; other site 319224000017 recombination protein F; Reviewed; Region: recF; PRK00064 319224000018 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000019 Walker A/P-loop; other site 319224000020 ATP binding site [chemical binding]; other site 319224000021 Q-loop/lid; other site 319224000022 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000023 ABC transporter signature motif; other site 319224000024 Walker B; other site 319224000025 D-loop; other site 319224000026 H-loop/switch region; other site 319224000027 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 319224000028 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 319224000029 Mg2+ binding site [ion binding]; other site 319224000030 G-X-G motif; other site 319224000031 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 319224000032 anchoring element; other site 319224000033 dimer interface [polypeptide binding]; other site 319224000034 ATP binding site [chemical binding]; other site 319224000035 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 319224000036 active site 319224000037 putative metal-binding site [ion binding]; other site 319224000038 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 319224000039 HDOD domain; Region: HDOD; pfam08668 319224000040 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224000041 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 319224000042 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 319224000043 dimer interface [polypeptide binding]; other site 319224000044 motif 1; other site 319224000045 active site 319224000046 motif 2; other site 319224000047 motif 3; other site 319224000048 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 319224000049 tol-pal system beta propeller repeat protein TolB; Region: propeller_TolB; TIGR02800 319224000050 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224000051 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 319224000052 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 319224000053 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 319224000054 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 319224000055 active site 319224000056 MOSC domain; Region: MOSC; pfam03473 319224000057 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 319224000058 CPxP motif; other site 319224000059 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 319224000060 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 319224000061 dimer interface [polypeptide binding]; other site 319224000062 active site 319224000063 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 319224000064 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 319224000065 substrate binding site [chemical binding]; other site 319224000066 oxyanion hole (OAH) forming residues; other site 319224000067 trimer interface [polypeptide binding]; other site 319224000068 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000069 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 319224000070 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 319224000071 proline dipeptidase; Provisional; Region: PRK13607 319224000072 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 319224000073 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 319224000074 active site 319224000075 hypothetical protein; Provisional; Region: PRK11568 319224000076 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 319224000077 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 319224000078 Cation transport protein; Region: TrkH; cl10514 319224000079 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 319224000080 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224000081 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 319224000082 dimerization interface [polypeptide binding]; other site 319224000083 putative DNA binding site [nucleotide binding]; other site 319224000084 putative Zn2+ binding site [ion binding]; other site 319224000085 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224000086 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 319224000087 Cation transport protein; Region: TrkH; cl10514 319224000088 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 319224000089 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000090 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 319224000091 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000092 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 319224000093 16S rRNA methyltransferase B; Provisional; Region: PRK10901 319224000094 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 319224000095 putative RNA binding site [nucleotide binding]; other site 319224000096 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 319224000097 S-adenosylmethionine binding site [chemical binding]; other site 319224000098 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 319224000099 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 319224000100 putative active site [active] 319224000101 substrate binding site [chemical binding]; other site 319224000102 putative cosubstrate binding site; other site 319224000103 catalytic site [active] 319224000104 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 319224000105 substrate binding site [chemical binding]; other site 319224000106 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 319224000107 active site 319224000108 catalytic residues [active] 319224000109 metal binding site [ion binding]; metal-binding site 319224000110 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224000111 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 319224000112 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 319224000113 Protein of unknown function (DUF494); Region: DUF494; cl01103 319224000114 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 319224000115 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 319224000116 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 319224000117 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 319224000118 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 319224000119 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 319224000120 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 319224000121 apolar tunnel; other site 319224000122 heme binding site [chemical binding]; other site 319224000123 dimerization interface [polypeptide binding]; other site 319224000124 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 319224000125 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 319224000126 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 319224000127 shikimate binding site; other site 319224000128 NAD(P) binding site [chemical binding]; other site 319224000129 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 319224000130 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 319224000131 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 319224000132 trimer interface [polypeptide binding]; other site 319224000133 putative metal binding site [ion binding]; other site 319224000134 Flagellin N-methylase; Region: FliB; cl00497 319224000135 Helix-turn-helix domains; Region: HTH; cl00088 319224000136 Rrf2 family protein; Region: rrf2_super; TIGR00738 319224000137 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 319224000138 NodB motif; other site 319224000139 putative active site [active] 319224000140 putative catalytic site [active] 319224000141 Zn binding site [ion binding]; other site 319224000142 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 319224000143 C-terminal peptidase (prc); Region: prc; TIGR00225 319224000144 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 319224000145 protein binding site [polypeptide binding]; other site 319224000146 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 319224000147 Catalytic dyad [active] 319224000148 AmiB activator; Provisional; Region: PRK11637 319224000149 Sulfatase; Region: Sulfatase; cl10460 319224000150 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 319224000151 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 319224000152 active site residue [active] 319224000153 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 319224000154 SecA binding site; other site 319224000155 Preprotein binding site; other site 319224000156 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 319224000157 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000158 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 319224000159 HI0933-like protein; Region: HI0933_like; pfam03486 319224000160 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000161 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 319224000162 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224000163 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 319224000164 Cation transport protein; Region: TrkH; cl10514 319224000165 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 319224000166 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000167 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224000168 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 319224000169 active site 319224000170 phosphorylation site [posttranslational modification] 319224000171 intermolecular recognition site; other site 319224000172 dimerization interface [polypeptide binding]; other site 319224000173 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 319224000174 DNA binding site [nucleotide binding] 319224000175 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 319224000176 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 319224000177 dimer interface [polypeptide binding]; other site 319224000178 phosphorylation site [posttranslational modification] 319224000179 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 319224000180 ATP binding site [chemical binding]; other site 319224000181 Mg2+ binding site [ion binding]; other site 319224000182 G-X-G motif; other site 319224000183 Pirin-related protein [General function prediction only]; Region: COG1741 319224000184 Cupin domain; Region: Cupin_2; cl09118 319224000185 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 319224000186 F plasmid transfer operon, TraF, protein; Region: TraF_2; pfam13729 319224000187 NlpC/P60 family; Region: NLPC_P60; cl11438 319224000188 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 319224000189 MPT binding site; other site 319224000190 trimer interface [polypeptide binding]; other site 319224000191 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 319224000192 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224000193 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 319224000194 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000195 Walker A/P-loop; other site 319224000196 ATP binding site [chemical binding]; other site 319224000197 Q-loop/lid; other site 319224000198 ABC transporter signature motif; other site 319224000199 Walker B; other site 319224000200 D-loop; other site 319224000201 H-loop/switch region; other site 319224000202 proline-specific peptidases, Bacillus coagulans-type subfamily; Region: pro_imino_pep_2; TIGR01250 319224000203 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 319224000204 Predicted transcriptional regulators [Transcription]; Region: COG1725 319224000205 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224000206 DNA-binding site [nucleotide binding]; DNA binding site 319224000207 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 319224000208 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 319224000209 Walker A/P-loop; other site 319224000210 ATP binding site [chemical binding]; other site 319224000211 Q-loop/lid; other site 319224000212 ABC transporter signature motif; other site 319224000213 Walker B; other site 319224000214 D-loop; other site 319224000215 H-loop/switch region; other site 319224000216 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 319224000217 AMP-binding enzyme; Region: AMP-binding; cl15778 319224000218 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224000219 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224000220 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 319224000221 active site 319224000222 HPP family; Region: HPP; pfam04982 319224000223 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224000224 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 319224000225 active site 319224000226 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 319224000227 2,3-diketo-5-methylthio-1-phosphopentane phosphatase; Region: enolase-ppase; TIGR01691 319224000228 Membrane domain of glycerophosphoryl diester phosphodiesterase; Region: GPDPase_memb; cl01974 319224000229 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 319224000230 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_memb_like; cd08579 319224000231 putative active site [active] 319224000232 catalytic site [active] 319224000233 putative metal binding site [ion binding]; other site 319224000234 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 319224000235 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 319224000236 Helix-turn-helix domains; Region: HTH; cl00088 319224000237 Helix-turn-helix domains; Region: HTH; cl00088 319224000238 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 319224000239 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 319224000240 FAD binding pocket [chemical binding]; other site 319224000241 FAD binding motif [chemical binding]; other site 319224000242 phosphate binding motif [ion binding]; other site 319224000243 NAD binding pocket [chemical binding]; other site 319224000244 imidazolonepropionase; Validated; Region: PRK09356 319224000245 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 319224000246 active site 319224000247 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 319224000248 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224000249 DNA-binding site [nucleotide binding]; DNA binding site 319224000250 UTRA domain; Region: UTRA; cl01230 319224000251 urocanate hydratase; Provisional; Region: PRK05414 319224000252 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 319224000253 active sites [active] 319224000254 tetramer interface [polypeptide binding]; other site 319224000255 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 319224000256 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 319224000257 putative catalytic cysteine [active] 319224000258 gamma-glutamyl kinase; Provisional; Region: PRK13402 319224000259 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 319224000260 nucleotide binding site [chemical binding]; other site 319224000261 homotetrameric interface [polypeptide binding]; other site 319224000262 putative phosphate binding site [ion binding]; other site 319224000263 putative allosteric binding site; other site 319224000264 PUA domain; Region: PUA; cl00607 319224000265 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 319224000266 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 319224000267 Na binding site [ion binding]; other site 319224000268 glutathione reductase; Validated; Region: PRK06116 319224000269 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224000270 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 319224000271 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 319224000272 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 319224000273 active site 319224000274 Zn binding site [ion binding]; other site 319224000275 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 319224000276 active site 319224000277 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 319224000278 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 319224000279 C-terminal domain interface [polypeptide binding]; other site 319224000280 GSH binding site (G-site) [chemical binding]; other site 319224000281 dimer interface [polypeptide binding]; other site 319224000282 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 319224000283 N-terminal domain interface [polypeptide binding]; other site 319224000284 dimer interface [polypeptide binding]; other site 319224000285 substrate binding pocket (H-site) [chemical binding]; other site 319224000286 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 319224000287 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 319224000288 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 319224000289 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 319224000290 Protein export membrane protein; Region: SecD_SecF; cl14618 319224000291 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224000292 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 319224000293 LemA family; Region: LemA; cl00742 319224000294 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 319224000295 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224000296 catalytic residue [active] 319224000297 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 319224000298 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 319224000299 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224000300 metal binding site [ion binding]; metal-binding site 319224000301 active site 319224000302 I-site; other site 319224000303 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 319224000304 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; cl16911 319224000305 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224000306 Protein export membrane protein; Region: SecD_SecF; cl14618 319224000307 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224000308 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 319224000309 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 319224000310 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 319224000311 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 319224000312 N-terminal plug; other site 319224000313 ligand-binding site [chemical binding]; other site 319224000314 Peptidase family M48; Region: Peptidase_M48; cl12018 319224000315 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 319224000316 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 319224000317 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224000318 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_16; cd07263 319224000319 Protein of unknown function (DUF3157); Region: DUF3157; pfam11355 319224000320 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224000321 Helix-turn-helix domains; Region: HTH; cl00088 319224000322 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_6; cd08475 319224000323 putative effector binding pocket; other site 319224000324 putative dimerization interface [polypeptide binding]; other site 319224000325 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 319224000326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000327 NAD(P) binding site [chemical binding]; other site 319224000328 active site 319224000329 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 319224000330 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 319224000331 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 319224000332 DsbD alpha interface [polypeptide binding]; other site 319224000333 catalytic residues [active] 319224000334 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 319224000335 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 319224000336 catalytic residues [active] 319224000337 TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif; Region: TlpA_like_ScsD_MtbDsbE; cd03011 319224000338 catalytic residues [active] 319224000339 Protein of unknown function (DUF1090); Region: DUF1090; pfam06476 319224000340 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 319224000341 Mechanosensitive ion channel; Region: MS_channel; pfam00924 319224000342 LysE type translocator; Region: LysE; cl00565 319224000343 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 319224000344 putative acyl-acceptor binding pocket; other site 319224000345 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 319224000346 NRDE protein; Region: NRDE; cl01315 319224000347 Glycogen synthase [Carbohydrate transport and metabolism]; Region: GlgA; COG0297 319224000348 ZIP Zinc transporter; Region: Zip; pfam02535 319224000349 MarC family integral membrane protein; Region: MarC; cl00919 319224000350 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4412 319224000351 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 319224000352 UTRA domain; Region: UTRA; cl01230 319224000353 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 319224000354 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; cl16911 319224000355 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 319224000356 BAX inhibitor (BI)-1/YccA-like protein family; Region: BI-1-like; cl00473 319224000357 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 319224000358 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 319224000359 ATP binding site [chemical binding]; other site 319224000360 substrate interface [chemical binding]; other site 319224000361 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 319224000362 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 319224000363 dimer interface [polypeptide binding]; other site 319224000364 putative functional site; other site 319224000365 putative MPT binding site; other site 319224000366 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 319224000367 Ferritin-like domain; Region: Ferritin; pfam00210 319224000368 ferroxidase diiron center [ion binding]; other site 319224000369 Nitrate and nitrite sensing; Region: NIT; pfam08376 319224000370 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 319224000371 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 319224000372 PAS domain; Region: PAS_9; pfam13426 319224000373 putative active site [active] 319224000374 heme pocket [chemical binding]; other site 319224000375 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224000376 metal binding site [ion binding]; metal-binding site 319224000377 active site 319224000378 I-site; other site 319224000379 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 319224000380 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 319224000381 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 319224000382 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 319224000383 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 319224000384 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 319224000385 GIY-YIG motif/motif A; other site 319224000386 putative active site [active] 319224000387 putative metal binding site [ion binding]; other site 319224000388 Resistant to P. syringae 6; Provisional; Region: PLN03210 319224000389 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 319224000390 S-adenosylmethionine binding site [chemical binding]; other site 319224000391 Peptidase M14-like domain; uncharacterized subgroup; Region: M14-like_1_4; cd06241 319224000392 putative active site [active] 319224000393 Zn binding site [ion binding]; other site 319224000394 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 319224000395 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 319224000396 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 319224000397 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 319224000398 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224000399 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 319224000400 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 319224000401 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 319224000402 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 319224000403 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 319224000404 HsdM N-terminal domain; Region: HsdM_N; pfam12161 319224000405 HsdM N-terminal domain; Region: HsdM_N; pfam12161 319224000406 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000407 AAA domain; Region: AAA_21; pfam13304 319224000408 Walker A/P-loop; other site 319224000409 ATP binding site [chemical binding]; other site 319224000410 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000411 Q-loop/lid; other site 319224000412 ABC transporter signature motif; other site 319224000413 Walker B; other site 319224000414 D-loop; other site 319224000415 H-loop/switch region; other site 319224000416 Protein of unknown function DUF45; Region: DUF45; cl00636 319224000417 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 319224000418 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 319224000419 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 319224000420 ATP binding site [chemical binding]; other site 319224000421 putative Mg++ binding site [ion binding]; other site 319224000422 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 319224000423 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 319224000424 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 319224000425 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224000426 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 319224000427 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 319224000428 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224000429 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224000430 HsdM N-terminal domain; Region: HsdM_N; pfam12161 319224000431 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 319224000432 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; cl16911 319224000433 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 319224000434 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 319224000435 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000436 Integrase core domain; Region: rve; cl01316 319224000437 multiple promoter invertase; Provisional; Region: mpi; PRK13413 319224000438 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 319224000439 catalytic residues [active] 319224000440 catalytic nucleophile [active] 319224000441 Presynaptic Site I dimer interface [polypeptide binding]; other site 319224000442 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 319224000443 Synaptic Flat tetramer interface [polypeptide binding]; other site 319224000444 Synaptic Site I dimer interface [polypeptide binding]; other site 319224000445 DNA binding site [nucleotide binding] 319224000446 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 319224000447 DNA-binding interface [nucleotide binding]; DNA binding site 319224000448 putative mercuric reductase; Provisional; Region: PRK13748 319224000449 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 319224000450 metal-binding site [ion binding] 319224000451 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224000452 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 319224000453 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 319224000454 metal-binding site [ion binding] 319224000455 MerT mercuric transport protein; Region: MerT; cl03578 319224000456 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 319224000457 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 319224000458 DNA binding residues [nucleotide binding] 319224000459 dimer interface [polypeptide binding]; other site 319224000460 mercury binding site [ion binding]; other site 319224000461 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 319224000462 active site 319224000463 putative transposase OrfB; Reviewed; Region: PHA02517 319224000464 HTH-like domain; Region: HTH_21; pfam13276 319224000465 Integrase core domain; Region: rve; cl01316 319224000466 Integrase core domain; Region: rve_3; cl15866 319224000467 Helix-turn-helix domains; Region: HTH; cl00088 319224000468 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 319224000469 Catalytic site [active] 319224000470 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 319224000471 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 319224000472 active site 319224000473 catalytic residues [active] 319224000474 DNA binding site [nucleotide binding] 319224000475 Int/Topo IB signature motif; other site 319224000476 Restriction endonuclease; Region: Mrr_cat; cl00516 319224000477 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 319224000478 Predicted transcriptional regulator [Transcription]; Region: COG2944 319224000479 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 319224000480 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 319224000481 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 319224000482 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224000483 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224000484 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 319224000485 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 319224000486 Ligand Binding Site [chemical binding]; other site 319224000487 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 319224000488 Ligand Binding Site [chemical binding]; other site 319224000489 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 319224000490 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 319224000491 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 319224000492 catalytic residues [active] 319224000493 catalytic nucleophile [active] 319224000494 Presynaptic Site I dimer interface [polypeptide binding]; other site 319224000495 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 319224000496 Synaptic Flat tetramer interface [polypeptide binding]; other site 319224000497 Synaptic Site I dimer interface [polypeptide binding]; other site 319224000498 DNA binding site [nucleotide binding] 319224000499 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 319224000500 DNA-binding interface [nucleotide binding]; DNA binding site 319224000501 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 319224000502 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 319224000503 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 319224000504 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 319224000505 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 319224000506 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 319224000507 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 319224000508 DNA binding residues [nucleotide binding] 319224000509 dimer interface [polypeptide binding]; other site 319224000510 putative metal binding site [ion binding]; other site 319224000511 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 319224000512 Cation efflux family; Region: Cation_efflux; cl00316 319224000513 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 319224000514 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 319224000515 Transposase; Region: DDE_Tnp_ISL3; pfam01610 319224000516 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 319224000517 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism; Region: PDD; cd08180 319224000518 putative active site [active] 319224000519 metal binding site [ion binding]; metal-binding site 319224000520 Ethanolamine utilization protein EutE-like; Region: ALDH_EutE; cd07121 319224000521 putative catalytic cysteine [active] 319224000522 Domain of unknown function (DUF336); Region: DUF336; cl01249 319224000523 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cd01614 319224000524 Hexamer/Pentamer interface [polypeptide binding]; other site 319224000525 central pore; other site 319224000526 putative propanediol utilization protein PduM; Provisional; Region: PRK15428 319224000527 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 319224000528 Propanediol utilisation protein PduL; Region: PduL; pfam06130 319224000529 Propanediol utilisation protein PduL; Region: PduL; pfam06130 319224000530 1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat 1l; Region: BMC_PduK; cd07056 319224000531 putative hexamer interface [polypeptide binding]; other site 319224000532 putative hexagonal pore; other site 319224000533 Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain; Region: BMC_CcmK_like; cd07045 319224000534 Hexamer interface [polypeptide binding]; other site 319224000535 Hexagonal pore residue; other site 319224000536 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 319224000537 amphipathic channel; other site 319224000538 Asn-Pro-Ala signature motifs; other site 319224000539 glycyl-radical enzyme activating protein family; Region: PFLE_PFLC; TIGR02494 319224000540 4Fe-4S binding domain; Region: Fer4; cl02805 319224000541 4Fe-4S binding domain; Region: Fer4; cl02805 319224000542 glycyl radical enzyme, PFL2/glycerol dehydratase family; Region: PFL2-3; TIGR01774 319224000543 Pyruvate formate lyase 2 and related enzymes; Region: PFL2_DhaB_BssA; cd01677 319224000544 dimer interface [polypeptide binding]; other site 319224000545 active site 319224000546 glycine loop; other site 319224000547 propanediol utilization protein PduB; Provisional; Region: PRK15415 319224000548 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1; Region: BMC_PduB_repeat1; cd07047 319224000549 putative hexamer interface [polypeptide binding]; other site 319224000550 putative hexagonal pore; other site 319224000551 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 2; Region: BMC_PduB_repeat2; cd07048 319224000552 putative hexamer interface [polypeptide binding]; other site 319224000553 putative hexagonal pore; other site 319224000554 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain; Region: BMC_PduA; cd07059 319224000555 Hexamer interface [polypeptide binding]; other site 319224000556 Putative hexagonal pore residue; other site 319224000557 PTS system mannose/fructose/sorbose family IID component; Region: EIID-AGA; cl01507 319224000558 PTS system sorbose-specific iic component; Region: EII-Sor; cl01506 319224000559 PTS_IIB, PTS system, Mannose/sorbose 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_man; cl00021 319224000560 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 319224000561 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 319224000562 IS1 transposase; Region: DDE_Tnp_IS1; cl00721 319224000563 InsA N-terminal domain; Region: Zn_Tnp_IS1; pfam03811 319224000564 InsA C-terminal domain; Region: HTH_Tnp_IS1; pfam12759 319224000565 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 319224000566 active site 319224000567 DNA binding site [nucleotide binding] 319224000568 Int/Topo IB signature motif; other site 319224000569 Helix-turn-helix domains; Region: HTH; cl00088 319224000570 Winged helix-turn helix; Region: HTH_29; pfam13551 319224000571 Helix-turn-helix domains; Region: HTH; cl00088 319224000572 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 319224000573 Integrase core domain; Region: rve; cl01316 319224000574 Sensory domain found in PocR; Region: PocR; pfam10114 319224000575 Predicted sensor domain [Signal transduction mechanisms / Transcription]; Region: PocR; COG4936 319224000576 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224000577 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 319224000578 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224000579 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 319224000580 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 319224000581 DNA binding residues [nucleotide binding] 319224000582 dimer interface [polypeptide binding]; other site 319224000583 putative metal binding site [ion binding]; other site 319224000584 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 319224000585 Cation efflux family; Region: Cation_efflux; cl00316 319224000586 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 319224000587 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3464 319224000588 Transposase; Region: DDE_Tnp_ISL3; pfam01610 319224000589 Protein of unknown function (DUF3703); Region: DUF3703; pfam12487 319224000590 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 319224000591 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 319224000592 carboxyltransferase (CT) interaction site; other site 319224000593 biotinylation site [posttranslational modification]; other site 319224000594 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 319224000595 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 319224000596 Cation efflux family; Region: Cation_efflux; cl00316 319224000597 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 319224000598 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 319224000599 DNA binding residues [nucleotide binding] 319224000600 dimer interface [polypeptide binding]; other site 319224000601 putative metal binding site [ion binding]; other site 319224000602 Cation efflux family; Region: Cation_efflux; cl00316 319224000603 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 319224000604 Competence protein CoiA-like family; Region: CoiA; cl11541 319224000605 Protein of unknown function (DUF2511); Region: DUF2511; pfam10709 319224000606 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 319224000607 DNA binding site [nucleotide binding] 319224000608 dimer interface [polypeptide binding]; other site 319224000609 active site 319224000610 Int/Topo IB signature motif; other site 319224000611 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG2263 319224000612 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; cl16911 319224000613 Methyltransferase domain; Region: Methyltransf_27; pfam13708 319224000614 Integrase core domain; Region: rve; cl01316 319224000615 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 319224000616 Helix-turn-helix domains; Region: HTH; cl00088 319224000617 Winged helix-turn helix; Region: HTH_33; pfam13592 319224000618 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 319224000619 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 319224000620 Protein of unknown function, DUF; Region: DUF411; cl01142 319224000621 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224000622 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224000623 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224000624 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 319224000625 Bacterial Ig-like domain; Region: Big_5; cl01012 319224000626 Copper resistance protein D; Region: CopD; cl00563 319224000627 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 319224000628 outer membrane porin, OprD family; Region: OprD; pfam03573 319224000629 DDE_Tnp_1-associated; Region: DDE_Tnp_1_assoc; pfam13808 319224000630 sensor kinase CusS; Provisional; Region: PRK09835 319224000631 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 319224000632 dimerization interface [polypeptide binding]; other site 319224000633 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 319224000634 dimer interface [polypeptide binding]; other site 319224000635 phosphorylation site [posttranslational modification] 319224000636 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 319224000637 ATP binding site [chemical binding]; other site 319224000638 Mg2+ binding site [ion binding]; other site 319224000639 G-X-G motif; other site 319224000640 DNA-binding transcriptional activator CusR; Provisional; Region: PRK09836 319224000641 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 319224000642 active site 319224000643 phosphorylation site [posttranslational modification] 319224000644 intermolecular recognition site; other site 319224000645 dimerization interface [polypeptide binding]; other site 319224000646 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 319224000647 DNA binding site [nucleotide binding] 319224000648 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 319224000649 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 319224000650 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 319224000651 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 319224000652 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 319224000653 Protein of unknown function, DUF; Region: DUF411; cl01142 319224000654 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 319224000655 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 319224000656 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224000657 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 319224000658 motif II; other site 319224000659 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 319224000660 putative peptidase; Provisional; Region: PRK11649 319224000661 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224000662 copper exporting ATPase; Provisional; Region: copA; PRK10671 319224000663 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 319224000664 metal-binding site [ion binding] 319224000665 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224000666 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224000667 Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR_unk; cd04787 319224000668 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 319224000669 DNA binding residues [nucleotide binding] 319224000670 dimer interface [polypeptide binding]; other site 319224000671 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 319224000672 RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable...; Region: RT_G2_intron; cd01651 319224000673 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 319224000674 putative active site [active] 319224000675 putative NTP binding site [chemical binding]; other site 319224000676 putative nucleic acid binding site [nucleotide binding]; other site 319224000677 Group II intron, maturase-specific domain; Region: GIIM; pfam08388 319224000678 putative transposase OrfB; Reviewed; Region: PHA02517 319224000679 HTH-like domain; Region: HTH_21; pfam13276 319224000680 Integrase core domain; Region: rve; cl01316 319224000681 Integrase core domain; Region: rve_3; cl15866 319224000682 Helix-turn-helix domains; Region: HTH; cl00088 319224000683 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 319224000684 DNA binding site [nucleotide binding] 319224000685 active site 319224000686 Int/Topo IB signature motif; other site 319224000687 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 319224000688 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 319224000689 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 319224000690 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 319224000691 Protein of unknown function (DUF1145); Region: DUF1145; cl11481 319224000692 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 319224000693 S-adenosylmethionine binding site [chemical binding]; other site 319224000694 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 319224000695 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 319224000696 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 319224000697 P loop; other site 319224000698 GTP binding site [chemical binding]; other site 319224000699 cell division protein FtsE; Provisional; Region: PRK10908 319224000700 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224000701 Walker A/P-loop; other site 319224000702 ATP binding site [chemical binding]; other site 319224000703 Q-loop/lid; other site 319224000704 ABC transporter signature motif; other site 319224000705 Walker B; other site 319224000706 D-loop; other site 319224000707 H-loop/switch region; other site 319224000708 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 319224000709 FtsX-like permease family; Region: FtsX; cl15850 319224000710 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 319224000711 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 319224000712 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224000713 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 319224000714 DNA binding residues [nucleotide binding] 319224000715 Fimbrial protein; Region: Fimbrial; cl01416 319224000716 Fimbrial protein; Region: Fimbrial; cl01416 319224000717 Fimbrial protein; Region: Fimbrial; cl01416 319224000718 Fimbrial protein; Region: Fimbrial; cl01416 319224000719 fimbrial chaperone protein StbB; Provisional; Region: PRK15249 319224000720 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 319224000721 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 319224000722 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 319224000723 PapC N-terminal domain; Region: PapC_N; pfam13954 319224000724 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 319224000725 PapC C-terminal domain; Region: PapC_C; pfam13953 319224000726 Fimbrial protein; Region: Fimbrial; cl01416 319224000727 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 319224000728 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 319224000729 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional; Region: PRK09959 319224000730 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 319224000731 substrate binding pocket [chemical binding]; other site 319224000732 membrane-bound complex binding site; other site 319224000733 hinge residues; other site 319224000734 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 319224000735 substrate binding pocket [chemical binding]; other site 319224000736 membrane-bound complex binding site; other site 319224000737 hinge residues; other site 319224000738 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 319224000739 putative active site [active] 319224000740 heme pocket [chemical binding]; other site 319224000741 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 319224000742 dimer interface [polypeptide binding]; other site 319224000743 phosphorylation site [posttranslational modification] 319224000744 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 319224000745 ATP binding site [chemical binding]; other site 319224000746 Mg2+ binding site [ion binding]; other site 319224000747 G-X-G motif; other site 319224000748 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 319224000749 active site 319224000750 phosphorylation site [posttranslational modification] 319224000751 intermolecular recognition site; other site 319224000752 dimerization interface [polypeptide binding]; other site 319224000753 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 319224000754 DNA-binding transcriptional activator EvgA; Provisional; Region: PRK09958 319224000755 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 319224000756 active site 319224000757 phosphorylation site [posttranslational modification] 319224000758 intermolecular recognition site; other site 319224000759 dimerization interface [polypeptide binding]; other site 319224000760 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 319224000761 DNA binding residues [nucleotide binding] 319224000762 dimerization interface [polypeptide binding]; other site 319224000763 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 319224000764 active site 319224000765 phosphorylation site [posttranslational modification] 319224000766 intermolecular recognition site; other site 319224000767 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 319224000768 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 319224000769 O-succinylbenzoic acid--CoA ligase; Provisional; Region: PRK09029 319224000770 AMP-binding enzyme; Region: AMP-binding; cl15778 319224000771 O-succinylbenzoate synthase; Provisional; Region: PRK05105 319224000772 o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway; Region: OSBS; cd03320 319224000773 active site 319224000774 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 319224000775 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 319224000776 nucleophilic elbow; other site 319224000777 catalytic triad; other site 319224000778 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase; Validated; Region: PRK07449 319224000779 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 319224000780 dimer interface [polypeptide binding]; other site 319224000781 tetramer interface [polypeptide binding]; other site 319224000782 PYR/PP interface [polypeptide binding]; other site 319224000783 TPP binding site [chemical binding]; other site 319224000784 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 319224000785 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 319224000786 TPP-binding site; other site 319224000787 Helix-turn-helix domains; Region: HTH; cl00088 319224000788 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 319224000789 dimerization interface [polypeptide binding]; other site 319224000790 cytochrome c nitrite reductase pentaheme subunit; Provisional; Region: PRK11659 319224000791 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 319224000792 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 319224000793 Polysulphide reductase, NrfD; Region: NrfD; cl01295 319224000794 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 319224000795 Helix-turn-helix domains; Region: HTH; cl00088 319224000796 AsnC family; Region: AsnC_trans_reg; pfam01037 319224000797 Spore germination protein; Region: Spore_permease; cl15802 319224000798 putative transporter; Provisional; Region: PRK11021 319224000799 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 319224000800 putative metal binding site [ion binding]; other site 319224000801 Protein of unknown function VcgC/VcgE (DUF2780); Region: DUF2780; pfam11075 319224000802 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 319224000803 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 319224000804 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 319224000805 Sel1 repeat; Region: Sel1; cl02723 319224000806 Cache domain; Region: Cache_1; pfam02743 319224000807 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 319224000808 dimerization interface [polypeptide binding]; other site 319224000809 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224000810 dimer interface [polypeptide binding]; other site 319224000811 putative CheW interface [polypeptide binding]; other site 319224000812 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 319224000813 Helix-turn-helix domains; Region: HTH; cl00088 319224000814 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 319224000815 substrate binding pocket [chemical binding]; other site 319224000816 dimerization interface [polypeptide binding]; other site 319224000817 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 319224000818 multidrug efflux system protein MdtL; Provisional; Region: PRK10473 319224000819 putative substrate translocation pore; other site 319224000820 DTW domain; Region: DTW; cl01221 319224000821 PAS domain S-box; Region: sensory_box; TIGR00229 319224000822 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 319224000823 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224000824 metal binding site [ion binding]; metal-binding site 319224000825 active site 319224000826 I-site; other site 319224000827 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 319224000828 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; cl16911 319224000829 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 319224000830 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 319224000831 N-terminal plug; other site 319224000832 ligand-binding site [chemical binding]; other site 319224000833 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 319224000834 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 319224000835 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 319224000836 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 319224000837 [4Fe-4S] binding site [ion binding]; other site 319224000838 molybdopterin cofactor binding site; other site 319224000839 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 319224000840 molybdopterin cofactor binding site; other site 319224000841 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 319224000842 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 319224000843 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 319224000844 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 319224000845 4Fe-4S binding domain; Region: Fer4; cl02805 319224000846 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 319224000847 [4Fe-4S] binding site [ion binding]; other site 319224000848 molybdopterin cofactor binding site; other site 319224000849 Molybdopterin-Binding, C-terminal (MopB_CT) 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-...; Region: MopB_CT; cl09929 319224000850 molybdopterin cofactor binding site; other site 319224000851 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 319224000852 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 319224000853 Ferredoxin [Energy production and conversion]; Region: COG1146 319224000854 4Fe-4S binding domain; Region: Fer4; cl02805 319224000855 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 319224000856 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 319224000857 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 319224000858 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 319224000859 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 319224000860 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 319224000861 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 319224000862 Domain of unknown function (DUF1993); Region: DUF1993; cl01567 319224000863 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 319224000864 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 319224000865 transmembrane helices; other site 319224000866 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 319224000867 Fumarase C-terminus; Region: Fumerase_C; cl00795 319224000868 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 319224000869 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 319224000870 active site 319224000871 phosphorylation site [posttranslational modification] 319224000872 intermolecular recognition site; other site 319224000873 dimerization interface [polypeptide binding]; other site 319224000874 Helix-turn-helix domains; Region: HTH; cl00088 319224000875 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 319224000876 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 319224000877 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 319224000878 ATP binding site [chemical binding]; other site 319224000879 Mg2+ binding site [ion binding]; other site 319224000880 G-X-G motif; other site 319224000881 Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitD; cd00547 319224000882 Iron-sulfur protein interface; other site 319224000883 proximal quinone binding site [chemical binding]; other site 319224000884 C-subunit interface; other site 319224000885 distal quinone binding site; other site 319224000886 Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine...; Region: QFR_TypeD_subunitC; cd00546 319224000887 D-subunit interface [polypeptide binding]; other site 319224000888 Iron-sulfur protein interface; other site 319224000889 proximal quinone binding site [chemical binding]; other site 319224000890 fumarate reductase iron-sulfur subunit; Provisional; Region: PRK12385 319224000891 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 319224000892 fumarate reductase flavoprotein subunit; Validated; Region: PRK09231 319224000893 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224000894 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 319224000895 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224000896 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224000897 Coenzyme A binding pocket [chemical binding]; other site 319224000898 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 319224000899 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 319224000900 ATP binding site [chemical binding]; other site 319224000901 Mg2+ binding site [ion binding]; other site 319224000902 G-X-G motif; other site 319224000903 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 319224000904 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 319224000905 active site 319224000906 phosphorylation site [posttranslational modification] 319224000907 intermolecular recognition site; other site 319224000908 dimerization interface [polypeptide binding]; other site 319224000909 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 319224000910 DNA binding site [nucleotide binding] 319224000911 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 319224000912 Dihaem cytochrome c; Region: DHC; pfam09626 319224000913 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 319224000914 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 319224000915 Protein of unknown function (DUF2809); Region: DUF2809; pfam10990 319224000916 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 319224000917 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 319224000918 NAD(P) binding site [chemical binding]; other site 319224000919 catalytic residues [active] 319224000920 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 319224000921 GAF domain; Region: GAF; cl15785 319224000922 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 319224000923 Walker A motif; other site 319224000924 ATP binding site [chemical binding]; other site 319224000925 Walker B motif; other site 319224000926 arginine finger; other site 319224000927 Helix-turn-helix domains; Region: HTH; cl00088 319224000928 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 319224000929 dimerization interface [polypeptide binding]; other site 319224000930 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 319224000931 dimer interface [polypeptide binding]; other site 319224000932 phosphorylation site [posttranslational modification] 319224000933 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 319224000934 ATP binding site [chemical binding]; other site 319224000935 Mg2+ binding site [ion binding]; other site 319224000936 G-X-G motif; other site 319224000937 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 319224000938 active site 319224000939 phosphorylation site [posttranslational modification] 319224000940 intermolecular recognition site; other site 319224000941 dimerization interface [polypeptide binding]; other site 319224000942 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 319224000943 DNA binding site [nucleotide binding] 319224000944 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 319224000945 dimer interface [polypeptide binding]; other site 319224000946 Cation efflux family; Region: Cation_efflux; cl00316 319224000947 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 319224000948 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 319224000949 active site 319224000950 phosphorylation site [posttranslational modification] 319224000951 intermolecular recognition site; other site 319224000952 dimerization interface [polypeptide binding]; other site 319224000953 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 319224000954 Walker A motif; other site 319224000955 ATP binding site [chemical binding]; other site 319224000956 Walker B motif; other site 319224000957 arginine finger; other site 319224000958 Helix-turn-helix domains; Region: HTH; cl00088 319224000959 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 319224000960 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 319224000961 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 319224000962 dimer interface [polypeptide binding]; other site 319224000963 phosphorylation site [posttranslational modification] 319224000964 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 319224000965 ATP binding site [chemical binding]; other site 319224000966 Mg2+ binding site [ion binding]; other site 319224000967 G-X-G motif; other site 319224000968 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 319224000969 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 319224000970 N-terminal domain interface [polypeptide binding]; other site 319224000971 dimer interface [polypeptide binding]; other site 319224000972 substrate binding pocket (H-site) [chemical binding]; other site 319224000973 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 319224000974 putative C-terminal domain interface [polypeptide binding]; other site 319224000975 putative GSH binding site (G-site) [chemical binding]; other site 319224000976 putative dimer interface [polypeptide binding]; other site 319224000977 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 319224000978 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 319224000979 potential catalytic triad [active] 319224000980 conserved cys residue [active] 319224000981 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 319224000982 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 319224000983 dimer interface [polypeptide binding]; other site 319224000984 active site 319224000985 metal binding site [ion binding]; metal-binding site 319224000986 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224000987 Helix-turn-helix domains; Region: HTH; cl00088 319224000988 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 319224000989 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224000990 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224000991 dimer interface [polypeptide binding]; other site 319224000992 putative CheW interface [polypeptide binding]; other site 319224000993 DinB superfamily; Region: DinB_2; pfam12867 319224000994 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 319224000995 phosphoethanolamine N-methyltransferase; Provisional; Region: PTZ00098 319224000996 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 319224000997 S-adenosylmethionine binding site [chemical binding]; other site 319224000998 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 319224000999 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 319224001000 substrate binding site [chemical binding]; other site 319224001001 ATP binding site [chemical binding]; other site 319224001002 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224001003 metal binding site [ion binding]; metal-binding site 319224001004 active site 319224001005 I-site; other site 319224001006 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 319224001007 MOSC domain; Region: MOSC; pfam03473 319224001008 3-alpha domain; Region: 3-alpha; pfam03475 319224001009 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296; cl15800 319224001010 Cache domain; Region: Cache_1; pfam02743 319224001011 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 319224001012 dimerization interface [polypeptide binding]; other site 319224001013 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224001014 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224001015 dimer interface [polypeptide binding]; other site 319224001016 putative CheW interface [polypeptide binding]; other site 319224001017 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224001018 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 319224001019 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 319224001020 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 319224001021 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 319224001022 FeS/SAM binding site; other site 319224001023 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 319224001024 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 319224001025 trimer interface [polypeptide binding]; other site 319224001026 dimer interface [polypeptide binding]; other site 319224001027 putative active site [active] 319224001028 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 319224001029 MoaE interaction surface [polypeptide binding]; other site 319224001030 MoeB interaction surface [polypeptide binding]; other site 319224001031 thiocarboxylated glycine; other site 319224001032 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 319224001033 MoaE homodimer interface [polypeptide binding]; other site 319224001034 MoaD interaction [polypeptide binding]; other site 319224001035 active site residues [active] 319224001036 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 319224001037 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 319224001038 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 319224001039 dimer interface [polypeptide binding]; other site 319224001040 conserved gate region; other site 319224001041 putative PBP binding loops; other site 319224001042 ABC-ATPase subunit interface; other site 319224001043 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 319224001044 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 319224001045 Walker A/P-loop; other site 319224001046 ATP binding site [chemical binding]; other site 319224001047 Q-loop/lid; other site 319224001048 ABC transporter signature motif; other site 319224001049 Walker B; other site 319224001050 D-loop; other site 319224001051 H-loop/switch region; other site 319224001052 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 319224001053 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224001054 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 319224001055 active site 319224001056 phosphorylation site [posttranslational modification] 319224001057 intermolecular recognition site; other site 319224001058 dimerization interface [polypeptide binding]; other site 319224001059 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 319224001060 DNA binding site [nucleotide binding] 319224001061 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224001062 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 319224001063 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 319224001064 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 319224001065 ATP binding site [chemical binding]; other site 319224001066 Mg2+ binding site [ion binding]; other site 319224001067 G-X-G motif; other site 319224001068 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224001069 active site 319224001070 Proteolipid membrane potential modulator; Region: Pmp3; cl00431 319224001071 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224001072 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 319224001073 N-terminal plug; other site 319224001074 ligand-binding site [chemical binding]; other site 319224001075 Protein of unknown function (DUF2986); Region: DUF2986; pfam11661 319224001076 Peptidase family M23; Region: Peptidase_M23; pfam01551 319224001077 NlpC/P60 family; Region: NLPC_P60; cl11438 319224001078 Domain of unknown function (DUF1864); Region: DUF1864; pfam08933 319224001079 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 319224001080 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 319224001081 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224001082 catalytic residue [active] 319224001083 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00144 319224001084 glutamine synthetase; Provisional; Region: glnA; PRK09469 319224001085 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 319224001086 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 319224001087 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 319224001088 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 319224001089 G1 box; other site 319224001090 putative GEF interaction site [polypeptide binding]; other site 319224001091 GTP/Mg2+ binding site [chemical binding]; other site 319224001092 Switch I region; other site 319224001093 G2 box; other site 319224001094 G3 box; other site 319224001095 Switch II region; other site 319224001096 G4 box; other site 319224001097 G5 box; other site 319224001098 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 319224001099 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 319224001100 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 319224001101 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224001102 metal binding site [ion binding]; metal-binding site 319224001103 active site 319224001104 I-site; other site 319224001105 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 319224001106 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 319224001107 dimer interface [polypeptide binding]; other site 319224001108 active site 319224001109 heme binding site [chemical binding]; other site 319224001110 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 319224001111 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 319224001112 4Fe-4S binding domain; Region: Fer4_5; pfam12801 319224001113 4Fe-4S binding domain; Region: Fer4_5; pfam12801 319224001114 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 319224001115 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 319224001116 putative active site [active] 319224001117 dimerization interface [polypeptide binding]; other site 319224001118 putative tRNAtyr binding site [nucleotide binding]; other site 319224001119 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 319224001120 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 319224001121 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224001122 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 319224001123 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 319224001124 non-specific DNA binding site [nucleotide binding]; other site 319224001125 salt bridge; other site 319224001126 sequence-specific DNA binding site [nucleotide binding]; other site 319224001127 Cupin domain; Region: Cupin_2; cl09118 319224001128 Benzoate membrane transport protein; Region: BenE; pfam03594 319224001129 benzoate transporter; Region: benE; TIGR00843 319224001130 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224001131 Coenzyme A binding pocket [chemical binding]; other site 319224001132 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 319224001133 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 319224001134 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 319224001135 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 319224001136 dimer interface [polypeptide binding]; other site 319224001137 active site 319224001138 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 319224001139 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 319224001140 NAD(P) binding site [chemical binding]; other site 319224001141 homotetramer interface [polypeptide binding]; other site 319224001142 homodimer interface [polypeptide binding]; other site 319224001143 active site 319224001144 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 319224001145 putative active site 1 [active] 319224001146 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 319224001147 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 319224001148 dimer interface [polypeptide binding]; other site 319224001149 active site 319224001150 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 319224001151 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 319224001152 Predicted exporter [General function prediction only]; Region: COG4258 319224001153 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 319224001154 active site 319224001155 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 319224001156 active sites [active] 319224001157 tetramer interface [polypeptide binding]; other site 319224001158 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 319224001159 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 319224001160 Ligand binding site; other site 319224001161 Putative Catalytic site; other site 319224001162 DXD motif; other site 319224001163 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 319224001164 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 319224001165 putative acyl-acceptor binding pocket; other site 319224001166 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 319224001167 active site 2 [active] 319224001168 active site 1 [active] 319224001169 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 319224001170 AMP-binding enzyme; Region: AMP-binding; cl15778 319224001171 Predicted membrane protein [Function unknown]; Region: COG4648 319224001172 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224001173 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224001174 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 319224001175 putative acyl-acceptor binding pocket; other site 319224001176 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 319224001177 Protein of unknown function (DUF3014); Region: DUF3014; pfam11219 319224001178 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 319224001179 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 319224001180 generic binding surface II; other site 319224001181 ssDNA binding site; other site 319224001182 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 319224001183 ATP binding site [chemical binding]; other site 319224001184 putative Mg++ binding site [ion binding]; other site 319224001185 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 319224001186 nucleotide binding region [chemical binding]; other site 319224001187 ATP-binding site [chemical binding]; other site 319224001188 MarC family integral membrane protein; Region: MarC; cl00919 319224001189 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224001190 ligand binding site [chemical binding]; other site 319224001191 hypothetical protein; Provisional; Region: PRK11820 319224001192 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 319224001193 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 319224001194 ribonuclease PH; Reviewed; Region: rph; PRK00173 319224001195 Ribonuclease PH; Region: RNase_PH_bact; cd11362 319224001196 hexamer interface [polypeptide binding]; other site 319224001197 active site 319224001198 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224001199 active site 319224001200 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 319224001201 GTP cyclohydrolase I; Provisional; Region: PLN03044 319224001202 active site 319224001203 division inhibitor protein; Provisional; Region: slmA; PRK09480 319224001204 Helix-turn-helix domains; Region: HTH; cl00088 319224001205 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 319224001206 trimer interface [polypeptide binding]; other site 319224001207 active site 319224001208 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 319224001209 Flavoprotein; Region: Flavoprotein; cl08021 319224001210 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 319224001211 hypothetical protein; Reviewed; Region: PRK00024 319224001212 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 319224001213 MPN+ (JAMM) motif; other site 319224001214 Zinc-binding site [ion binding]; other site 319224001215 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 319224001216 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 319224001217 N-acetylglutamate synthase; Validated; Region: PRK05279 319224001218 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 319224001219 putative feedback inhibition sensing region; other site 319224001220 putative nucleotide binding site [chemical binding]; other site 319224001221 putative substrate binding site [chemical binding]; other site 319224001222 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224001223 Coenzyme A binding pocket [chemical binding]; other site 319224001224 putative chloramphenical resistance permease RarD; Provisional; Region: PRK15430 319224001225 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 319224001226 CoenzymeA binding site [chemical binding]; other site 319224001227 subunit interaction site [polypeptide binding]; other site 319224001228 PHB binding site; other site 319224001229 ATP-dependent DNA helicase RecQ; Provisional; Region: PRK11057 319224001230 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 319224001231 ATP binding site [chemical binding]; other site 319224001232 putative Mg++ binding site [ion binding]; other site 319224001233 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 319224001234 nucleotide binding region [chemical binding]; other site 319224001235 ATP-binding site [chemical binding]; other site 319224001236 RQC domain; Region: RQC; cl09632 319224001237 HRDC domain; Region: HRDC; cl02578 319224001238 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 319224001239 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224001240 active site 319224001241 I-site; other site 319224001242 metal binding site [ion binding]; metal-binding site 319224001243 2-isopropylmalate synthase; Validated; Region: PRK00915 319224001244 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 319224001245 active site 319224001246 catalytic residues [active] 319224001247 metal binding site [ion binding]; metal-binding site 319224001248 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 319224001249 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 319224001250 tartrate dehydrogenase; Provisional; Region: PRK08194 319224001251 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 319224001252 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 319224001253 substrate binding site [chemical binding]; other site 319224001254 ligand binding site [chemical binding]; other site 319224001255 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 319224001256 substrate binding site [chemical binding]; other site 319224001257 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; cl01155 319224001258 glycerol kinase; Provisional; Region: glpK; PRK00047 319224001259 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 319224001260 N- and C-terminal domain interface [polypeptide binding]; other site 319224001261 active site 319224001262 MgATP binding site [chemical binding]; other site 319224001263 catalytic site [active] 319224001264 metal binding site [ion binding]; metal-binding site 319224001265 glycerol binding site [chemical binding]; other site 319224001266 homotetramer interface [polypeptide binding]; other site 319224001267 homodimer interface [polypeptide binding]; other site 319224001268 FBP binding site [chemical binding]; other site 319224001269 protein IIAGlc interface [polypeptide binding]; other site 319224001270 cell division protein MraZ; Reviewed; Region: PRK00326 319224001271 MraZ protein; Region: MraZ; pfam02381 319224001272 MraZ protein; Region: MraZ; pfam02381 319224001273 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 319224001274 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; cl16911 319224001275 Septum formation initiator; Region: DivIC; cl11433 319224001276 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 319224001277 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 319224001278 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224001279 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 319224001280 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 319224001281 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 319224001282 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 319224001283 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 319224001284 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 319224001285 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 319224001286 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 319224001287 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 319224001288 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 319224001289 Mg++ binding site [ion binding]; other site 319224001290 putative catalytic motif [active] 319224001291 putative substrate binding site [chemical binding]; other site 319224001292 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 319224001293 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 319224001294 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 319224001295 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 319224001296 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 319224001297 active site 319224001298 homodimer interface [polypeptide binding]; other site 319224001299 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 319224001300 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 319224001301 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 319224001302 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 319224001303 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 319224001304 Cell division protein FtsQ; Region: FtsQ; pfam03799 319224001305 cell division protein FtsA; Reviewed; Region: ftsA; PRK09472 319224001306 Cell division protein FtsA; Region: FtsA; cl11496 319224001307 Cell division protein FtsA; Region: FtsA; cl11496 319224001308 cell division protein FtsZ; Validated; Region: PRK09330 319224001309 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 319224001310 nucleotide binding site [chemical binding]; other site 319224001311 SulA interaction site; other site 319224001312 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 319224001313 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 319224001314 Protein of unknown function (DUF721); Region: DUF721; cl02324 319224001315 Peptidase family M23; Region: Peptidase_M23; pfam01551 319224001316 preprotein translocase subunit SecA; Reviewed; Region: PRK13107 319224001317 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001318 ATP binding site [chemical binding]; other site 319224001319 putative Mg++ binding site [ion binding]; other site 319224001320 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 319224001321 SEC-C motif; Region: SEC-C; pfam02810 319224001322 Integrase core domain; Region: rve; cl01316 319224001323 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 319224001324 dimer interface [polypeptide binding]; other site 319224001325 allosteric magnesium binding site [ion binding]; other site 319224001326 active site 319224001327 aspartate-rich active site metal binding site; other site 319224001328 Schiff base residues; other site 319224001329 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 319224001330 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 319224001331 hypothetical protein; Region: PHA02277 319224001332 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224001333 metal binding site [ion binding]; metal-binding site 319224001334 active site 319224001335 I-site; other site 319224001336 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 319224001337 active site 319224001338 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 319224001339 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 319224001340 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 319224001341 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 319224001342 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224001343 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 319224001344 SCP-2 sterol transfer family; Region: SCP2; cl01225 319224001345 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 319224001346 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 319224001347 S-adenosylmethionine binding site [chemical binding]; other site 319224001348 Arginase family; Region: Arginase; cl00306 319224001349 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 319224001350 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 319224001351 active site 319224001352 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 319224001353 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 319224001354 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224001355 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224001356 dimer interface [polypeptide binding]; other site 319224001357 putative CheW interface [polypeptide binding]; other site 319224001358 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 319224001359 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 319224001360 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 319224001361 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 319224001362 DHHA2 domain; Region: DHHA2; pfam02833 319224001363 Domain of unknown function (DUF386); Region: DUF386; cl01047 319224001364 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 319224001365 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 319224001366 N-terminal plug; other site 319224001367 ligand-binding site [chemical binding]; other site 319224001368 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 319224001369 Pseudouridine synthase, a subgroup of the RluA family; Region: PSRA_1; cd02558 319224001370 probable active site [active] 319224001371 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 319224001372 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 319224001373 ATP binding site [chemical binding]; other site 319224001374 Mg2+ binding site [ion binding]; other site 319224001375 G-X-G motif; other site 319224001376 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 319224001377 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 319224001378 active site 319224001379 phosphorylation site [posttranslational modification] 319224001380 intermolecular recognition site; other site 319224001381 dimerization interface [polypeptide binding]; other site 319224001382 Helix-turn-helix domains; Region: HTH; cl00088 319224001383 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 319224001384 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 319224001385 NADP binding site [chemical binding]; other site 319224001386 homodimer interface [polypeptide binding]; other site 319224001387 active site 319224001388 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 319224001389 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 319224001390 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 319224001391 Protein of unknown function (DUF971); Region: DUF971; cl01414 319224001392 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 319224001393 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 319224001394 Walker A motif; other site 319224001395 ATP binding site [chemical binding]; other site 319224001396 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001397 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 319224001398 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 319224001399 active site 319224001400 HslU subunit interaction site [polypeptide binding]; other site 319224001401 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 319224001402 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 319224001403 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 319224001404 active site 319224001405 phosphorylation site [posttranslational modification] 319224001406 intermolecular recognition site; other site 319224001407 dimerization interface [polypeptide binding]; other site 319224001408 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 319224001409 DNA binding residues [nucleotide binding] 319224001410 dimerization interface [polypeptide binding]; other site 319224001411 NMT1-like family; Region: NMT1_2; cl15260 319224001412 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 319224001413 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 319224001414 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 319224001415 ATP binding site [chemical binding]; other site 319224001416 Mg2+ binding site [ion binding]; other site 319224001417 G-X-G motif; other site 319224001418 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 319224001419 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 319224001420 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 319224001421 substrate binding pocket [chemical binding]; other site 319224001422 membrane-bound complex binding site; other site 319224001423 hinge residues; other site 319224001424 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 319224001425 Sel1 repeat; Region: Sel1; cl02723 319224001426 Sel1 repeat; Region: Sel1; cl02723 319224001427 Mechanosensitive ion channel; Region: MS_channel; pfam00924 319224001428 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 319224001429 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 319224001430 dimer interface [polypeptide binding]; other site 319224001431 active site 319224001432 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 319224001433 catalytic residues [active] 319224001434 substrate binding site [chemical binding]; other site 319224001435 Protein of unknown function (DUF465); Region: DUF465; cl01070 319224001436 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 319224001437 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 319224001438 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 319224001439 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 319224001440 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 319224001441 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 319224001442 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 319224001443 cell division protein FtsN; Region: ftsN; TIGR02223 319224001444 Sporulation related domain; Region: SPOR; cl10051 319224001445 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 319224001446 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 319224001447 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 319224001448 active site 319224001449 HIGH motif; other site 319224001450 KMSK motif region; other site 319224001451 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 319224001452 tRNA binding surface [nucleotide binding]; other site 319224001453 anticodon binding site; other site 319224001454 primosome assembly protein PriA; Validated; Region: PRK05580 319224001455 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 319224001456 ATP binding site [chemical binding]; other site 319224001457 putative Mg++ binding site [ion binding]; other site 319224001458 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001459 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 319224001460 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 319224001461 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 319224001462 Malic enzyme, N-terminal domain; Region: malic; pfam00390 319224001463 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 319224001464 putative NAD(P) binding site [chemical binding]; other site 319224001465 regulatory protein CsrD; Provisional; Region: PRK11059 319224001466 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 319224001467 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 319224001468 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 319224001469 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 319224001470 putative outer membrane porin HofQ; Provisional; Region: hofQ; PRK13568 319224001471 Secretin N-terminal domain; Region: Secretin_N_2; pfam07655 319224001472 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 319224001473 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 319224001474 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 319224001475 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001476 ribonuclease E; Reviewed; Region: rne; PRK10811 319224001477 TPR repeat; Region: TPR_11; pfam13414 319224001478 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 319224001479 TPR motif; other site 319224001480 binding surface 319224001481 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 319224001482 binding surface 319224001483 TPR motif; other site 319224001484 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 319224001485 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 319224001486 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 319224001487 Walker A motif; other site 319224001488 ATP binding site [chemical binding]; other site 319224001489 Walker B motif; other site 319224001490 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 319224001491 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 319224001492 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 319224001493 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224001494 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 319224001495 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 319224001496 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224001497 legume lectins; Region: lectin_L-type; cl14058 319224001498 homotetramer interaction site [polypeptide binding]; other site 319224001499 homodimer interaction site [polypeptide binding]; other site 319224001500 carbohydrate binding site [chemical binding]; other site 319224001501 metal binding site [ion binding]; metal-binding site 319224001502 rod shape-determining protein MreB; Provisional; Region: PRK13927 319224001503 hypothetical protein; Provisional; Region: PRK10039 319224001504 Cell division protein FtsA; Region: FtsA; cl11496 319224001505 rod shape-determining protein MreC; Region: mreC; TIGR00219 319224001506 rod shape-determining protein MreC; Region: MreC; pfam04085 319224001507 rod shape-determining protein MreD; Region: MreD; cl01087 319224001508 Maf-like protein; Region: Maf; pfam02545 319224001509 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 319224001510 active site 319224001511 dimer interface [polypeptide binding]; other site 319224001512 ribonuclease G; Provisional; Region: PRK11712 319224001513 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 319224001514 homodimer interface [polypeptide binding]; other site 319224001515 oligonucleotide binding site [chemical binding]; other site 319224001516 TIGR02099 family protein; Region: TIGR02099 319224001517 AsmA-like C-terminal region; Region: AsmA_2; cl15864 319224001518 Predicted amidohydrolase [General function prediction only]; Region: COG0388 319224001519 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 319224001520 putative active site [active] 319224001521 catalytic triad [active] 319224001522 dimer interface [polypeptide binding]; other site 319224001523 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 319224001524 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 319224001525 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 319224001526 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 319224001527 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 319224001528 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 319224001529 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 319224001530 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224001531 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 319224001532 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 319224001533 Ion transport protein; Region: Ion_trans; pfam00520 319224001534 amino acid transporter; Region: 2A0306; TIGR00909 319224001535 Spore germination protein; Region: Spore_permease; cl15802 319224001536 hydroperoxidase II; Provisional; Region: katE; PRK11249 319224001537 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 319224001538 tetramer interface [polypeptide binding]; other site 319224001539 heme binding pocket [chemical binding]; other site 319224001540 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 319224001541 domain interactions; other site 319224001542 MgtC family; Region: MgtC; pfam02308 319224001543 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 319224001544 Protein of unknown function (DUF615); Region: DUF615; cl01147 319224001545 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 319224001546 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 319224001547 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 319224001548 N-terminal plug; other site 319224001549 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 319224001550 ligand-binding site [chemical binding]; other site 319224001551 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224001552 Domain of unknown function; Region: DUF331; cl01149 319224001553 fumarate hydratase; Reviewed; Region: fumC; PRK00485 319224001554 Class II fumarases; Region: Fumarase_classII; cd01362 319224001555 active site 319224001556 tetramer interface [polypeptide binding]; other site 319224001557 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 319224001558 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 319224001559 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 319224001560 FeS/SAM binding site; other site 319224001561 Protein of unknown function (DUF541); Region: SIMPL; cl01077 319224001562 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 319224001563 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 319224001564 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 319224001565 S-adenosylmethionine binding site [chemical binding]; other site 319224001566 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 319224001567 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 319224001568 N-terminal plug; other site 319224001569 ligand-binding site [chemical binding]; other site 319224001570 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; cl01155 319224001571 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224001572 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224001573 Transposase Tn5 dimerisation domain; Region: Dimer_Tnp_Tn5; pfam02281 319224001574 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 319224001575 ATP binding site [chemical binding]; other site 319224001576 active site 319224001577 substrate binding site [chemical binding]; other site 319224001578 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 319224001579 cytochrome c nitrite reductase, Fe-S protein; Region: cyt_nit_nrfC; TIGR03149 319224001580 4Fe-4S binding domain; Region: Fer4; cl02805 319224001581 Polysulphide reductase, NrfD; Region: NrfD; cl01295 319224001582 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 319224001583 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 319224001584 Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ...; Region: Met_repressor_MetJ; cd00490 319224001585 dimerization interface [polypeptide binding]; other site 319224001586 DNA binding site [nucleotide binding] 319224001587 corepressor binding sites; other site 319224001588 O-succinylhomoserine (thiol)-lyase; Region: O_succ_thio_ly; TIGR02080 319224001589 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 319224001590 homodimer interface [polypeptide binding]; other site 319224001591 substrate-cofactor binding pocket; other site 319224001592 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224001593 catalytic residue [active] 319224001594 bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional; Region: metL; PRK09466 319224001595 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 319224001596 nucleotide binding site [chemical binding]; other site 319224001597 substrate binding site [chemical binding]; other site 319224001598 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 319224001599 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 319224001600 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 319224001601 FAD binding site [chemical binding]; other site 319224001602 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 319224001603 dimerization interface [polypeptide binding]; other site 319224001604 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224001605 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224001606 dimer interface [polypeptide binding]; other site 319224001607 putative CheW interface [polypeptide binding]; other site 319224001608 transcriptional regulator SlyA; Provisional; Region: PRK03573 319224001609 Helix-turn-helix domains; Region: HTH; cl00088 319224001610 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 319224001611 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 319224001612 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 319224001613 Protein of unknown function (DUF2955); Region: DUF2955; pfam11168 319224001614 Ethanolamine utilisation protein, EutH; Region: EutH; cl01248 319224001615 Cytochrome c; Region: Cytochrom_C; cl11414 319224001616 Cytochrome c; Region: Cytochrom_C; cl11414 319224001617 Cytochrome c [Energy production and conversion]; Region: COG3258 319224001618 Cytochrome c; Region: Cytochrom_C; cl11414 319224001619 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 319224001620 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 319224001621 This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_DmsA-EC; cd02770 319224001622 putative [Fe4-S4] binding site [ion binding]; other site 319224001623 putative molybdopterin cofactor binding site [chemical binding]; other site 319224001624 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_CT_DmsA-EC; cd02794 319224001625 putative molybdopterin cofactor binding site; other site 319224001626 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 319224001627 4Fe-4S binding domain; Region: Fer4; cl02805 319224001628 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 319224001629 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 319224001630 Gram-negative bacterial tonB protein; Region: TonB; cl10048 319224001631 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 319224001632 EamA-like transporter family; Region: EamA; cl01037 319224001633 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 319224001634 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 319224001635 active site 319224001636 motif I; other site 319224001637 motif II; other site 319224001638 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 319224001639 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 319224001640 ATP binding site [chemical binding]; other site 319224001641 Mg++ binding site [ion binding]; other site 319224001642 motif III; other site 319224001643 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 319224001644 nucleotide binding region [chemical binding]; other site 319224001645 ATP-binding site [chemical binding]; other site 319224001646 DbpA RNA binding domain; Region: DbpA; pfam03880 319224001647 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 319224001648 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 319224001649 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 319224001650 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 319224001651 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 319224001652 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224001653 putative substrate translocation pore; other site 319224001654 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 319224001655 dimer interface [polypeptide binding]; other site 319224001656 ssDNA binding site [nucleotide binding]; other site 319224001657 tetramer (dimer of dimers) interface [polypeptide binding]; other site 319224001658 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 319224001659 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 319224001660 glutamine binding [chemical binding]; other site 319224001661 catalytic triad [active] 319224001662 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 319224001663 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 319224001664 HDOD domain; Region: HDOD; pfam08668 319224001665 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 319224001666 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 319224001667 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 319224001668 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 319224001669 inhibitor-cofactor binding pocket; inhibition site 319224001670 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224001671 catalytic residue [active] 319224001672 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 319224001673 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 319224001674 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 319224001675 NAD(P) binding site [chemical binding]; other site 319224001676 catalytic residues [active] 319224001677 Domain of unknown function (DUF1338); Region: DUF1338; cl02226 319224001678 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224001679 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 319224001680 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 319224001681 dimer interface [polypeptide binding]; other site 319224001682 phosphorylation site [posttranslational modification] 319224001683 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 319224001684 ATP binding site [chemical binding]; other site 319224001685 Mg2+ binding site [ion binding]; other site 319224001686 G-X-G motif; other site 319224001687 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224001688 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 319224001689 active site 319224001690 phosphorylation site [posttranslational modification] 319224001691 intermolecular recognition site; other site 319224001692 dimerization interface [polypeptide binding]; other site 319224001693 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 319224001694 DNA binding site [nucleotide binding] 319224001695 Predicted membrane protein [Function unknown]; Region: COG3212 319224001696 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 319224001697 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 319224001698 ligand binding site [chemical binding]; other site 319224001699 flexible hinge region; other site 319224001700 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 319224001701 putative switch regulator; other site 319224001702 non-specific DNA interactions [nucleotide binding]; other site 319224001703 DNA binding site [nucleotide binding] 319224001704 sequence specific DNA binding site [nucleotide binding]; other site 319224001705 putative cAMP binding site [chemical binding]; other site 319224001706 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 319224001707 Sel1 repeat; Region: Sel1; cl02723 319224001708 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 319224001709 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224001710 metal binding site [ion binding]; metal-binding site 319224001711 active site 319224001712 I-site; other site 319224001713 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 319224001714 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 319224001715 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 319224001716 ATP binding site [chemical binding]; other site 319224001717 putative Mg++ binding site [ion binding]; other site 319224001718 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 319224001719 nucleotide binding region [chemical binding]; other site 319224001720 Helicase associated domain (HA2); Region: HA2; cl04503 319224001721 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 319224001722 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 319224001723 Transglycosylase; Region: Transgly; cl07896 319224001724 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224001725 PPIC-type PPIASE domain; Region: Rotamase; cl08278 319224001726 Putative integral membrane protein (DUF2391); Region: DUF2391; cl01935 319224001727 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 319224001728 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 319224001729 PAS domain; Region: PAS_9; pfam13426 319224001730 putative active site [active] 319224001731 heme pocket [chemical binding]; other site 319224001732 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 319224001733 PAS domain; Region: PAS_9; pfam13426 319224001734 putative active site [active] 319224001735 heme pocket [chemical binding]; other site 319224001736 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224001737 dimer interface [polypeptide binding]; other site 319224001738 putative CheW interface [polypeptide binding]; other site 319224001739 tetrathionate reductase subunit A; Provisional; Region: PRK14991 319224001740 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 319224001741 molybdopterin cofactor binding site; other site 319224001742 The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong...; Region: MopB_Tetrathionate-Ra; cd02758 319224001743 putative molybdopterin cofactor binding site [chemical binding]; other site 319224001744 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 319224001745 putative molybdopterin cofactor binding site; other site 319224001746 Polysulphide reductase, NrfD; Region: NrfD; cl01295 319224001747 tetrathionate reductase subunit B; Provisional; Region: PRK14993 319224001748 4Fe-4S binding domain; Region: Fer4; cl02805 319224001749 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 319224001750 NMT1-like family; Region: NMT1_2; cl15260 319224001751 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224001752 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 319224001753 dimer interface [polypeptide binding]; other site 319224001754 phosphorylation site [posttranslational modification] 319224001755 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 319224001756 ATP binding site [chemical binding]; other site 319224001757 Mg2+ binding site [ion binding]; other site 319224001758 G-X-G motif; other site 319224001759 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 319224001760 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 319224001761 active site 319224001762 phosphorylation site [posttranslational modification] 319224001763 intermolecular recognition site; other site 319224001764 dimerization interface [polypeptide binding]; other site 319224001765 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 319224001766 DNA binding residues [nucleotide binding] 319224001767 dimerization interface [polypeptide binding]; other site 319224001768 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 319224001769 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 319224001770 active site 319224001771 metal binding site [ion binding]; metal-binding site 319224001772 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 319224001773 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 319224001774 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 319224001775 Cache domain; Region: Cache_2; cl07034 319224001776 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224001777 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224001778 dimer interface [polypeptide binding]; other site 319224001779 putative CheW interface [polypeptide binding]; other site 319224001780 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 319224001781 BON domain; Region: BON; cl02771 319224001782 Restriction endonuclease; Region: Mrr_cat; cl00516 319224001783 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 319224001784 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 319224001785 AMP binding site [chemical binding]; other site 319224001786 metal binding site [ion binding]; metal-binding site 319224001787 active site 319224001788 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 319224001789 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 319224001790 two-component response regulator; Provisional; Region: PRK11173 319224001791 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 319224001792 active site 319224001793 phosphorylation site [posttranslational modification] 319224001794 intermolecular recognition site; other site 319224001795 dimerization interface [polypeptide binding]; other site 319224001796 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 319224001797 DNA binding site [nucleotide binding] 319224001798 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 319224001799 aspartate kinase III; Validated; Region: PRK09084 319224001800 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 319224001801 nucleotide binding site [chemical binding]; other site 319224001802 substrate binding site [chemical binding]; other site 319224001803 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC-like_1; cd04912 319224001804 dimer interface [polypeptide binding]; other site 319224001805 allosteric regulatory binding pocket; other site 319224001806 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII; Region: ACT_AKiii-LysC-EC_2; cd04917 319224001807 dimer interface [polypeptide binding]; other site 319224001808 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 319224001809 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 319224001810 Uncharacterized protein family (UPF0231); Region: UPF0231; cl11474 319224001811 transcriptional regulator NarL; Provisional; Region: PRK10651 319224001812 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 319224001813 active site 319224001814 phosphorylation site [posttranslational modification] 319224001815 intermolecular recognition site; other site 319224001816 dimerization interface [polypeptide binding]; other site 319224001817 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 319224001818 DNA binding residues [nucleotide binding] 319224001819 dimerization interface [polypeptide binding]; other site 319224001820 nitrate/nitrite sensor protein NarQ; Provisional; Region: PRK10935 319224001821 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 319224001822 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 319224001823 Histidine kinase; Region: HisKA_3; pfam07730 319224001824 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 319224001825 cytochrome c nitrite reductase subunit c552; Provisional; Region: nrfA; PRK11125 319224001826 putative molybdenum transport ATP-binding protein ModF; Provisional; Region: PRK10938 319224001827 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001828 Q-loop/lid; other site 319224001829 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001830 ABC transporter signature motif; other site 319224001831 ABC transporter signature motif; other site 319224001832 Walker B; other site 319224001833 Walker B; other site 319224001834 D-loop; other site 319224001835 D-loop; other site 319224001836 H-loop/switch region; other site 319224001837 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224001838 Walker A/P-loop; other site 319224001839 ATP binding site [chemical binding]; other site 319224001840 Q-loop/lid; other site 319224001841 ABC transporter signature motif; other site 319224001842 Walker B; other site 319224001843 D-loop; other site 319224001844 H-loop/switch region; other site 319224001845 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 319224001846 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 319224001847 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 319224001848 catalytic residues [active] 319224001849 Helix-turn-helix domains; Region: HTH; cl00088 319224001850 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 319224001851 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 319224001852 N-terminal plug; other site 319224001853 ligand-binding site [chemical binding]; other site 319224001854 Cupin domain; Region: Cupin_2; cl09118 319224001855 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224001856 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 319224001857 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224001858 LysE type translocator; Region: LysE; cl00565 319224001859 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 319224001860 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224001861 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224001862 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 319224001863 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224001864 Helix-turn-helix domains; Region: HTH; cl00088 319224001865 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 319224001866 putative effector binding pocket; other site 319224001867 dimerization interface [polypeptide binding]; other site 319224001868 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 319224001869 MatE; Region: MatE; cl10513 319224001870 MatE; Region: MatE; cl10513 319224001871 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 319224001872 oligomerisation interface [polypeptide binding]; other site 319224001873 mobile loop; other site 319224001874 roof hairpin; other site 319224001875 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 319224001876 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 319224001877 ring oligomerisation interface [polypeptide binding]; other site 319224001878 ATP/Mg binding site [chemical binding]; other site 319224001879 stacking interactions; other site 319224001880 hinge regions; other site 319224001881 SIR2 superfamily 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; cl00195 319224001882 Uncharacterized conserved protein [Function unknown]; Region: COG1432 319224001883 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 319224001884 putative metal binding site [ion binding]; other site 319224001885 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 319224001886 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 319224001887 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 319224001888 ATP binding site [chemical binding]; other site 319224001889 Helix-turn-helix domains; Region: HTH; cl00088 319224001890 putative outer membrane lipoprotein; Provisional; Region: PRK10510 319224001891 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224001892 ligand binding site [chemical binding]; other site 319224001893 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 319224001894 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 319224001895 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 319224001896 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 319224001897 MgtE intracellular N domain; Region: MgtE_N; cl15244 319224001898 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 319224001899 Divalent cation transporter; Region: MgtE; cl00786 319224001900 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 319224001901 dimerization domain swap beta strand [polypeptide binding]; other site 319224001902 regulatory protein interface [polypeptide binding]; other site 319224001903 active site 319224001904 regulatory phosphorylation site [posttranslational modification]; other site 319224001905 P-loop ATPase protein family; Region: ATP_bind_2; cl15794 319224001906 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 319224001907 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 319224001908 active site 319224001909 phosphorylation site [posttranslational modification] 319224001910 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 319224001911 30S subunit binding site; other site 319224001912 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 319224001913 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 319224001914 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 319224001915 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 319224001916 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 319224001917 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 319224001918 Walker A/P-loop; other site 319224001919 ATP binding site [chemical binding]; other site 319224001920 Q-loop/lid; other site 319224001921 ABC transporter signature motif; other site 319224001922 Walker B; other site 319224001923 D-loop; other site 319224001924 H-loop/switch region; other site 319224001925 OstA-like protein; Region: OstA; cl00844 319224001926 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 319224001927 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 319224001928 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224001929 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 319224001930 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 319224001931 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 319224001932 putative active site [active] 319224001933 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 319224001934 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 319224001935 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 319224001936 Walker A/P-loop; other site 319224001937 ATP binding site [chemical binding]; other site 319224001938 Q-loop/lid; other site 319224001939 ABC transporter signature motif; other site 319224001940 Walker B; other site 319224001941 D-loop; other site 319224001942 H-loop/switch region; other site 319224001943 Permease; Region: Permease; cl00510 319224001944 mce related protein; Region: MCE; pfam02470 319224001945 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 319224001946 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 319224001947 anti sigma factor interaction site; other site 319224001948 regulatory phosphorylation site [posttranslational modification]; other site 319224001949 BolA-like protein; Region: BolA; cl00386 319224001950 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 319224001951 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 319224001952 hinge; other site 319224001953 active site 319224001954 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 319224001955 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 319224001956 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 319224001957 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 319224001958 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 319224001959 homodimer interface [polypeptide binding]; other site 319224001960 substrate-cofactor binding pocket; other site 319224001961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224001962 catalytic residue [active] 319224001963 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 319224001964 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 319224001965 Walker A/P-loop; other site 319224001966 ATP binding site [chemical binding]; other site 319224001967 Q-loop/lid; other site 319224001968 ABC transporter signature motif; other site 319224001969 Walker B; other site 319224001970 D-loop; other site 319224001971 H-loop/switch region; other site 319224001972 TOBE-like domain; Region: TOBE_3; pfam12857 319224001973 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 319224001974 dimer interface [polypeptide binding]; other site 319224001975 conserved gate region; other site 319224001976 putative PBP binding loops; other site 319224001977 ABC-ATPase subunit interface; other site 319224001978 sulfate transport protein; Provisional; Region: cysT; CHL00187 319224001979 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 319224001980 dimer interface [polypeptide binding]; other site 319224001981 conserved gate region; other site 319224001982 putative PBP binding loops; other site 319224001983 ABC-ATPase subunit interface; other site 319224001984 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 319224001985 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 319224001986 Uncharacterized small protein (DUF2292); Region: DUF2292; cl02371 319224001987 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 319224001988 His-Xaa-Ser system protein HsxD; Region: chp_LLNDYxLRE; TIGR03976 319224001989 His-Xaa-Ser system radical SAM maturase HxsB; Region: rSAM_paired_1; TIGR03978 319224001990 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 319224001991 FeS/SAM binding site; other site 319224001992 HSF-type DNA-binding; Region: HSF_DNA-bind; cl12113 319224001993 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 319224001994 putative transposase OrfB; Reviewed; Region: PHA02517 319224001995 HTH-like domain; Region: HTH_21; pfam13276 319224001996 Integrase core domain; Region: rve; cl01316 319224001997 Integrase core domain; Region: rve_3; cl15866 319224001998 Helix-turn-helix domains; Region: HTH; cl00088 319224001999 His-Xaa-Ser system radical SAM maturase HxsC; Region: rSAM_pair_HxsC; TIGR03977 319224002000 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 319224002001 FeS/SAM binding site; other site 319224002002 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 319224002003 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 319224002004 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 319224002005 protein binding site [polypeptide binding]; other site 319224002006 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 319224002007 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 319224002008 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 319224002009 protein binding site [polypeptide binding]; other site 319224002010 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 319224002011 Predicted ATPase [General function prediction only]; Region: COG1485 319224002012 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 319224002013 23S rRNA interface [nucleotide binding]; other site 319224002014 L3 interface [polypeptide binding]; other site 319224002015 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 319224002016 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 319224002017 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 319224002018 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 319224002019 GDP-binding site [chemical binding]; other site 319224002020 ACT binding site; other site 319224002021 IMP binding site; other site 319224002022 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 319224002023 Sel1 repeat; Region: Sel1; cl02723 319224002024 exoribonuclease R; Provisional; Region: PRK11642 319224002025 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 319224002026 RNB domain; Region: RNB; pfam00773 319224002027 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 319224002028 RNA binding site [nucleotide binding]; other site 319224002029 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 319224002030 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 319224002031 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 319224002032 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 319224002033 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224002034 putative substrate translocation pore; other site 319224002035 Protein of unknown function, DUF481; Region: DUF481; cl01213 319224002036 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 319224002037 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 319224002038 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 319224002039 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 319224002040 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 319224002041 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 319224002042 Peptidase S46; Region: Peptidase_S46; pfam10459 319224002043 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 319224002044 replicative DNA helicase; Provisional; Region: PRK08006 319224002045 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 319224002046 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 319224002047 Walker A motif; other site 319224002048 ATP binding site [chemical binding]; other site 319224002049 Walker B motif; other site 319224002050 DNA binding loops [nucleotide binding] 319224002051 alanine racemase; Reviewed; Region: alr; PRK00053 319224002052 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 319224002053 active site 319224002054 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 319224002055 substrate binding site [chemical binding]; other site 319224002056 catalytic residues [active] 319224002057 dimer interface [polypeptide binding]; other site 319224002058 Predicted inhibitor of MCP methylation, homolog of CheC [Cell motility and secretion]; Region: COG1406 319224002059 Chemotaxis phosphatase CheX; Region: CheX; cl15816 319224002060 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 319224002061 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 319224002062 FMN binding site [chemical binding]; other site 319224002063 active site 319224002064 catalytic residues [active] 319224002065 substrate binding site [chemical binding]; other site 319224002066 PspC domain; Region: PspC; cl00864 319224002067 enoyl-CoA hydratase; Provisional; Region: PRK06688 319224002068 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 319224002069 substrate binding site [chemical binding]; other site 319224002070 oxyanion hole (OAH) forming residues; other site 319224002071 trimer interface [polypeptide binding]; other site 319224002072 Protein of unknown function (DUF461); Region: DUF461; cl01071 319224002073 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 319224002074 outer membrane protein; Region: OMP_w_GlyGly; TIGR04219 319224002075 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 319224002076 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 319224002077 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 319224002078 dimer interface [polypeptide binding]; other site 319224002079 ADP-ribose binding site [chemical binding]; other site 319224002080 active site 319224002081 nudix motif; other site 319224002082 metal binding site [ion binding]; metal-binding site 319224002083 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 319224002084 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 319224002085 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 319224002086 active site 319224002087 metal binding site [ion binding]; metal-binding site 319224002088 hexamer interface [polypeptide binding]; other site 319224002089 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 319224002090 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 319224002091 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 319224002092 ATP binding site [chemical binding]; other site 319224002093 Mg2+ binding site [ion binding]; other site 319224002094 G-X-G motif; other site 319224002095 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 319224002096 anchoring element; other site 319224002097 dimer interface [polypeptide binding]; other site 319224002098 ATP binding site [chemical binding]; other site 319224002099 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 319224002100 active site 319224002101 metal binding site [ion binding]; metal-binding site 319224002102 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 319224002103 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 319224002104 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 319224002105 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 319224002106 CAP-like domain; other site 319224002107 active site 319224002108 primary dimer interface [polypeptide binding]; other site 319224002109 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224002110 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002111 dimer interface [polypeptide binding]; other site 319224002112 putative CheW interface [polypeptide binding]; other site 319224002113 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; cl15774 319224002114 octamerization interface [polypeptide binding]; other site 319224002115 diferric-oxygen binding site [ion binding]; other site 319224002116 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 319224002117 Superinfection exclusion protein B; Region: SieB; pfam14163 319224002118 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 319224002119 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 319224002120 dimer interface [polypeptide binding]; other site 319224002121 phosphorylation site [posttranslational modification] 319224002122 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 319224002123 ATP binding site [chemical binding]; other site 319224002124 Mg2+ binding site [ion binding]; other site 319224002125 G-X-G motif; other site 319224002126 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 319224002127 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 319224002128 putative ATP binding site [chemical binding]; other site 319224002129 putative substrate interface [chemical binding]; other site 319224002130 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 319224002131 eyelet of channel; other site 319224002132 trimer interface [polypeptide binding]; other site 319224002133 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 319224002134 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 319224002135 Protein of unknown function (DUF3069); Region: DUF3069; pfam11269 319224002136 malate dehydrogenase; Provisional; Region: PRK13529 319224002137 Malic enzyme, N-terminal domain; Region: malic; pfam00390 319224002138 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 319224002139 NAD(P) binding site [chemical binding]; other site 319224002140 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 319224002141 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 319224002142 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 319224002143 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 319224002144 Bacterial PH domain; Region: DUF304; cl01348 319224002145 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224002146 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 319224002147 synthetase active site [active] 319224002148 NTP binding site [chemical binding]; other site 319224002149 metal binding site [ion binding]; metal-binding site 319224002150 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 319224002151 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 319224002152 active site 319224002153 Zn binding site [ion binding]; other site 319224002154 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 319224002155 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 319224002156 RNA binding surface [nucleotide binding]; other site 319224002157 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 319224002158 active site 319224002159 uracil binding [chemical binding]; other site 319224002160 Domain of unknown function (DUF4097); Region: DUF4097; pfam13349 319224002161 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 319224002162 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 319224002163 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 319224002164 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224002165 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 319224002166 DNA binding residues [nucleotide binding] 319224002167 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 319224002168 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224002169 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002170 dimer interface [polypeptide binding]; other site 319224002171 putative CheW interface [polypeptide binding]; other site 319224002172 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 319224002173 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 319224002174 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224002175 active site 319224002176 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 319224002177 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 319224002178 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 319224002179 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 319224002180 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 319224002181 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 319224002182 tRNA; other site 319224002183 putative tRNA binding site [nucleotide binding]; other site 319224002184 putative NADP binding site [chemical binding]; other site 319224002185 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 319224002186 peptide chain release factor 1; Validated; Region: prfA; PRK00591 319224002187 RF-1 domain; Region: RF-1; cl02875 319224002188 RF-1 domain; Region: RF-1; cl02875 319224002189 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 319224002190 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; cl16911 319224002191 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224002192 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224002193 Invasion gene expression up-regulator, SirB; Region: SirB; cl01184 319224002194 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 319224002195 Tetratricopeptide repeat; Region: TPR_9; pfam13371 319224002196 Protein of unknown function (DUF819); Region: DUF819; cl02317 319224002197 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 319224002198 NeuB family; Region: NeuB; cl00496 319224002199 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 319224002200 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002201 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 319224002202 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 319224002203 trimer interface [polypeptide binding]; other site 319224002204 eyelet of channel; other site 319224002205 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 319224002206 Helix-turn-helix domains; Region: HTH; cl00088 319224002207 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 319224002208 dimerization interface [polypeptide binding]; other site 319224002209 Protein of unknown function (DUF819); Region: DUF819; cl02317 319224002210 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 319224002211 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 319224002212 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 319224002213 Nitrogen regulatory protein P-II; Region: P-II; cl00412 319224002214 Nitrogen regulatory protein P-II; Region: P-II; smart00938 319224002215 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 319224002216 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002217 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 319224002218 VanZ like family; Region: VanZ; cl01971 319224002219 Protein of unknown function (DUF520); Region: DUF520; cl00723 319224002220 muropeptide transporter; Validated; Region: ampG; PRK11010 319224002221 AmpG-like permease; Region: 2A0125; TIGR00901 319224002222 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 319224002223 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 319224002224 substrate binding site [chemical binding]; other site 319224002225 Uncharacterized lipoprotein; Region: Lipoprotein_16; pfam03923 319224002226 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; cl01155 319224002227 Protein of unknown function (DUF2804); Region: DUF2804; pfam10974 319224002228 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 319224002229 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 319224002230 The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the...; Region: DnaQ_like_exo; cl10012 319224002231 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 319224002232 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 319224002233 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 319224002234 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 319224002235 aromatic acid decarboxylase; Validated; Region: PRK05920 319224002236 Flavoprotein; Region: Flavoprotein; cl08021 319224002237 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224002238 active site 319224002239 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 319224002240 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224002241 Walker A/P-loop; other site 319224002242 ATP binding site [chemical binding]; other site 319224002243 Q-loop/lid; other site 319224002244 ABC transporter signature motif; other site 319224002245 Walker B; other site 319224002246 D-loop; other site 319224002247 H-loop/switch region; other site 319224002248 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224002249 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 319224002250 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 319224002251 catalytic residues [active] 319224002252 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined; Region: PA_subtilisin_1; cd04818 319224002253 PA/protease or protease-like domain interface [polypeptide binding]; other site 319224002254 Peptidase S8 family domain in Vpr-like proteins; Region: Peptidases_S8_subtilisin_Vpr-like; cd07474 319224002255 Fn3-like domain (DUF1034); Region: DUF1034; pfam06280 319224002256 DNA-binding transcriptional regulator AsnC; Provisional; Region: PRK11179 319224002257 Helix-turn-helix domains; Region: HTH; cl00088 319224002258 AsnC family; Region: AsnC_trans_reg; pfam01037 319224002259 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224002260 active site 319224002261 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 319224002262 Peptidase family U32; Region: Peptidase_U32; cl03113 319224002263 Collagenase; Region: DUF3656; pfam12392 319224002264 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224002265 Protein of unknown function (DUF2004); Region: DUF2004; pfam09406 319224002266 Cupin domain; Region: Cupin_2; cl09118 319224002267 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 319224002268 active site 319224002269 Fe-S metabolism associated domain; Region: SufE; cl00951 319224002270 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 319224002271 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 319224002272 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224002273 catalytic residue [active] 319224002274 MltA-interacting protein MipA; Region: MipA; cl01504 319224002275 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 319224002276 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224002277 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 319224002278 active site 319224002279 phosphorylation site [posttranslational modification] 319224002280 intermolecular recognition site; other site 319224002281 dimerization interface [polypeptide binding]; other site 319224002282 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 319224002283 DNA binding site [nucleotide binding] 319224002284 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224002285 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 319224002286 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 319224002287 dimer interface [polypeptide binding]; other site 319224002288 phosphorylation site [posttranslational modification] 319224002289 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 319224002290 ATP binding site [chemical binding]; other site 319224002291 Mg2+ binding site [ion binding]; other site 319224002292 G-X-G motif; other site 319224002293 MltA-interacting protein MipA; Region: MipA; cl01504 319224002294 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 319224002295 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 319224002296 active site 319224002297 catalytic tetrad [active] 319224002298 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 319224002299 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 319224002300 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 319224002301 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 319224002302 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 319224002303 FMN-binding domain; Region: FMN_bind; cl01081 319224002304 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 319224002305 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 319224002306 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 319224002307 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 319224002308 catalytic loop [active] 319224002309 iron binding site [ion binding]; other site 319224002310 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 319224002311 FAD binding pocket [chemical binding]; other site 319224002312 FAD binding motif [chemical binding]; other site 319224002313 phosphate binding motif [ion binding]; other site 319224002314 beta-alpha-beta structure motif; other site 319224002315 NAD binding pocket [chemical binding]; other site 319224002316 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 319224002317 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 319224002318 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224002319 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 319224002320 Helix-turn-helix domains; Region: HTH; cl00088 319224002321 Predicted acetyltransferase [General function prediction only]; Region: COG3153 319224002322 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224002323 Coenzyme A binding pocket [chemical binding]; other site 319224002324 Protein of unknown function DUF84; Region: NTPase_I-T; cl00866 319224002325 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 319224002326 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 319224002327 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 319224002328 active site 319224002329 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 319224002330 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 319224002331 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 319224002332 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 319224002333 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224002334 Coenzyme A binding pocket [chemical binding]; other site 319224002335 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 319224002336 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 319224002337 META domain; Region: META; cl01245 319224002338 S-adenosylmethionine synthetase; Validated; Region: PRK05250 319224002339 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 319224002340 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 319224002341 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 319224002342 transketolase; Reviewed; Region: PRK12753 319224002343 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 319224002344 TPP-binding site [chemical binding]; other site 319224002345 dimer interface [polypeptide binding]; other site 319224002346 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 319224002347 PYR/PP interface [polypeptide binding]; other site 319224002348 dimer interface [polypeptide binding]; other site 319224002349 TPP binding site [chemical binding]; other site 319224002350 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 319224002351 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 319224002352 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002353 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224002354 Phosphoglycerate kinase; Region: PGK; pfam00162 319224002355 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; cd00318 319224002356 substrate binding site [chemical binding]; other site 319224002357 hinge regions; other site 319224002358 ADP binding site [chemical binding]; other site 319224002359 catalytic site [active] 319224002360 hypothetical protein; Provisional; Region: PRK08185 319224002361 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 319224002362 intersubunit interface [polypeptide binding]; other site 319224002363 active site 319224002364 zinc binding site [ion binding]; other site 319224002365 Na+ binding site [ion binding]; other site 319224002366 Protein of unknown function, DUF481; Region: DUF481; cl01213 319224002367 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 319224002368 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 319224002369 transmembrane helices; other site 319224002370 Helix-turn-helix domains; Region: HTH; cl00088 319224002371 DNA binding site [nucleotide binding] 319224002372 PAS domain; Region: PAS_9; pfam13426 319224002373 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224002374 radical SAM protein, TatD family-associated; Region: tatD_link_rSAM; TIGR04038 319224002375 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 319224002376 FeS/SAM binding site; other site 319224002377 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224002378 Protein export membrane protein; Region: SecD_SecF; cl14618 319224002379 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224002380 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 319224002381 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 319224002382 DEAD-like helicases superfamily; Region: DEXDc; smart00487 319224002383 ATP binding site [chemical binding]; other site 319224002384 Mg++ binding site [ion binding]; other site 319224002385 motif III; other site 319224002386 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 319224002387 nucleotide binding region [chemical binding]; other site 319224002388 ATP-binding site [chemical binding]; other site 319224002389 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 319224002390 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 319224002391 S-adenosylmethionine binding site [chemical binding]; other site 319224002392 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 319224002393 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 319224002394 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 319224002395 active site 319224002396 Int/Topo IB signature motif; other site 319224002397 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 319224002398 dimerization domain [polypeptide binding]; other site 319224002399 dimer interface [polypeptide binding]; other site 319224002400 catalytic residues [active] 319224002401 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 319224002402 DHH family; Region: DHH; pfam01368 319224002403 DHHA1 domain; Region: DHHA1; pfam02272 319224002404 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224002405 Coenzyme A binding pocket [chemical binding]; other site 319224002406 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 319224002407 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 319224002408 catalytic residue [active] 319224002409 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 319224002410 catalytic residues [active] 319224002411 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224002412 peroxiredoxin; Region: AhpC; TIGR03137 319224002413 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 319224002414 dimer interface [polypeptide binding]; other site 319224002415 decamer (pentamer of dimers) interface [polypeptide binding]; other site 319224002416 catalytic triad [active] 319224002417 peroxidatic and resolving cysteines [active] 319224002418 multifunctional aminopeptidase A; Provisional; Region: PRK00913 319224002419 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 319224002420 interface (dimer of trimers) [polypeptide binding]; other site 319224002421 Substrate-binding/catalytic site; other site 319224002422 Zn-binding sites [ion binding]; other site 319224002423 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 319224002424 Mechanosensitive ion channel; Region: MS_channel; pfam00924 319224002425 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 319224002426 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 319224002427 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002428 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 319224002429 heme-binding residues [chemical binding]; other site 319224002430 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 319224002431 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002432 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 319224002433 S-adenosylmethionine binding site [chemical binding]; other site 319224002434 Rhomboid family; Region: Rhomboid; cl11446 319224002435 calcium/sodium:proton antiporter; Provisional; Region: PRK10599 319224002436 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 319224002437 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224002438 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224002439 Predicted membrane protein [Function unknown]; Region: COG2119 319224002440 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 319224002441 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 319224002442 yybP-ykoY element as predicted by Rfam (RF00080), score 63.83 319224002443 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 319224002444 Peptidase S46; Region: Peptidase_S46; pfam10459 319224002445 Protein of unknown function (DUF2931); Region: DUF2931; pfam11153 319224002446 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224002447 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 319224002448 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 319224002449 RNA binding surface [nucleotide binding]; other site 319224002450 Pseudouridine synthase, Escherichia coli RluF like; Region: PseudoU_synth_RluF; cd02554 319224002451 probable active site [active] 319224002452 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 319224002453 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224002454 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 319224002455 dimerization interface [polypeptide binding]; other site 319224002456 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224002457 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002458 dimer interface [polypeptide binding]; other site 319224002459 putative CheW interface [polypeptide binding]; other site 319224002460 EamA-like transporter family; Region: EamA; cl01037 319224002461 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 319224002462 Helix-turn-helix domain; Region: HTH_18; pfam12833 319224002463 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 319224002464 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 319224002465 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 319224002466 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 319224002467 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 319224002468 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224002469 DNA-binding site [nucleotide binding]; DNA binding site 319224002470 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 319224002471 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224002472 homodimer interface [polypeptide binding]; other site 319224002473 catalytic residue [active] 319224002474 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 319224002475 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 319224002476 homodimer interface [polypeptide binding]; other site 319224002477 substrate-cofactor binding pocket; other site 319224002478 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224002479 catalytic residue [active] 319224002480 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 319224002481 SAM-dependent 23S ribosomal RNA mG1835 methyltransferase; Provisional; Region: PRK15001 319224002482 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 319224002483 S-adenosylmethionine binding site [chemical binding]; other site 319224002484 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 319224002485 BolA-like protein; Region: BolA; cl00386 319224002486 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 319224002487 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 319224002488 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 319224002489 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; cl01155 319224002490 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 319224002491 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 319224002492 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 319224002493 FMN-binding domain; Region: FMN_bind; cl01081 319224002494 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 319224002495 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 319224002496 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 319224002497 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 319224002498 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 319224002499 FAD binding pocket [chemical binding]; other site 319224002500 FAD binding motif [chemical binding]; other site 319224002501 phosphate binding motif [ion binding]; other site 319224002502 beta-alpha-beta structure motif; other site 319224002503 NAD binding pocket [chemical binding]; other site 319224002504 ApbE family; Region: ApbE; cl00643 319224002505 Protein of unknown function (DUF539); Region: DUF539; cl01129 319224002506 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 319224002507 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 319224002508 heme binding site [chemical binding]; other site 319224002509 ferroxidase pore; other site 319224002510 ferroxidase diiron center [ion binding]; other site 319224002511 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 319224002512 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 319224002513 heme binding site [chemical binding]; other site 319224002514 ferroxidase pore; other site 319224002515 ferroxidase diiron center [ion binding]; other site 319224002516 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 319224002517 dimerization interface [polypeptide binding]; other site 319224002518 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002519 dimer interface [polypeptide binding]; other site 319224002520 putative CheW interface [polypeptide binding]; other site 319224002521 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 319224002522 active site 319224002523 DNA polymerase IV; Validated; Region: PRK02406 319224002524 DNA binding site [nucleotide binding] 319224002525 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224002526 Helix-turn-helix domains; Region: HTH; cl00088 319224002527 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 319224002528 putative effector binding pocket; other site 319224002529 dimerization interface [polypeptide binding]; other site 319224002530 EamA-like transporter family; Region: EamA; cl01037 319224002531 EamA-like transporter family; Region: EamA; cl01037 319224002532 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 319224002533 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 319224002534 metal binding site [ion binding]; metal-binding site 319224002535 dimer interface [polypeptide binding]; other site 319224002536 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 319224002537 interface (dimer of trimers) [polypeptide binding]; other site 319224002538 Substrate-binding/catalytic site; other site 319224002539 Zn-binding sites [ion binding]; other site 319224002540 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4994 319224002541 Protein of unknown function (DUF2956); Region: DUF2956; pfam11169 319224002542 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 319224002543 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 319224002544 Walker A/P-loop; other site 319224002545 ATP binding site [chemical binding]; other site 319224002546 Q-loop/lid; other site 319224002547 ABC transporter signature motif; other site 319224002548 Walker B; other site 319224002549 D-loop; other site 319224002550 H-loop/switch region; other site 319224002551 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 319224002552 ABC-ATPase subunit interface; other site 319224002553 dimer interface [polypeptide binding]; other site 319224002554 putative PBP binding regions; other site 319224002555 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 319224002556 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 319224002557 putative hemin binding site; other site 319224002558 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 319224002559 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224002560 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 319224002561 Gram-negative bacterial tonB protein; Region: TonB; cl10048 319224002562 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 319224002563 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 319224002564 N-terminal plug; other site 319224002565 ligand-binding site [chemical binding]; other site 319224002566 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 319224002567 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 319224002568 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 319224002569 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224002570 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224002571 Walker A/P-loop; other site 319224002572 ATP binding site [chemical binding]; other site 319224002573 Q-loop/lid; other site 319224002574 ABC transporter signature motif; other site 319224002575 Walker B; other site 319224002576 D-loop; other site 319224002577 H-loop/switch region; other site 319224002578 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 319224002579 AMP-binding enzyme; Region: AMP-binding; cl15778 319224002580 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224002581 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 319224002582 4Fe-4S binding domain; Region: Fer4_5; pfam12801 319224002583 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 319224002584 PAS domain S-box; Region: sensory_box; TIGR00229 319224002585 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 319224002586 putative active site [active] 319224002587 heme pocket [chemical binding]; other site 319224002588 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 319224002589 phage shock protein operon transcriptional activator; Provisional; Region: pspF; PRK11608 319224002590 Walker A motif; other site 319224002591 ATP binding site [chemical binding]; other site 319224002592 Walker B motif; other site 319224002593 arginine finger; other site 319224002594 Helix-turn-helix domains; Region: HTH; cl00088 319224002595 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 319224002596 DsbD alpha interface [polypeptide binding]; other site 319224002597 catalytic residues [active] 319224002598 LysE type translocator; Region: LysE; cl00565 319224002599 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 319224002600 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 319224002601 ligand binding site [chemical binding]; other site 319224002602 active site 319224002603 UGI interface [polypeptide binding]; other site 319224002604 catalytic site [active] 319224002605 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 319224002606 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 319224002607 substrate binding pocket [chemical binding]; other site 319224002608 chain length determination region; other site 319224002609 substrate-Mg2+ binding site; other site 319224002610 catalytic residues [active] 319224002611 aspartate-rich region 1; other site 319224002612 active site lid residues [active] 319224002613 aspartate-rich region 2; other site 319224002614 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 319224002615 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 319224002616 GTPase CgtA; Reviewed; Region: obgE; PRK12298 319224002617 GTP1/OBG; Region: GTP1_OBG; pfam01018 319224002618 Obg GTPase; Region: Obg; cd01898 319224002619 G1 box; other site 319224002620 GTP/Mg2+ binding site [chemical binding]; other site 319224002621 Switch I region; other site 319224002622 G2 box; other site 319224002623 G3 box; other site 319224002624 Switch II region; other site 319224002625 G4 box; other site 319224002626 G5 box; other site 319224002627 Uncharacterized conserved protein [Function unknown]; Region: COG2966 319224002628 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 319224002629 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 319224002630 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 319224002631 NADP+ binding site [chemical binding]; other site 319224002632 folate binding site [chemical binding]; other site 319224002633 Protein of unknown function (DUF3718); Region: DUF3718; pfam12514 319224002634 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 319224002635 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224002636 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002637 dimer interface [polypeptide binding]; other site 319224002638 putative CheW interface [polypeptide binding]; other site 319224002639 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 319224002640 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 319224002641 active site 319224002642 metal binding site [ion binding]; metal-binding site 319224002643 Protein of unknown function (DUF525); Region: DUF525; cl01119 319224002644 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; cl16911 319224002645 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 319224002646 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 319224002647 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 319224002648 SurA N-terminal domain; Region: SurA_N_3; cl07813 319224002649 PPIC-type PPIASE domain; Region: Rotamase; cl08278 319224002650 PPIC-type PPIASE domain; Region: Rotamase; cl08278 319224002651 LPS assembly outer membrane complex protein LptD; Provisional; Region: PRK03761 319224002652 OstA-like protein; Region: OstA; cl00844 319224002653 Organic solvent tolerance protein; Region: OstA_C; pfam04453 319224002654 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224002655 Phosphotransferase enzyme family; Region: APH; pfam01636 319224002656 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 319224002657 Substrate binding site; other site 319224002658 metal-binding site 319224002659 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 319224002660 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 319224002661 putative metal binding site [ion binding]; other site 319224002662 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 319224002663 HSP70 interaction site [polypeptide binding]; other site 319224002664 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; cl01155 319224002665 glycerate dehydrogenase; Provisional; Region: PRK06487 319224002666 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002667 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 319224002668 binding surface 319224002669 TPR motif; other site 319224002670 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 319224002671 Protein of unknown function (DUF3142); Region: DUF3142; pfam11340 319224002672 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224002673 active site 319224002674 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 319224002675 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002676 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224002677 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 319224002678 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 319224002679 Walker A/P-loop; other site 319224002680 ATP binding site [chemical binding]; other site 319224002681 Q-loop/lid; other site 319224002682 ABC transporter signature motif; other site 319224002683 Walker B; other site 319224002684 D-loop; other site 319224002685 H-loop/switch region; other site 319224002686 TOBE-like domain; Region: TOBE_3; pfam12857 319224002687 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 319224002688 dimer interface [polypeptide binding]; other site 319224002689 conserved gate region; other site 319224002690 putative PBP binding loops; other site 319224002691 ABC-ATPase subunit interface; other site 319224002692 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 319224002693 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 319224002694 dimer interface [polypeptide binding]; other site 319224002695 conserved gate region; other site 319224002696 putative PBP binding loops; other site 319224002697 ABC-ATPase subunit interface; other site 319224002698 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 319224002699 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 319224002700 cysteine synthase B; Region: cysM; TIGR01138 319224002701 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 319224002702 dimer interface [polypeptide binding]; other site 319224002703 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224002704 catalytic residue [active] 319224002705 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 319224002706 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 319224002707 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224002708 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 319224002709 dimer interface [polypeptide binding]; other site 319224002710 phosphorylation site [posttranslational modification] 319224002711 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 319224002712 ATP binding site [chemical binding]; other site 319224002713 Mg2+ binding site [ion binding]; other site 319224002714 G-X-G motif; other site 319224002715 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 319224002716 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 319224002717 active site 319224002718 phosphorylation site [posttranslational modification] 319224002719 intermolecular recognition site; other site 319224002720 dimerization interface [polypeptide binding]; other site 319224002721 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 319224002722 DNA binding site [nucleotide binding] 319224002723 Protein of unknown function (DUF3019); Region: DUF3019; pfam11456 319224002724 MltA-interacting protein MipA; Region: MipA; cl01504 319224002725 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 319224002726 YcxB-like protein; Region: YcxB; pfam14317 319224002727 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224002728 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 319224002729 active site 319224002730 metal binding site [ion binding]; metal-binding site 319224002731 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224002732 Predicted transcriptional regulator [Transcription]; Region: COG2345 319224002733 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 319224002734 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 319224002735 RNA binding surface [nucleotide binding]; other site 319224002736 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 319224002737 active site 319224002738 uracil binding [chemical binding]; other site 319224002739 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 319224002740 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002741 dimer interface [polypeptide binding]; other site 319224002742 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 319224002743 putative CheW interface [polypeptide binding]; other site 319224002744 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 319224002745 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 319224002746 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 319224002747 RNA binding surface [nucleotide binding]; other site 319224002748 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224002749 active site 319224002750 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 319224002751 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 319224002752 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 319224002753 Clp amino terminal domain; Region: Clp_N; pfam02861 319224002754 Clp amino terminal domain; Region: Clp_N; pfam02861 319224002755 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 319224002756 Walker A motif; other site 319224002757 ATP binding site [chemical binding]; other site 319224002758 Walker B motif; other site 319224002759 arginine finger; other site 319224002760 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 319224002761 Walker A motif; other site 319224002762 ATP binding site [chemical binding]; other site 319224002763 Walker B motif; other site 319224002764 arginine finger; other site 319224002765 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 319224002766 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 319224002767 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 319224002768 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 319224002769 Integrase core domain; Region: rve; cl01316 319224002770 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 319224002771 oxaloacetate decarboxylase; Provisional; Region: PRK14040 319224002772 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 319224002773 active site 319224002774 catalytic residues [active] 319224002775 metal binding site [ion binding]; metal-binding site 319224002776 homodimer binding site [polypeptide binding]; other site 319224002777 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 319224002778 carboxyltransferase (CT) interaction site; other site 319224002779 biotinylation site [posttranslational modification]; other site 319224002780 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 319224002781 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 319224002782 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 319224002783 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 319224002784 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 319224002785 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 319224002786 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224002787 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 319224002788 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 319224002789 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224002790 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 319224002791 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 319224002792 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224002793 catalytic residue [active] 319224002794 GAF domain; Region: GAF_2; pfam13185 319224002795 GAF domain; Region: GAF; cl15785 319224002796 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224002797 metal binding site [ion binding]; metal-binding site 319224002798 active site 319224002799 I-site; other site 319224002800 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 319224002801 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224002802 AIR carboxylase; Region: AIRC; cl00310 319224002803 putative transporter; Provisional; Region: PRK11660 319224002804 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224002805 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224002806 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 319224002807 von Willebrand factor; Region: vWF_A; pfam12450 319224002808 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 319224002809 VWA subgroup: 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...; Region: vWA_subgroup; cd01465 319224002810 metal ion-dependent adhesion site (MIDAS); other site 319224002811 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 319224002812 RNA polymerase sigma factor; Provisional; Region: PRK12513 319224002813 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224002814 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 319224002815 DNA binding residues [nucleotide binding] 319224002816 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; cl15774 319224002817 Protein of unknown function (DUF3545); Region: DUF3545; pfam12065 319224002818 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 319224002819 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 319224002820 active site 319224002821 dimer interface [polypeptide binding]; other site 319224002822 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 319224002823 dimer interface [polypeptide binding]; other site 319224002824 active site 319224002825 transaldolase-like protein; Provisional; Region: PTZ00411 319224002826 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 319224002827 active site 319224002828 dimer interface [polypeptide binding]; other site 319224002829 catalytic residue [active] 319224002830 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; cl01155 319224002831 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224002832 ligand binding site [chemical binding]; other site 319224002833 putative phosphoketolase; Provisional; Region: PRK05261 319224002834 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 319224002835 TPP-binding site; other site 319224002836 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; Region: XFP; pfam03894 319224002837 XFP C-terminal domain; Region: XFP_C; pfam09363 319224002838 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 319224002839 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 319224002840 Protein of unknown function (DUF328); Region: DUF328; cl01143 319224002841 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 319224002842 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions; Region: PA_M28_2; cd04815 319224002843 PA/protease or protease-like domain interface [polypeptide binding]; other site 319224002844 M28 Zn-Peptidase Plasma glutamate carboxypeptidase; Region: M28_Pgcp_like; cd03883 319224002845 metal binding site [ion binding]; metal-binding site 319224002846 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 319224002847 dimerization interface [polypeptide binding]; other site 319224002848 putative DNA binding site [nucleotide binding]; other site 319224002849 putative Zn2+ binding site [ion binding]; other site 319224002850 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 319224002851 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 319224002852 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 319224002853 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 319224002854 active site 319224002855 Riboflavin kinase; Region: Flavokinase; cl03312 319224002856 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 319224002857 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 319224002858 HIGH motif; other site 319224002859 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 319224002860 active site 319224002861 KMSKS motif; other site 319224002862 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 319224002863 tRNA binding surface [nucleotide binding]; other site 319224002864 anticodon binding site; other site 319224002865 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 319224002866 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 319224002867 lipoprotein signal peptidase; Provisional; Region: PRK14787 319224002868 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224002869 LytB protein; Region: LYTB; cl00507 319224002870 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 319224002871 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 319224002872 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 319224002873 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224002874 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 319224002875 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 319224002876 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 319224002877 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224002878 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 319224002879 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224002880 Type II transport protein GspH; Region: GspH; pfam12019 319224002881 Type II transport protein GspH; Region: GspH; pfam12019 319224002882 Nitrogen regulatory protein P-II; Region: P-II; cl00412 319224002883 Nitrogen regulatory protein P-II; Region: P-II; smart00938 319224002884 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 319224002885 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224002886 Transcriptional regulators [Transcription]; Region: PurR; COG1609 319224002887 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 319224002888 DNA binding site [nucleotide binding] 319224002889 domain linker motif; other site 319224002890 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 319224002891 putative ligand binding site [chemical binding]; other site 319224002892 putative dimerization interface [polypeptide binding]; other site 319224002893 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 319224002894 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; cl01155 319224002895 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 319224002896 Putative carbohydrate binding domain; Region: CHB_HEX; cl03918 319224002897 The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a...; Region: GH20_Sm-chitobiase-like; cd06569 319224002898 Glycosyl hydrolase family 20, catalytic domain; Region: Glyco_hydro_20; pfam00728 319224002899 active site 319224002900 C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase); Region: E_set_Chitobiase_C; cd02847 319224002901 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 319224002902 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 319224002903 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 319224002904 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 319224002905 dimer interface [polypeptide binding]; other site 319224002906 active site 319224002907 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 319224002908 dimer interface [polypeptide binding]; other site 319224002909 active site 319224002910 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 319224002911 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 319224002912 active site 319224002913 dimer interface [polypeptide binding]; other site 319224002914 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 319224002915 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 319224002916 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 319224002917 putative substrate translocation pore; other site 319224002918 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 319224002919 Cupin domain; Region: Cupin_2; cl09118 319224002920 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 319224002921 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 319224002922 tetrameric interface [polypeptide binding]; other site 319224002923 NAD binding site [chemical binding]; other site 319224002924 catalytic residues [active] 319224002925 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 319224002926 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 319224002927 inhibitor-cofactor binding pocket; inhibition site 319224002928 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224002929 catalytic residue [active] 319224002930 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 319224002931 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 319224002932 NAD(P) binding site [chemical binding]; other site 319224002933 catalytic residues [active] 319224002934 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 319224002935 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 319224002936 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 319224002937 active site residue [active] 319224002938 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 319224002939 active site residue [active] 319224002940 Protein of unknown function (DUF2937); Region: DUF2937; pfam11157 319224002941 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002942 FAD dependent oxidoreductase; Region: DAO; pfam01266 319224002943 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 319224002944 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 319224002945 non-specific DNA binding site [nucleotide binding]; other site 319224002946 salt bridge; other site 319224002947 sequence-specific DNA binding site [nucleotide binding]; other site 319224002948 Cupin domain; Region: Cupin_2; cl09118 319224002949 Peptidase C26; Region: Peptidase_C26; pfam07722 319224002950 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 319224002951 catalytic triad [active] 319224002952 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 319224002953 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 319224002954 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 319224002955 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 319224002956 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 319224002957 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224002958 Walker A/P-loop; other site 319224002959 ATP binding site [chemical binding]; other site 319224002960 Q-loop/lid; other site 319224002961 ABC transporter signature motif; other site 319224002962 Walker B; other site 319224002963 D-loop; other site 319224002964 H-loop/switch region; other site 319224002965 TOBE domain; Region: TOBE_2; cl01440 319224002966 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 319224002967 dimer interface [polypeptide binding]; other site 319224002968 conserved gate region; other site 319224002969 putative PBP binding loops; other site 319224002970 ABC-ATPase subunit interface; other site 319224002971 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 319224002972 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 319224002973 dimer interface [polypeptide binding]; other site 319224002974 conserved gate region; other site 319224002975 putative PBP binding loops; other site 319224002976 ABC-ATPase subunit interface; other site 319224002977 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224002978 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 319224002979 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 319224002980 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 319224002981 tetramerization interface [polypeptide binding]; other site 319224002982 NAD(P) binding site [chemical binding]; other site 319224002983 catalytic residues [active] 319224002984 4-aminobutyrate aminotransferase; Validated; Region: PRK08088 319224002985 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 319224002986 inhibitor-cofactor binding pocket; inhibition site 319224002987 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224002988 catalytic residue [active] 319224002989 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 319224002990 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 319224002991 dipeptide/tripeptide permease B; Provisional; Region: PRK10207 319224002992 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 319224002993 putative substrate translocation pore; other site 319224002994 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 319224002995 Cache domain; Region: Cache_1; pfam02743 319224002996 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 319224002997 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224002998 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224002999 dimer interface [polypeptide binding]; other site 319224003000 putative CheW interface [polypeptide binding]; other site 319224003001 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 319224003002 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 319224003003 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 319224003004 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 319224003005 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224003006 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 319224003007 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 319224003008 DNA binding residues [nucleotide binding] 319224003009 DNA primase; Validated; Region: dnaG; PRK05667 319224003010 CHC2 zinc finger; Region: zf-CHC2; cl15369 319224003011 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 319224003012 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 319224003013 active site 319224003014 metal binding site [ion binding]; metal-binding site 319224003015 interdomain interaction site; other site 319224003016 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 319224003017 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 319224003018 GatB domain; Region: GatB_Yqey; cl11497 319224003019 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 319224003020 UGMP family protein; Validated; Region: PRK09604 319224003021 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 319224003022 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 319224003023 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 319224003024 homooctamer interface [polypeptide binding]; other site 319224003025 active site 319224003026 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 319224003027 catalytic center binding site [active] 319224003028 ATP binding site [chemical binding]; other site 319224003029 Bacitracin resistance protein BacA; Region: BacA; cl00858 319224003030 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 319224003031 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; cl16911 319224003032 Murein lipoprotein [Cell envelope biogenesis, outer membrane]; Region: COG4238; cl11539 319224003033 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 319224003034 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 319224003035 active site 319224003036 NTP binding site [chemical binding]; other site 319224003037 metal binding triad [ion binding]; metal-binding site 319224003038 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 319224003039 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224003040 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 319224003041 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 319224003042 Walker A motif; other site 319224003043 ATP binding site [chemical binding]; other site 319224003044 Walker B motif; other site 319224003045 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 319224003046 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 319224003047 transmembrane helices; other site 319224003048 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 319224003049 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 319224003050 inhibitor-cofactor binding pocket; inhibition site 319224003051 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224003052 catalytic residue [active] 319224003053 aspartate carbamoyltransferase; Provisional; Region: PRK08192 319224003054 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 319224003055 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003056 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 319224003057 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 319224003058 Cl- selectivity filter; other site 319224003059 Cl- binding residues [ion binding]; other site 319224003060 pore gating glutamate residue; other site 319224003061 dimer interface [polypeptide binding]; other site 319224003062 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 319224003063 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 319224003064 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 319224003065 putative peptidase; Provisional; Region: PRK11649 319224003066 Opacity-associated protein A N-terminal motif; Region: OapA_N; pfam08525 319224003067 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 319224003068 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 319224003069 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 319224003070 active site 319224003071 HIGH motif; other site 319224003072 dimer interface [polypeptide binding]; other site 319224003073 KMSKS motif; other site 319224003074 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; cl09940 319224003075 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 319224003076 hypothetical protein; Provisional; Region: PRK10578 319224003077 UPF0126 domain; Region: UPF0126; pfam03458 319224003078 UPF0126 domain; Region: UPF0126; pfam03458 319224003079 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 319224003080 CobD/Cbib protein; Region: CobD_Cbib; cl00561 319224003081 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 319224003082 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 319224003083 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 319224003084 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003085 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224003086 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 319224003087 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 319224003088 active site 319224003089 dimer interface [polypeptide binding]; other site 319224003090 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 319224003091 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 319224003092 active site 319224003093 FMN binding site [chemical binding]; other site 319224003094 substrate binding site [chemical binding]; other site 319224003095 3Fe-4S cluster binding site [ion binding]; other site 319224003096 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 319224003097 domain interface; other site 319224003098 radical SAM protein, TIGR01212 family; Region: TIGR01212 319224003099 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 319224003100 FeS/SAM binding site; other site 319224003101 aerobic respiration control sensor protein ArcB; Provisional; Region: PRK11091 319224003102 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 319224003103 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224003104 Helix-turn-helix domains; Region: HTH; cl00088 319224003105 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 319224003106 dimerization interface [polypeptide binding]; other site 319224003107 cyclase homology domain; Region: CHD; cd07302 319224003108 nucleotidyl binding site; other site 319224003109 metal binding site [ion binding]; metal-binding site 319224003110 dimer interface [polypeptide binding]; other site 319224003111 MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH...; Region: MutH_Sau3AI; cd00583 319224003112 putative DNA-binding cleft [nucleotide binding]; other site 319224003113 putative DNA clevage site; other site 319224003114 molecular lever; other site 319224003115 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 319224003116 putative active site [active] 319224003117 Ap4A binding site [chemical binding]; other site 319224003118 nudix motif; other site 319224003119 putative metal binding site [ion binding]; other site 319224003120 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 319224003121 GAF domain; Region: GAF; cl15785 319224003122 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 319224003123 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 319224003124 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 319224003125 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 319224003126 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 319224003127 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 319224003128 dimerization interface [polypeptide binding]; other site 319224003129 active site 319224003130 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 319224003131 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 319224003132 Helix-turn-helix domains; Region: HTH; cl00088 319224003133 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 319224003134 dimerization interface [polypeptide binding]; other site 319224003135 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 319224003136 L-aspartate oxidase; Provisional; Region: PRK09077 319224003137 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003138 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 319224003139 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 319224003140 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224003141 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 319224003142 DNA binding residues [nucleotide binding] 319224003143 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 319224003144 Anti sigma-E protein RseA, C-terminal domain; Region: RseA_C; pfam03873 319224003145 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 319224003146 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 319224003147 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 319224003148 GTP-binding protein LepA; Provisional; Region: PRK05433 319224003149 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 319224003150 G1 box; other site 319224003151 putative GEF interaction site [polypeptide binding]; other site 319224003152 GTP/Mg2+ binding site [chemical binding]; other site 319224003153 Switch I region; other site 319224003154 G2 box; other site 319224003155 G3 box; other site 319224003156 Switch II region; other site 319224003157 G4 box; other site 319224003158 G5 box; other site 319224003159 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 319224003160 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 319224003161 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 319224003162 signal peptidase I; Provisional; Region: PRK10861 319224003163 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 319224003164 Catalytic site [active] 319224003165 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 319224003166 ribonuclease III; Reviewed; Region: rnc; PRK00102 319224003167 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 319224003168 dimerization interface [polypeptide binding]; other site 319224003169 active site 319224003170 metal binding site [ion binding]; metal-binding site 319224003171 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 319224003172 dsRNA binding site [nucleotide binding]; other site 319224003173 GTPase Era; Reviewed; Region: era; PRK00089 319224003174 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 319224003175 G1 box; other site 319224003176 GTP/Mg2+ binding site [chemical binding]; other site 319224003177 Switch I region; other site 319224003178 G2 box; other site 319224003179 Switch II region; other site 319224003180 G3 box; other site 319224003181 G4 box; other site 319224003182 G5 box; other site 319224003183 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 319224003184 Recombination protein O N terminal; Region: RecO_N; cl15812 319224003185 Recombination protein O C terminal; Region: RecO_C; pfam02565 319224003186 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 319224003187 active site 319224003188 hydrophilic channel; other site 319224003189 dimerization interface [polypeptide binding]; other site 319224003190 catalytic residues [active] 319224003191 active site lid [active] 319224003192 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 319224003193 Protein of unknown function (DUF962); Region: DUF962; cl01879 319224003194 Domain of unknown function DUF21; Region: DUF21; pfam01595 319224003195 hypothetical protein; Provisional; Region: PRK11573 319224003196 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 319224003197 Transporter associated domain; Region: CorC_HlyC; cl08393 319224003198 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 319224003199 signal recognition particle protein; Provisional; Region: PRK10867 319224003200 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 319224003201 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 319224003202 P loop; other site 319224003203 GTP binding site [chemical binding]; other site 319224003204 Signal peptide binding domain; Region: SRP_SPB; pfam02978 319224003205 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 319224003206 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 319224003207 RimM N-terminal domain; Region: RimM; pfam01782 319224003208 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 319224003209 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 319224003210 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 319224003211 NeuB family; Region: NeuB; cl00496 319224003212 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 319224003213 bifunctional chorismate mutase/prephenate dehydrogenase; Provisional; Region: tyrA; PRK11199 319224003214 Chorismate mutase type II; Region: CM_2; cl00693 319224003215 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003216 hybrid cluster protein; Provisional; Region: PRK05290 319224003217 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 319224003218 ACS interaction site; other site 319224003219 CODH interaction site; other site 319224003220 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 319224003221 hybrid metal cluster; other site 319224003222 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 319224003223 HCP oxidoreductase, NADH-dependent; Provisional; Region: PRK10684 319224003224 FAD binding pocket [chemical binding]; other site 319224003225 FAD binding motif [chemical binding]; other site 319224003226 phosphate binding motif [ion binding]; other site 319224003227 beta-alpha-beta structure motif; other site 319224003228 NAD binding pocket [chemical binding]; other site 319224003229 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 319224003230 catalytic loop [active] 319224003231 iron binding site [ion binding]; other site 319224003232 bifunctional chorismate mutase/prephenate dehydratase; Provisional; Region: pheA; PRK10622 319224003233 Chorismate mutase type II; Region: CM_2; cl00693 319224003234 Prephenate dehydratase; Region: PDT; pfam00800 319224003235 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 319224003236 putative L-Phe binding site [chemical binding]; other site 319224003237 NeuB family; Region: NeuB; cl00496 319224003238 multifunctional aminopeptidase A; Provisional; Region: PRK00913 319224003239 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 319224003240 interface (dimer of trimers) [polypeptide binding]; other site 319224003241 Substrate-binding/catalytic site; other site 319224003242 Zn-binding sites [ion binding]; other site 319224003243 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 319224003244 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 319224003245 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 319224003246 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 319224003247 RDD family; Region: RDD; cl00746 319224003248 Protein of unknown function (DUF2960); Region: DUF2960; pfam11173 319224003249 Protein of unknown function, DUF486; Region: DUF486; cl01236 319224003250 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 319224003251 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224003252 Coenzyme A binding pocket [chemical binding]; other site 319224003253 Protein of unknown function (DUF1449); Region: DUF1449; pfam07290 319224003254 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 319224003255 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 319224003256 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 319224003257 hypothetical protein; Provisional; Region: PRK09898 319224003258 4Fe-4S binding domain; Region: Fer4; cl02805 319224003259 putative oxidoreductase; Provisional; Region: PRK09849 319224003260 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; cl08354 319224003261 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 319224003262 hypothetical protein; Provisional; Region: PRK09947 319224003263 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 319224003264 intracellular protease, PfpI family; Region: PfpI; TIGR01382 319224003265 conserved cys residue [active] 319224003266 Ribbon-helix-helix domain; Region: RHH_4; cl01775 319224003267 Protein of unknown function (DUF2913); Region: DUF2913; pfam11140 319224003268 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 319224003269 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 319224003270 ATP binding site [chemical binding]; other site 319224003271 Mg++ binding site [ion binding]; other site 319224003272 motif III; other site 319224003273 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 319224003274 nucleotide binding region [chemical binding]; other site 319224003275 ATP-binding site [chemical binding]; other site 319224003276 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 319224003277 PAS fold; Region: PAS_3; pfam08447 319224003278 putative active site [active] 319224003279 heme pocket [chemical binding]; other site 319224003280 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224003281 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224003282 dimer interface [polypeptide binding]; other site 319224003283 putative CheW interface [polypeptide binding]; other site 319224003284 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 319224003285 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 319224003286 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 319224003287 active site 319224003288 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 319224003289 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 319224003290 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224003291 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224003292 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 319224003293 Predicted membrane protein [Function unknown]; Region: COG2311 319224003294 Protein of unknown function (DUF418); Region: DUF418; cl12135 319224003295 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 319224003296 nucleoside/Zn binding site; other site 319224003297 dimer interface [polypeptide binding]; other site 319224003298 catalytic motif [active] 319224003299 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 319224003300 CoenzymeA binding site [chemical binding]; other site 319224003301 subunit interaction site [polypeptide binding]; other site 319224003302 PHB binding site; other site 319224003303 Domain of unknown function (DUF368); Region: DUF368; cl00893 319224003304 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 319224003305 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 319224003306 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 319224003307 YheO-like PAS domain; Region: PAS_6; pfam08348 319224003308 Helix-turn-helix domains; Region: HTH; cl00088 319224003309 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 319224003310 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 319224003311 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 319224003312 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 319224003313 dimerization interface [polypeptide binding]; other site 319224003314 putative DNA binding site [nucleotide binding]; other site 319224003315 putative Zn2+ binding site [ion binding]; other site 319224003316 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224003317 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 319224003318 ArsC family; Region: ArsC; pfam03960 319224003319 catalytic residues [active] 319224003320 arsenical pump membrane protein; Provisional; Region: PRK15445 319224003321 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 319224003322 transmembrane helices; other site 319224003323 Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily; Region: eu-GS; cl00170 319224003324 glutathione (GSH) binding pocket [chemical binding]; other site 319224003325 active site residues [active] 319224003326 ATP binding pocket [chemical binding]; other site 319224003327 magnesium binding site [ion binding]; other site 319224003328 glycine rich loop; other site 319224003329 alanine rich loop; other site 319224003330 Predicted permease; Region: DUF318; pfam03773 319224003331 Predicted permeases [General function prediction only]; Region: COG0701 319224003332 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 319224003333 dimerization interface [polypeptide binding]; other site 319224003334 putative DNA binding site [nucleotide binding]; other site 319224003335 putative Zn2+ binding site [ion binding]; other site 319224003336 Low molecular weight phosphatase family; Region: LMWPc; cd00115 319224003337 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 319224003338 active site 319224003339 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 319224003340 dimerization interface [polypeptide binding]; other site 319224003341 putative DNA binding site [nucleotide binding]; other site 319224003342 putative Zn2+ binding site [ion binding]; other site 319224003343 Predicted permease; Region: DUF318; pfam03773 319224003344 Predicted permeases [General function prediction only]; Region: COG0701 319224003345 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224003346 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 319224003347 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003348 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224003349 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224003350 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 319224003351 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 319224003352 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224003353 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224003354 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 319224003355 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 319224003356 Ligand Binding Site [chemical binding]; other site 319224003357 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 319224003358 Ligand Binding Site [chemical binding]; other site 319224003359 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 319224003360 SmpB-tmRNA interface; other site 319224003361 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 319224003362 putative coenzyme Q binding site [chemical binding]; other site 319224003363 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 319224003364 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 319224003365 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 319224003366 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 319224003367 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224003368 metal binding site [ion binding]; metal-binding site 319224003369 active site 319224003370 I-site; other site 319224003371 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 319224003372 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 319224003373 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003374 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224003375 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; cl01155 319224003376 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; cl01155 319224003377 malate synthase A; Region: malate_syn_A; TIGR01344 319224003378 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 319224003379 active site 319224003380 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 319224003381 tetramer interface [polypeptide binding]; other site 319224003382 active site 319224003383 Mg2+/Mn2+ binding site [ion binding]; other site 319224003384 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 319224003385 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 319224003386 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224003387 putative alcohol dehydrogenase; Provisional; Region: PRK09860 319224003388 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 319224003389 dimer interface [polypeptide binding]; other site 319224003390 active site 319224003391 metal binding site [ion binding]; metal-binding site 319224003392 Transcriptional regulators [Transcription]; Region: MarR; COG1846 319224003393 Helix-turn-helix domains; Region: HTH; cl00088 319224003394 Helix-turn-helix domains; Region: HTH; cl00088 319224003395 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 319224003396 active site 319224003397 4-alpha-glucanotransferase; Region: Glyco_hydro_77; cl00711 319224003398 glycogen branching enzyme; Provisional; Region: PRK05402 319224003399 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 319224003400 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 319224003401 active site 319224003402 catalytic site [active] 319224003403 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 319224003404 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 319224003405 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 319224003406 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 319224003407 active site 319224003408 catalytic site [active] 319224003409 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 319224003410 homodimer interface [polypeptide binding]; other site 319224003411 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 319224003412 active site pocket [active] 319224003413 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 319224003414 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 319224003415 ligand binding site; other site 319224003416 oligomer interface; other site 319224003417 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 319224003418 dimer interface [polypeptide binding]; other site 319224003419 N-terminal domain interface [polypeptide binding]; other site 319224003420 sulfate 1 binding site; other site 319224003421 glycogen synthase; Provisional; Region: glgA; PRK00654 319224003422 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 319224003423 ADP-binding pocket [chemical binding]; other site 319224003424 homodimer interface [polypeptide binding]; other site 319224003425 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 319224003426 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 319224003427 PAS fold; Region: PAS_3; pfam08447 319224003428 putative active site [active] 319224003429 heme pocket [chemical binding]; other site 319224003430 PAS fold; Region: PAS_3; pfam08447 319224003431 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 319224003432 PAS domain; Region: PAS_9; pfam13426 319224003433 putative active site [active] 319224003434 heme pocket [chemical binding]; other site 319224003435 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224003436 metal binding site [ion binding]; metal-binding site 319224003437 active site 319224003438 I-site; other site 319224003439 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 319224003440 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 319224003441 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 319224003442 ATP binding site [chemical binding]; other site 319224003443 Mg++ binding site [ion binding]; other site 319224003444 motif III; other site 319224003445 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 319224003446 nucleotide binding region [chemical binding]; other site 319224003447 ATP-binding site [chemical binding]; other site 319224003448 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 319224003449 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224003450 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 319224003451 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 319224003452 substrate binding pocket [chemical binding]; other site 319224003453 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224003454 membrane-bound complex binding site; other site 319224003455 hinge residues; other site 319224003456 Protein of unknown function (DUF3087); Region: DUF3087; pfam11286 319224003457 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 319224003458 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224003459 putative substrate translocation pore; other site 319224003460 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 319224003461 MatE; Region: MatE; cl10513 319224003462 MatE; Region: MatE; cl10513 319224003463 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 319224003464 Putative esterase; Region: Esterase; pfam00756 319224003465 putative acetyltransferase YhhY; Provisional; Region: PRK10140 319224003466 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224003467 Coenzyme A binding pocket [chemical binding]; other site 319224003468 BCS1 N terminal; Region: BCS1_N; cl07381 319224003469 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224003470 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 319224003471 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 319224003472 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; cl00674 319224003473 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 319224003474 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 319224003475 Cysteine-rich domain; Region: CCG; pfam02754 319224003476 Cysteine-rich domain; Region: CCG; pfam02754 319224003477 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 319224003478 FAD binding domain; Region: FAD_binding_4; pfam01565 319224003479 4Fe-4S binding domain; Region: Fer4; cl02805 319224003480 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 319224003481 L-lactate permease; Region: Lactate_perm; cl00701 319224003482 glycolate transporter; Provisional; Region: PRK09695 319224003483 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 319224003484 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 319224003485 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 319224003486 dimer interface [polypeptide binding]; other site 319224003487 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 319224003488 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 319224003489 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 319224003490 TPP-binding site; other site 319224003491 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 319224003492 PYR/PP interface [polypeptide binding]; other site 319224003493 dimer interface [polypeptide binding]; other site 319224003494 TPP binding site [chemical binding]; other site 319224003495 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 319224003496 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 319224003497 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 319224003498 substrate binding pocket [chemical binding]; other site 319224003499 chain length determination region; other site 319224003500 substrate-Mg2+ binding site; other site 319224003501 catalytic residues [active] 319224003502 aspartate-rich region 1; other site 319224003503 active site lid residues [active] 319224003504 aspartate-rich region 2; other site 319224003505 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 319224003506 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 319224003507 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224003508 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 319224003509 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 319224003510 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224003511 ligand binding site [chemical binding]; other site 319224003512 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 319224003513 THUMP domain; Region: THUMP; cl12076 319224003514 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 319224003515 Ligand Binding Site [chemical binding]; other site 319224003516 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 319224003517 active site residue [active] 319224003518 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 319224003519 Helix-turn-helix domains; Region: HTH; cl00088 319224003520 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 319224003521 dimerization interface [polypeptide binding]; other site 319224003522 substrate binding pocket [chemical binding]; other site 319224003523 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG3571 319224003524 Protein of unknown function (DUF423); Region: DUF423; cl01008 319224003525 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 319224003526 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; cl16911 319224003527 tartrate dehydrogenase; Provisional; Region: PRK08194 319224003528 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 319224003529 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 319224003530 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 319224003531 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 319224003532 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 319224003533 flap endonuclease-like protein; Provisional; Region: PRK09482 319224003534 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 319224003535 active site 319224003536 metal binding site 1 [ion binding]; metal-binding site 319224003537 putative 5' ssDNA interaction site; other site 319224003538 metal binding site 3; metal-binding site 319224003539 metal binding site 2 [ion binding]; metal-binding site 319224003540 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 319224003541 putative DNA binding site [nucleotide binding]; other site 319224003542 putative metal binding site [ion binding]; other site 319224003543 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 319224003544 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 319224003545 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 319224003546 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224003547 metal binding site [ion binding]; metal-binding site 319224003548 active site 319224003549 I-site; other site 319224003550 Tetratricopeptide repeat; Region: TPR_12; pfam13424 319224003551 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 319224003552 binding surface 319224003553 TPR motif; other site 319224003554 Tetratricopeptide repeat; Region: TPR_12; pfam13424 319224003555 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 319224003556 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 319224003557 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 319224003558 protein binding site [polypeptide binding]; other site 319224003559 Putative exonuclease, RdgC; Region: RdgC; cl01122 319224003560 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 319224003561 trimer interface [polypeptide binding]; other site 319224003562 eyelet of channel; other site 319224003563 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 319224003564 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 319224003565 active site 319224003566 phosphorylation site [posttranslational modification] 319224003567 intermolecular recognition site; other site 319224003568 dimerization interface [polypeptide binding]; other site 319224003569 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 319224003570 DNA binding site [nucleotide binding] 319224003571 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 319224003572 phosphate regulon sensor protein; Provisional; Region: phoR; PRK11006 319224003573 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 319224003574 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 319224003575 dimer interface [polypeptide binding]; other site 319224003576 phosphorylation site [posttranslational modification] 319224003577 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 319224003578 ATP binding site [chemical binding]; other site 319224003579 Mg2+ binding site [ion binding]; other site 319224003580 G-X-G motif; other site 319224003581 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 319224003582 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 319224003583 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 319224003584 active site 319224003585 Zn binding site [ion binding]; other site 319224003586 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 319224003587 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 319224003588 catalytic residues [active] 319224003589 dimer interface [polypeptide binding]; other site 319224003590 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 319224003591 MgtE intracellular N domain; Region: MgtE_N; cl15244 319224003592 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 319224003593 Divalent cation transporter; Region: MgtE; cl00786 319224003594 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 319224003595 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224003596 Coenzyme A binding pocket [chemical binding]; other site 319224003597 YfaZ precursor; Region: YfaZ; pfam07437 319224003598 16S rRNA methyltransferase B; Provisional; Region: PRK14902 319224003599 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 319224003600 S-adenosylmethionine binding site [chemical binding]; other site 319224003601 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 319224003602 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 319224003603 C-terminal domain interface [polypeptide binding]; other site 319224003604 GSH binding site (G-site) [chemical binding]; other site 319224003605 dimer interface [polypeptide binding]; other site 319224003606 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 319224003607 N-terminal domain interface [polypeptide binding]; other site 319224003608 putative dimer interface [polypeptide binding]; other site 319224003609 active site 319224003610 Conserved hypothetical protein (DUF2461); Region: DUF2461; cl02374 319224003611 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 319224003612 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 319224003613 N-terminal plug; other site 319224003614 ligand-binding site [chemical binding]; other site 319224003615 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; smart00782 319224003616 PhnA protein; Region: PhnA; pfam03831 319224003617 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 319224003618 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 319224003619 putative substrate translocation pore; other site 319224003620 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 319224003621 Helix-turn-helix domains; Region: HTH; cl00088 319224003622 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 319224003623 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 319224003624 putative active site [active] 319224003625 Zn binding site [ion binding]; other site 319224003626 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 319224003627 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224003628 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224003629 dimer interface [polypeptide binding]; other site 319224003630 putative CheW interface [polypeptide binding]; other site 319224003631 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 319224003632 BON domain; Region: BON; cl02771 319224003633 BON domain; Region: BON; cl02771 319224003634 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 319224003635 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 319224003636 Walker A motif; other site 319224003637 ATP binding site [chemical binding]; other site 319224003638 Walker B motif; other site 319224003639 arginine finger; other site 319224003640 Helix-turn-helix domains; Region: HTH; cl00088 319224003641 hypothetical protein; Provisional; Region: PRK12361 319224003642 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 319224003643 active site 319224003644 catalytic residues [active] 319224003645 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 319224003646 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding...; Region: NPD_FabD; cd04742 319224003647 FMN binding site [chemical binding]; other site 319224003648 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 319224003649 substrate binding site [chemical binding]; other site 319224003650 putative catalytic residue [active] 319224003651 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 319224003652 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 319224003653 active site 319224003654 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 319224003655 active site 319224003656 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 319224003657 dimer interface [polypeptide binding]; other site 319224003658 active site 2 [active] 319224003659 active site 1 [active] 319224003660 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 319224003661 active site 1 [active] 319224003662 dimer interface [polypeptide binding]; other site 319224003663 active site 2 [active] 319224003664 Acyl transferase domain; Region: Acyl_transf_1; cl08282 319224003665 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 319224003666 3-oxoacyl-acyl carrier protein synthase; Provisional; Region: PTZ00050 319224003667 active site 319224003668 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 319224003669 Acyl transferase domain; Region: Acyl_transf_1; cl08282 319224003670 polyketide-type polyunsaturated fatty acid synthase PfaA; Region: omega_3_PfaA; TIGR02813 319224003671 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224003672 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224003673 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224003674 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224003675 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 319224003676 putative NADP binding site [chemical binding]; other site 319224003677 active site 319224003678 Winged helix-turn helix; Region: HTH_29; pfam13551 319224003679 Helix-turn-helix domains; Region: HTH; cl00088 319224003680 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 319224003681 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 319224003682 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 319224003683 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 319224003684 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 319224003685 Syd protein (SUKH-2); Region: Syd; cl06405 319224003686 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 319224003687 Protein of unknown function (DUF3192); Region: DUF3192; pfam11399 319224003688 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 319224003689 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224003690 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 319224003691 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 319224003692 tRNA pseudouridine synthase C; Region: DUF446; cl01187 319224003693 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 319224003694 probable active site [active] 319224003695 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224003696 PTS system glucose-specific transporter subunits IIBC; Provisional; Region: PRK11089 319224003697 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 319224003698 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 319224003699 active site turn [active] 319224003700 phosphorylation site [posttranslational modification] 319224003701 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 319224003702 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 319224003703 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 319224003704 putative active site [active] 319224003705 putative substrate binding site [chemical binding]; other site 319224003706 putative cosubstrate binding site; other site 319224003707 catalytic site [active] 319224003708 PAS domain; Region: PAS_9; pfam13426 319224003709 GAF domain; Region: GAF_2; pfam13185 319224003710 GAF domain; Region: GAF; cl15785 319224003711 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 319224003712 Zn2+ binding site [ion binding]; other site 319224003713 Mg2+ binding site [ion binding]; other site 319224003714 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 319224003715 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 319224003716 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 319224003717 trimer interface [polypeptide binding]; other site 319224003718 active site 319224003719 substrate binding site [chemical binding]; other site 319224003720 CoA binding site [chemical binding]; other site 319224003721 PII uridylyl-transferase; Provisional; Region: PRK05007 319224003722 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 319224003723 metal binding triad; other site 319224003724 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 319224003725 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224003726 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 319224003727 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 319224003728 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 319224003729 active site 319224003730 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 319224003731 rRNA interaction site [nucleotide binding]; other site 319224003732 S8 interaction site; other site 319224003733 putative laminin-1 binding site; other site 319224003734 elongation factor Ts; Provisional; Region: tsf; PRK09377 319224003735 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 319224003736 Elongation factor TS; Region: EF_TS; pfam00889 319224003737 Elongation factor TS; Region: EF_TS; pfam00889 319224003738 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 319224003739 putative nucleotide binding site [chemical binding]; other site 319224003740 uridine monophosphate binding site [chemical binding]; other site 319224003741 homohexameric interface [polypeptide binding]; other site 319224003742 ribosome recycling factor; Reviewed; Region: frr; PRK00083 319224003743 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 319224003744 hinge region; other site 319224003745 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; cd00475 319224003746 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 319224003747 catalytic residue [active] 319224003748 putative FPP diphosphate binding site; other site 319224003749 putative FPP binding hydrophobic cleft; other site 319224003750 dimer interface [polypeptide binding]; other site 319224003751 putative IPP diphosphate binding site; other site 319224003752 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 319224003753 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 319224003754 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 319224003755 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 319224003756 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 319224003757 zinc metallopeptidase RseP; Provisional; Region: PRK10779 319224003758 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 319224003759 active site 319224003760 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 319224003761 protein binding site [polypeptide binding]; other site 319224003762 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 319224003763 protein binding site [polypeptide binding]; other site 319224003764 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 319224003765 putative substrate binding region [chemical binding]; other site 319224003766 outer membrane protein assembly factor YaeT; Provisional; Region: PRK11067 319224003767 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224003768 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224003769 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224003770 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224003771 Surface antigen; Region: Bac_surface_Ag; cl03097 319224003772 periplasmic chaperone; Provisional; Region: PRK10780 319224003773 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 319224003774 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 319224003775 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 319224003776 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 319224003777 trimer interface [polypeptide binding]; other site 319224003778 active site 319224003779 UDP-GlcNAc binding site [chemical binding]; other site 319224003780 lipid binding site [chemical binding]; lipid-binding site 319224003781 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 319224003782 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 319224003783 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 319224003784 active site 319224003785 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 319224003786 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 319224003787 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 319224003788 RNA/DNA hybrid binding site [nucleotide binding]; other site 319224003789 active site 319224003790 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 319224003791 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 319224003792 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 319224003793 generic binding surface II; other site 319224003794 generic binding surface I; other site 319224003795 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 319224003796 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 319224003797 Ligand Binding Site [chemical binding]; other site 319224003798 TilS substrate binding domain; Region: TilS; pfam09179 319224003799 B3/4 domain; Region: B3_4; cl11458 319224003800 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224003801 metal binding site [ion binding]; metal-binding site 319224003802 active site 319224003803 I-site; other site 319224003804 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 319224003805 DNA-binding site [nucleotide binding]; DNA binding site 319224003806 RNA-binding motif; other site 319224003807 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 319224003808 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 319224003809 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 319224003810 ATP binding site [chemical binding]; other site 319224003811 putative Mg++ binding site [ion binding]; other site 319224003812 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 319224003813 nucleotide binding region [chemical binding]; other site 319224003814 ATP-binding site [chemical binding]; other site 319224003815 putative hydrolase; Validated; Region: PRK09248 319224003816 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 319224003817 active site 319224003818 fructokinase; Reviewed; Region: PRK09557 319224003819 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 319224003820 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 319224003821 putative active site [active] 319224003822 Protein of unknown function (DUF2982); Region: DUF2982; pfam11201 319224003823 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224003824 Putative transposase; Region: Y2_Tnp; pfam04986 319224003825 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 319224003826 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224003827 Helix-turn-helix domains; Region: HTH; cl00088 319224003828 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 319224003829 dimerization interface [polypeptide binding]; other site 319224003830 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 319224003831 ferredoxin-type protein; Provisional; Region: PRK10194 319224003832 UDP-glucose 4-epimerase; Region: PLN02240 319224003833 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 319224003834 NAD binding site [chemical binding]; other site 319224003835 homodimer interface [polypeptide binding]; other site 319224003836 active site 319224003837 substrate binding site [chemical binding]; other site 319224003838 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 319224003839 active site 319224003840 tetramer interface; other site 319224003841 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 319224003842 cofactor binding site; other site 319224003843 metal binding site [ion binding]; metal-binding site 319224003844 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 319224003845 aromatic arch; other site 319224003846 DCoH dimer interaction site [polypeptide binding]; other site 319224003847 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 319224003848 DCoH tetramer interaction site [polypeptide binding]; other site 319224003849 substrate binding site [chemical binding]; other site 319224003850 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 319224003851 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 319224003852 putative aromatic amino acid binding site; other site 319224003853 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 319224003854 Walker A motif; other site 319224003855 ATP binding site [chemical binding]; other site 319224003856 Walker B motif; other site 319224003857 arginine finger; other site 319224003858 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 319224003859 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 319224003860 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 319224003861 maleylacetoacetate isomerase; Region: maiA; TIGR01262 319224003862 C-terminal domain interface [polypeptide binding]; other site 319224003863 GSH binding site (G-site) [chemical binding]; other site 319224003864 putative dimer interface [polypeptide binding]; other site 319224003865 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 319224003866 dimer interface [polypeptide binding]; other site 319224003867 N-terminal domain interface [polypeptide binding]; other site 319224003868 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 319224003869 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 319224003870 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; cl01155 319224003871 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 319224003872 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003873 NAD(P) binding site [chemical binding]; other site 319224003874 active site 319224003875 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 319224003876 homoserine O-succinyltransferase; Provisional; Region: PRK05368 319224003877 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 319224003878 proposed active site lysine [active] 319224003879 conserved cys residue [active] 319224003880 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 319224003881 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 319224003882 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224003883 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224003884 dimer interface [polypeptide binding]; other site 319224003885 putative CheW interface [polypeptide binding]; other site 319224003886 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 319224003887 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 319224003888 dimer interface [polypeptide binding]; other site 319224003889 active site 319224003890 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 319224003891 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 319224003892 tetrameric interface [polypeptide binding]; other site 319224003893 NAD binding site [chemical binding]; other site 319224003894 catalytic residues [active] 319224003895 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 319224003896 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 319224003897 active site 319224003898 enoyl-CoA hydratase; Provisional; Region: PRK09076 319224003899 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 319224003900 substrate binding site [chemical binding]; other site 319224003901 oxyanion hole (OAH) forming residues; other site 319224003902 trimer interface [polypeptide binding]; other site 319224003903 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 319224003904 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 319224003905 substrate binding site [chemical binding]; other site 319224003906 oxyanion hole (OAH) forming residues; other site 319224003907 trimer interface [polypeptide binding]; other site 319224003908 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 319224003909 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003910 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 319224003911 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 319224003912 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224003913 NAD(P) binding site [chemical binding]; other site 319224003914 active site 319224003915 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 319224003916 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 319224003917 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 319224003918 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 319224003919 DNA binding residues [nucleotide binding] 319224003920 dimer interface [polypeptide binding]; other site 319224003921 copper binding site [ion binding]; other site 319224003922 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 319224003923 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 319224003924 metal-binding site [ion binding] 319224003925 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224003926 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224003927 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 319224003928 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224003929 Walker A/P-loop; other site 319224003930 ATP binding site [chemical binding]; other site 319224003931 Q-loop/lid; other site 319224003932 ABC transporter signature motif; other site 319224003933 Walker B; other site 319224003934 D-loop; other site 319224003935 H-loop/switch region; other site 319224003936 ABC transporter; Region: ABC_tran_2; pfam12848 319224003937 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 319224003938 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 319224003939 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 319224003940 FAD binding domain; Region: FAD_binding_4; pfam01565 319224003941 Berberine and berberine like; Region: BBE; pfam08031 319224003942 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 319224003943 PAS domain S-box; Region: sensory_box; TIGR00229 319224003944 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224003945 metal binding site [ion binding]; metal-binding site 319224003946 active site 319224003947 I-site; other site 319224003948 Domain of unknown function (DUF1888); Region: DUF1888; pfam08985 319224003949 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 319224003950 DNA binding site [nucleotide binding] 319224003951 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224003952 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224003953 Helix-turn-helix domains; Region: HTH; cl00088 319224003954 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 319224003955 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 319224003956 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 319224003957 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 319224003958 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 319224003959 Walker A/P-loop; other site 319224003960 ATP binding site [chemical binding]; other site 319224003961 Q-loop/lid; other site 319224003962 ABC transporter signature motif; other site 319224003963 Walker B; other site 319224003964 D-loop; other site 319224003965 H-loop/switch region; other site 319224003966 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 319224003967 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 319224003968 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224003969 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 319224003970 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 319224003971 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 319224003972 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 319224003973 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 319224003974 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224003975 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224003976 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224003977 dimer interface [polypeptide binding]; other site 319224003978 putative CheW interface [polypeptide binding]; other site 319224003979 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 319224003980 LysE type translocator; Region: LysE; cl00565 319224003981 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_24; cd09012 319224003982 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224003983 Histone chaperone Rttp106-like; Region: Rtt106; pfam08512 319224003984 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 319224003985 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 319224003986 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 319224003987 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 319224003988 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 319224003989 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 319224003990 conserved gate region; other site 319224003991 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 319224003992 ABC-ATPase subunit interface; other site 319224003993 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 319224003994 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 319224003995 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 319224003996 dimer interface [polypeptide binding]; other site 319224003997 conserved gate region; other site 319224003998 putative PBP binding loops; other site 319224003999 ABC-ATPase subunit interface; other site 319224004000 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 319224004001 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 319224004002 Walker A/P-loop; other site 319224004003 ATP binding site [chemical binding]; other site 319224004004 Q-loop/lid; other site 319224004005 ABC transporter signature motif; other site 319224004006 Walker B; other site 319224004007 D-loop; other site 319224004008 H-loop/switch region; other site 319224004009 transcriptional regulator PhoU; Provisional; Region: PRK11115 319224004010 PhoU domain; Region: PhoU; pfam01895 319224004011 PhoU domain; Region: PhoU; pfam01895 319224004012 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 319224004013 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 319224004014 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224004015 dimer interface [polypeptide binding]; other site 319224004016 putative CheW interface [polypeptide binding]; other site 319224004017 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 319224004018 dimer interface [polypeptide binding]; other site 319224004019 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224004020 metal binding site [ion binding]; metal-binding site 319224004021 Protein of unknown function (DUF502); Region: DUF502; cl01107 319224004022 BCCT family transporter; Region: BCCT; cl00569 319224004023 hypothetical protein; Provisional; Region: PRK11295 319224004024 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; cl00083 319224004025 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 319224004026 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; cl16911 319224004027 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09258 319224004028 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 319224004029 dimer interface [polypeptide binding]; other site 319224004030 active site 319224004031 CoA binding pocket [chemical binding]; other site 319224004032 haloalkane dehalogenase; Provisional; Region: PRK03592 319224004033 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 319224004034 peptide synthase; Provisional; Region: PRK09274 319224004035 AMP-binding enzyme; Region: AMP-binding; cl15778 319224004036 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224004037 3-beta hydroxysteroid dehydrogenase/isomerase family; Region: 3Beta_HSD; pfam01073 319224004038 NAD(P) binding site [chemical binding]; other site 319224004039 active site 319224004040 GSCFA family; Region: GSCFA; pfam08885 319224004041 Protein of unknown function (DUF3624); Region: DUF3624; pfam12292 319224004042 Integral membrane protein TerC family; Region: TerC; cl10468 319224004043 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 319224004044 ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the...; Region: ABC_drug_resistance_like; cd03264 319224004045 Walker A/P-loop; other site 319224004046 ATP binding site [chemical binding]; other site 319224004047 Q-loop/lid; other site 319224004048 ABC transporter signature motif; other site 319224004049 Walker B; other site 319224004050 D-loop; other site 319224004051 H-loop/switch region; other site 319224004052 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224004053 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224004054 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 319224004055 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 319224004056 Zn binding site [ion binding]; other site 319224004057 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 319224004058 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 319224004059 active site 319224004060 substrate binding site [chemical binding]; other site 319224004061 metal binding site [ion binding]; metal-binding site 319224004062 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 319224004063 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224004064 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 319224004065 Helix-turn-helix domains; Region: HTH; cl00088 319224004066 WYL domain; Region: WYL; cl14852 319224004067 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 319224004068 AzlC protein; Region: AzlC; cl00570 319224004069 Cupin domain; Region: Cupin_2; cl09118 319224004070 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224004071 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 319224004072 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224004073 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 319224004074 trimer interface [polypeptide binding]; other site 319224004075 active site 319224004076 substrate binding site [chemical binding]; other site 319224004077 CoA binding site [chemical binding]; other site 319224004078 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 319224004079 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 319224004080 putative transposase OrfB; Reviewed; Region: PHA02517 319224004081 HTH-like domain; Region: HTH_21; pfam13276 319224004082 Integrase core domain; Region: rve; cl01316 319224004083 Integrase core domain; Region: rve_3; cl15866 319224004084 Helix-turn-helix domains; Region: HTH; cl00088 319224004085 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 319224004086 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 319224004087 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224004088 catalytic residue [active] 319224004089 Glycerate kinase family; Region: Gly_kinase; cl00841 319224004090 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 319224004091 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 319224004092 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 319224004093 putative heme binding pocket [chemical binding]; other site 319224004094 carbohydrate diacid transcriptional activator CdaR; Provisional; Region: PRK11477 319224004095 Putative sugar diacid recognition; Region: Diacid_rec; pfam05651 319224004096 Helix-turn-helix domains; Region: HTH; cl00088 319224004097 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 319224004098 putative uracil binding site [chemical binding]; other site 319224004099 putative active site [active] 319224004100 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 319224004101 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 319224004102 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 319224004103 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 319224004104 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 319224004105 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 319224004106 heme-binding residues [chemical binding]; other site 319224004107 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 319224004108 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 319224004109 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 319224004110 heme-binding residues [chemical binding]; other site 319224004111 FeoA domain; Region: FeoA; cl00838 319224004112 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 319224004113 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 319224004114 G1 box; other site 319224004115 GTP/Mg2+ binding site [chemical binding]; other site 319224004116 Switch I region; other site 319224004117 G2 box; other site 319224004118 G3 box; other site 319224004119 Switch II region; other site 319224004120 G4 box; other site 319224004121 G5 box; other site 319224004122 Nucleoside recognition; Region: Gate; cl00486 319224004123 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 319224004124 Nucleoside recognition; Region: Gate; cl00486 319224004125 Nucleoside recognition; Region: Gate; cl00486 319224004126 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 319224004127 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 319224004128 active site 319224004129 HIGH motif; other site 319224004130 nucleotide binding site [chemical binding]; other site 319224004131 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 319224004132 KMSKS motif; other site 319224004133 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 319224004134 Yip1 domain; Region: Yip1; cl12048 319224004135 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 319224004136 active site 319224004137 dinuclear metal binding site [ion binding]; other site 319224004138 dimerization interface [polypeptide binding]; other site 319224004139 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 319224004140 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 319224004141 putative active site [active] 319224004142 putative metal binding site [ion binding]; other site 319224004143 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 319224004144 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 319224004145 substrate binding site [chemical binding]; other site 319224004146 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 319224004147 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 319224004148 active site 319224004149 HIGH motif; other site 319224004150 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 319224004151 KMSKS motif; other site 319224004152 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 319224004153 tRNA binding surface [nucleotide binding]; other site 319224004154 anticodon binding site; other site 319224004155 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 319224004156 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 319224004157 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 319224004158 homodimer interface [polypeptide binding]; other site 319224004159 NADP binding site [chemical binding]; other site 319224004160 substrate binding site [chemical binding]; other site 319224004161 trigger factor; Provisional; Region: tig; PRK01490 319224004162 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224004163 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 319224004164 Clp protease; Region: CLP_protease; pfam00574 319224004165 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 319224004166 oligomer interface [polypeptide binding]; other site 319224004167 active site residues [active] 319224004168 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 319224004169 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 319224004170 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 319224004171 Walker A motif; other site 319224004172 ATP binding site [chemical binding]; other site 319224004173 Walker B motif; other site 319224004174 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 319224004175 DNA-binding ATP-dependent protease La; Provisional; Region: PRK10787 319224004176 Found in ATP-dependent protease La (LON); Region: LON; smart00464 319224004177 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 319224004178 Walker A motif; other site 319224004179 ATP binding site [chemical binding]; other site 319224004180 Walker B motif; other site 319224004181 arginine finger; other site 319224004182 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 319224004183 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 319224004184 IHF dimer interface [polypeptide binding]; other site 319224004185 IHF - DNA interface [nucleotide binding]; other site 319224004186 periplasmic folding chaperone; Provisional; Region: PRK10788 319224004187 SurA N-terminal domain; Region: SurA_N_3; cl07813 319224004188 PPIC-type PPIASE domain; Region: Rotamase; cl08278 319224004189 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 319224004190 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 319224004191 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224004192 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 319224004193 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 319224004194 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 319224004195 Walker A/P-loop; other site 319224004196 ATP binding site [chemical binding]; other site 319224004197 Q-loop/lid; other site 319224004198 ABC transporter signature motif; other site 319224004199 Walker B; other site 319224004200 D-loop; other site 319224004201 H-loop/switch region; other site 319224004202 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 319224004203 antimicrobial peptide ABC transporter ATP-binding protein; Provisional; Region: PRK15093 319224004204 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 319224004205 Walker A/P-loop; other site 319224004206 ATP binding site [chemical binding]; other site 319224004207 Q-loop/lid; other site 319224004208 ABC transporter signature motif; other site 319224004209 Walker B; other site 319224004210 D-loop; other site 319224004211 H-loop/switch region; other site 319224004212 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 319224004213 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SapC; COG4171 319224004214 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 319224004215 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 319224004216 dimer interface [polypeptide binding]; other site 319224004217 conserved gate region; other site 319224004218 putative PBP binding loops; other site 319224004219 ABC-ATPase subunit interface; other site 319224004220 antimicrobial peptide ABC transporter permease SapB; Provisional; Region: PRK15110 319224004221 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 319224004222 dimer interface [polypeptide binding]; other site 319224004223 conserved gate region; other site 319224004224 putative PBP binding loops; other site 319224004225 ABC-ATPase subunit interface; other site 319224004226 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 319224004227 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 319224004228 peptide binding site [polypeptide binding]; other site 319224004229 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 319224004230 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 319224004231 Walker A motif; other site 319224004232 ATP binding site [chemical binding]; other site 319224004233 Walker B motif; other site 319224004234 arginine finger; other site 319224004235 Helix-turn-helix domains; Region: HTH; cl00088 319224004236 phage shock protein A; Region: phageshock_pspA; TIGR02977 319224004237 Phage shock protein B; Region: PspB; cl05946 319224004238 phage shock protein C; Region: phageshock_pspC; TIGR02978 319224004239 PspC domain; Region: PspC; cl00864 319224004240 YcjX-like family, DUF463; Region: DUF463; cl01193 319224004241 hypothetical protein; Provisional; Region: PRK05415 319224004242 Domain of unknown function (DUF697); Region: DUF697; cl12064 319224004243 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 319224004244 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 319224004245 homodimer interface [polypeptide binding]; other site 319224004246 substrate-cofactor binding pocket; other site 319224004247 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224004248 catalytic residue [active] 319224004249 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 319224004250 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 319224004251 Late competence development protein ComFB; Region: ComFB; pfam10719 319224004252 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 319224004253 Primosomal replication protein priB and priC; Region: priB_priC; cl11483 319224004254 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 319224004255 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 319224004256 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 319224004257 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224004258 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224004259 DNA polymerase II; Reviewed; Region: PRK05762 319224004260 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 319224004261 active site 319224004262 catalytic site [active] 319224004263 substrate binding site [chemical binding]; other site 319224004264 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 319224004265 active site 319224004266 metal-binding site 319224004267 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 319224004268 trimer interface [polypeptide binding]; other site 319224004269 eyelet of channel; other site 319224004270 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; cl01155 319224004271 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; cl01155 319224004272 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 319224004273 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224004274 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224004275 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 319224004276 Gram-negative bacterial tonB protein; Region: TonB; cl10048 319224004277 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 319224004278 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 319224004279 TPR motif; other site 319224004280 binding surface 319224004281 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224004282 metal binding site [ion binding]; metal-binding site 319224004283 active site 319224004284 I-site; other site 319224004285 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 319224004286 PPIC-type PPIASE domain; Region: Rotamase; cl08278 319224004287 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 319224004288 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224004289 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 319224004290 RNA binding surface [nucleotide binding]; other site 319224004291 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 319224004292 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 319224004293 Helix-turn-helix domains; Region: HTH; cl00088 319224004294 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 319224004295 dimerization interface [polypeptide binding]; other site 319224004296 substrate binding pocket [chemical binding]; other site 319224004297 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 319224004298 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 319224004299 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 319224004300 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 319224004301 active site 319224004302 metal binding site [ion binding]; metal-binding site 319224004303 DNA binding site [nucleotide binding] 319224004304 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 319224004305 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 319224004306 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 319224004307 Walker A/P-loop; other site 319224004308 ATP binding site [chemical binding]; other site 319224004309 Q-loop/lid; other site 319224004310 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 319224004311 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 319224004312 ABC transporter signature motif; other site 319224004313 Walker B; other site 319224004314 D-loop; other site 319224004315 H-loop/switch region; other site 319224004316 putative peptidase; Provisional; Region: PRK11649 319224004317 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 319224004318 Protein of unknown function DUF45; Region: DUF45; cl00636 319224004319 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 319224004320 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 319224004321 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 319224004322 ATP binding site [chemical binding]; other site 319224004323 Mg++ binding site [ion binding]; other site 319224004324 motif III; other site 319224004325 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 319224004326 nucleotide binding region [chemical binding]; other site 319224004327 ATP-binding site [chemical binding]; other site 319224004328 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 319224004329 active site 319224004330 nucleophile elbow; other site 319224004331 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 319224004332 ATP cone domain; Region: ATP-cone; pfam03477 319224004333 Class III ribonucleotide reductase; Region: RNR_III; cd01675 319224004334 effector binding site; other site 319224004335 active site 319224004336 Zn binding site [ion binding]; other site 319224004337 glycine loop; other site 319224004338 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 319224004339 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 319224004340 Protein of unknown function (DUF2810); Region: DUF2810; cl08159 319224004341 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 319224004342 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 319224004343 dimerization interface [polypeptide binding]; other site 319224004344 active site 319224004345 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 319224004346 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 319224004347 Carbon starvation protein CstA; Region: CstA; pfam02554 319224004348 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 319224004349 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 319224004350 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 319224004351 active site 319224004352 phosphorylation site [posttranslational modification] 319224004353 intermolecular recognition site; other site 319224004354 dimerization interface [polypeptide binding]; other site 319224004355 LytTr DNA-binding domain; Region: LytTR; cl04498 319224004356 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 319224004357 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 319224004358 GAF domain; Region: GAF; cl15785 319224004359 Histidine kinase; Region: His_kinase; pfam06580 319224004360 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 319224004361 ATP binding site [chemical binding]; other site 319224004362 Mg2+ binding site [ion binding]; other site 319224004363 G-X-G motif; other site 319224004364 Protein of unknown function (DUF2492); Region: DUF2492; cl11278 319224004365 ParA-like protein; Provisional; Region: PHA02518 319224004366 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 319224004367 P-loop; other site 319224004368 Magnesium ion binding site [ion binding]; other site 319224004369 PilZ domain; Region: PilZ; cl01260 319224004370 Phosphate-starvation-inducible E; Region: PsiE; cl01264 319224004371 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 319224004372 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 319224004373 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 319224004374 Competence protein; Region: Competence; cl00471 319224004375 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 319224004376 lipid transporter ATP-binding/permease protein; Provisional; Region: PRK11176 319224004377 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224004378 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 319224004379 Walker A/P-loop; other site 319224004380 ATP binding site [chemical binding]; other site 319224004381 Q-loop/lid; other site 319224004382 ABC transporter signature motif; other site 319224004383 Walker B; other site 319224004384 D-loop; other site 319224004385 H-loop/switch region; other site 319224004386 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 319224004387 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 319224004388 Trm112p-like protein; Region: Trm112p; cl01066 319224004389 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 319224004390 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224004391 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 319224004392 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 319224004393 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 319224004394 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 319224004395 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 319224004396 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224004397 Protein of unknown function (DUF445); Region: DUF445; pfam04286 319224004398 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 319224004399 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224004400 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 319224004401 cytidine deaminase; Provisional; Region: PRK09027 319224004402 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 319224004403 active site 319224004404 catalytic motif [active] 319224004405 Zn binding site [ion binding]; other site 319224004406 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 319224004407 exonuclease I; Provisional; Region: sbcB; PRK11779 319224004408 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 319224004409 active site 319224004410 catalytic site [active] 319224004411 substrate binding site [chemical binding]; other site 319224004412 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 319224004413 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 319224004414 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 319224004415 S-adenosylmethionine binding site [chemical binding]; other site 319224004416 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 319224004417 DNA-binding site [nucleotide binding]; DNA binding site 319224004418 RNA-binding motif; other site 319224004419 ribonuclease E; Reviewed; Region: rne; PRK10811 319224004420 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 319224004421 homodimer interface [polypeptide binding]; other site 319224004422 oligonucleotide binding site [chemical binding]; other site 319224004423 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 319224004424 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 319224004425 RNA binding surface [nucleotide binding]; other site 319224004426 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224004427 active site 319224004428 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 319224004429 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 319224004430 motif II; other site 319224004431 Maf-like protein; Region: Maf; pfam02545 319224004432 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 319224004433 active site 319224004434 dimer interface [polypeptide binding]; other site 319224004435 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 319224004436 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 319224004437 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 319224004438 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 319224004439 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 319224004440 dimer interface [polypeptide binding]; other site 319224004441 active site 319224004442 CoA binding pocket [chemical binding]; other site 319224004443 Acyl transferase domain; Region: Acyl_transf_1; cl08282 319224004444 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 319224004445 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 319224004446 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 319224004447 NAD(P) binding site [chemical binding]; other site 319224004448 homotetramer interface [polypeptide binding]; other site 319224004449 homodimer interface [polypeptide binding]; other site 319224004450 active site 319224004451 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224004452 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 319224004453 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 319224004454 dimer interface [polypeptide binding]; other site 319224004455 active site 319224004456 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 319224004457 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224004458 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 319224004459 NAD(P) binding pocket [chemical binding]; other site 319224004460 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 319224004461 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 319224004462 active site 319224004463 phosphate binding residues; other site 319224004464 catalytic residues [active] 319224004465 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 319224004466 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 319224004467 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 319224004468 active site 319224004469 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 319224004470 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 319224004471 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 319224004472 N-terminal plug; other site 319224004473 ligand-binding site [chemical binding]; other site 319224004474 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 319224004475 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 319224004476 active site 319224004477 nucleophile elbow; other site 319224004478 asparagine synthetase B; Provisional; Region: asnB; PRK09431 319224004479 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 319224004480 active site 319224004481 dimer interface [polypeptide binding]; other site 319224004482 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 319224004483 Ligand Binding Site [chemical binding]; other site 319224004484 Molecular Tunnel; other site 319224004485 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 319224004486 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 319224004487 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 319224004488 PA/protease or protease-like domain interface [polypeptide binding]; other site 319224004489 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 319224004490 metal binding site [ion binding]; metal-binding site 319224004491 UMP phosphatase; Provisional; Region: PRK10444 319224004492 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 319224004493 active site 319224004494 motif I; other site 319224004495 motif II; other site 319224004496 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 319224004497 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 319224004498 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 319224004499 active site 319224004500 substrate binding site [chemical binding]; other site 319224004501 cosubstrate binding site; other site 319224004502 catalytic site [active] 319224004503 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 319224004504 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 319224004505 dimerization interface [polypeptide binding]; other site 319224004506 putative ATP binding site [chemical binding]; other site 319224004507 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224004508 active site 319224004509 Predicted permease [General function prediction only]; Region: COG2056 319224004510 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 319224004511 peroxidase; Provisional; Region: PRK15000 319224004512 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 319224004513 dimer interface [polypeptide binding]; other site 319224004514 decamer (pentamer of dimers) interface [polypeptide binding]; other site 319224004515 catalytic triad [active] 319224004516 peroxidatic and resolving cysteines [active] 319224004517 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 319224004518 dimer interface [polypeptide binding]; other site 319224004519 catalytic site [active] 319224004520 putative active site [active] 319224004521 putative substrate binding site [chemical binding]; other site 319224004522 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224004523 ligand binding site [chemical binding]; other site 319224004524 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 319224004525 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 319224004526 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 319224004527 active site 319224004528 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224004529 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 319224004530 Gram-negative bacterial tonB protein; Region: TonB; cl10048 319224004531 translocation protein TolB; Provisional; Region: tolB; PRK04792 319224004532 TolB amino-terminal domain; Region: TolB_N; cl00639 319224004533 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224004534 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224004535 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224004536 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 319224004537 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224004538 ligand binding site [chemical binding]; other site 319224004539 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 319224004540 Tetratricopeptide repeat; Region: TPR_6; pfam13174 319224004541 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 319224004542 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 319224004543 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 319224004544 active site 319224004545 metal binding site [ion binding]; metal-binding site 319224004546 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 319224004547 dipeptidyl carboxypeptidase II; Provisional; Region: PRK10280 319224004548 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 319224004549 active site 319224004550 Zn binding site [ion binding]; other site 319224004551 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 319224004552 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 319224004553 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224004554 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224004555 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 319224004556 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224004557 substrate binding pocket [chemical binding]; other site 319224004558 membrane-bound complex binding site; other site 319224004559 hinge residues; other site 319224004560 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 319224004561 Predicted membrane protein [Function unknown]; Region: COG4984 319224004562 Domain of unknown function (DUF4401); Region: DUF4401; pfam14351 319224004563 GDYXXLXY protein; Region: GDYXXLXY; cl02066 319224004564 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 319224004565 Lamin Tail Domain; Region: LTD; pfam00932 319224004566 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 319224004567 generic binding surface II; other site 319224004568 generic binding surface I; other site 319224004569 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 319224004570 putative active site [active] 319224004571 putative catalytic site [active] 319224004572 putative Mg binding site IVb [ion binding]; other site 319224004573 putative phosphate binding site [ion binding]; other site 319224004574 putative DNA binding site [nucleotide binding]; other site 319224004575 putative Mg binding site IVa [ion binding]; other site 319224004576 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 319224004577 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 319224004578 active site 319224004579 Int/Topo IB signature motif; other site 319224004580 DNA binding site [nucleotide binding] 319224004581 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 319224004582 Putative transposase; Region: Y2_Tnp; pfam04986 319224004583 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 319224004584 HSP70 interaction site [polypeptide binding]; other site 319224004585 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 319224004586 THUMP domain; Region: THUMP; cl12076 319224004587 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; cl16911 319224004588 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 319224004589 S-adenosylmethionine binding site [chemical binding]; other site 319224004590 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 319224004591 catalytic residues [active] 319224004592 ABC transporter ATPase component; Reviewed; Region: PRK11147 319224004593 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 319224004594 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 319224004595 ABC transporter; Region: ABC_tran_2; pfam12848 319224004596 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 319224004597 Protein of unknown function (DUF3466); Region: DUF3466; pfam11949 319224004598 Ribosome modulation factor; Region: RMF; cl01207 319224004599 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 319224004600 active site 1 [active] 319224004601 dimer interface [polypeptide binding]; other site 319224004602 active site 2 [active] 319224004603 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 319224004604 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 319224004605 response regulator; Provisional; Region: PRK09483 319224004606 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 319224004607 active site 319224004608 phosphorylation site [posttranslational modification] 319224004609 intermolecular recognition site; other site 319224004610 dimerization interface [polypeptide binding]; other site 319224004611 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 319224004612 DNA binding residues [nucleotide binding] 319224004613 dimerization interface [polypeptide binding]; other site 319224004614 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 319224004615 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 319224004616 GIY-YIG motif/motif A; other site 319224004617 active site 319224004618 catalytic site [active] 319224004619 putative DNA binding site [nucleotide binding]; other site 319224004620 metal binding site [ion binding]; metal-binding site 319224004621 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 319224004622 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 319224004623 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 319224004624 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224004625 Walker A/P-loop; other site 319224004626 ATP binding site [chemical binding]; other site 319224004627 Q-loop/lid; other site 319224004628 ABC transporter signature motif; other site 319224004629 Walker B; other site 319224004630 D-loop; other site 319224004631 H-loop/switch region; other site 319224004632 hypothetical protein; Provisional; Region: PRK11239 319224004633 Protein of unknown function, DUF480; Region: DUF480; cl01209 319224004634 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 319224004635 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 319224004636 arginine decarboxylase; Provisional; Region: PRK05354 319224004637 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 319224004638 dimer interface [polypeptide binding]; other site 319224004639 active site 319224004640 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 319224004641 catalytic residues [active] 319224004642 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 319224004643 Adenosylmethionine decarboxylase; Region: SAM_decarbox; cl03253 319224004644 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 319224004645 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 319224004646 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 319224004647 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 319224004648 YceI-like domain; Region: YceI; cl01001 319224004649 Protein of unknown function (DUF3802); Region: DUF3802; pfam12290 319224004650 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 319224004651 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 319224004652 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 319224004653 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 319224004654 nucleotide binding site/active site [active] 319224004655 HIT family signature motif; other site 319224004656 catalytic residue [active] 319224004657 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 319224004658 CoenzymeA binding site [chemical binding]; other site 319224004659 subunit interaction site [polypeptide binding]; other site 319224004660 PHB binding site; other site 319224004661 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 319224004662 CoenzymeA binding site [chemical binding]; other site 319224004663 subunit interaction site [polypeptide binding]; other site 319224004664 PHB binding site; other site 319224004665 Predicted periplasmic lipoprotein [General function prediction only]; Region: COG5633 319224004666 Putative periplasmic lipoprotein; Region: DUF1425; cd09030 319224004667 putative dimer interface [polypeptide binding]; other site 319224004668 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 319224004669 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 319224004670 putative transporter; Provisional; Region: PRK03699 319224004671 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 319224004672 putative substrate translocation pore; other site 319224004673 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 319224004674 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 319224004675 ligand binding site [chemical binding]; other site 319224004676 flexible hinge region; other site 319224004677 Helix-turn-helix domains; Region: HTH; cl00088 319224004678 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224004679 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 319224004680 N-terminal plug; other site 319224004681 ligand-binding site [chemical binding]; other site 319224004682 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 319224004683 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224004684 Phosphotransferase enzyme family; Region: APH; pfam01636 319224004685 active site 319224004686 ATP binding site [chemical binding]; other site 319224004687 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224004688 substrate binding site [chemical binding]; other site 319224004689 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 319224004690 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 319224004691 putative FMN binding site [chemical binding]; other site 319224004692 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 319224004693 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224004694 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 319224004695 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 319224004696 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224004697 Protein of unknown function, DUF482; Region: DUF482; pfam04339 319224004698 LysE type translocator; Region: LysE; cl00565 319224004699 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 319224004700 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 319224004701 dimer interface [polypeptide binding]; other site 319224004702 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 319224004703 active site 319224004704 Fe binding site [ion binding]; other site 319224004705 Cupin domain; Region: Cupin_2; cl09118 319224004706 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224004707 Helix-turn-helix domains; Region: HTH; cl00088 319224004708 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 319224004709 dimerization interface [polypeptide binding]; other site 319224004710 Mitochondrial biogenesis AIM24; Region: AIM24; cl00884 319224004711 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; cl01155 319224004712 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; cl01155 319224004713 MatE; Region: MatE; cl10513 319224004714 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 319224004715 EVE domain; Region: EVE; cl00728 319224004716 AMP-binding domain protein; Validated; Region: PRK08315 319224004717 AMP-binding enzyme; Region: AMP-binding; cl15778 319224004718 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224004719 Cache domain; Region: Cache_1; pfam02743 319224004720 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 319224004721 putative active site [active] 319224004722 heme pocket [chemical binding]; other site 319224004723 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224004724 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 319224004725 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 319224004726 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 319224004727 transmembrane helices; other site 319224004728 fatty acid metabolism regulator; Provisional; Region: PRK04984 319224004729 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224004730 DNA-binding site [nucleotide binding]; DNA binding site 319224004731 FCD domain; Region: FCD; cl11656 319224004732 SpoVR family protein; Provisional; Region: PRK11767 319224004733 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 319224004734 Uncharacterized conserved protein [Function unknown]; Region: COG2718 319224004735 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 319224004736 PrkA family serine protein kinase; Provisional; Region: PRK15455 319224004737 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224004738 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 319224004739 superoxide dismutase; Provisional; Region: PRK10543 319224004740 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 319224004741 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 319224004742 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 319224004743 putative GSH binding site [chemical binding]; other site 319224004744 catalytic residues [active] 319224004745 uracil-xanthine permease; Region: ncs2; TIGR00801 319224004746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 319224004747 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 319224004748 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 319224004749 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 319224004750 Walker A motif; other site 319224004751 ATP binding site [chemical binding]; other site 319224004752 Walker B motif; other site 319224004753 arginine finger; other site 319224004754 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 319224004755 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 319224004756 ArsC family; Region: ArsC; pfam03960 319224004757 catalytic residues [active] 319224004758 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 319224004759 Peptidase family M48; Region: Peptidase_M48; cl12018 319224004760 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 319224004761 binding surface 319224004762 TPR motif; other site 319224004763 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 319224004764 CPxP motif; other site 319224004765 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 319224004766 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 319224004767 Helix-turn-helix domains; Region: HTH; cl00088 319224004768 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 319224004769 putative dimerization interface [polypeptide binding]; other site 319224004770 LysE type translocator; Region: LysE; cl00565 319224004771 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 319224004772 catalytic triad [active] 319224004773 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 319224004774 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_1; cd04893 319224004775 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 319224004776 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 319224004777 dihydrodipicolinate synthase; Region: dapA; TIGR00674 319224004778 dimer interface [polypeptide binding]; other site 319224004779 active site 319224004780 catalytic residue [active] 319224004781 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 319224004782 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 319224004783 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224004784 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 319224004785 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 319224004786 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224004787 Protein export membrane protein; Region: SecD_SecF; cl14618 319224004788 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 319224004789 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224004790 Coenzyme A binding pocket [chemical binding]; other site 319224004791 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 319224004792 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 319224004793 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 319224004794 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 319224004795 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 319224004796 conserved cys residue [active] 319224004797 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 319224004798 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 319224004799 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 319224004800 active site 319224004801 catalytic residues [active] 319224004802 metal binding site [ion binding]; metal-binding site 319224004803 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 319224004804 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 319224004805 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224004806 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 319224004807 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 319224004808 carboxyltransferase (CT) interaction site; other site 319224004809 biotinylation site [posttranslational modification]; other site 319224004810 enoyl-CoA hydratase; Provisional; Region: PRK05995 319224004811 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 319224004812 substrate binding site [chemical binding]; other site 319224004813 oxyanion hole (OAH) forming residues; other site 319224004814 trimer interface [polypeptide binding]; other site 319224004815 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 319224004816 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 319224004817 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 319224004818 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 319224004819 isovaleryl-CoA dehydrogenase; Region: PLN02519 319224004820 substrate binding site [chemical binding]; other site 319224004821 FAD binding site [chemical binding]; other site 319224004822 catalytic base [active] 319224004823 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 319224004824 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 319224004825 DNA binding residues [nucleotide binding] 319224004826 putative dimer interface [polypeptide binding]; other site 319224004827 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 319224004828 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 319224004829 AMP-binding enzyme; Region: AMP-binding; cl15778 319224004830 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224004831 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 319224004832 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224004833 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 319224004834 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 319224004835 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224004836 Helix-turn-helix domains; Region: HTH; cl00088 319224004837 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 319224004838 dimerization interface [polypeptide binding]; other site 319224004839 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 319224004840 putative active site [active] 319224004841 metal binding site [ion binding]; metal-binding site 319224004842 UbiA prenyltransferase family; Region: UbiA; cl00337 319224004843 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 319224004844 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224004845 NAD(P) binding site [chemical binding]; other site 319224004846 active site 319224004847 acyl-CoA thioesterase II; Provisional; Region: PRK10526 319224004848 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 319224004849 active site 319224004850 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 319224004851 catalytic triad [active] 319224004852 dimer interface [polypeptide binding]; other site 319224004853 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 319224004854 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224004855 Helix-turn-helix domains; Region: HTH; cl00088 319224004856 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 319224004857 dimerization interface [polypeptide binding]; other site 319224004858 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 319224004859 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224004860 putative substrate translocation pore; other site 319224004861 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 319224004862 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 319224004863 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 319224004864 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 319224004865 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 319224004866 domain interface [polypeptide binding]; other site 319224004867 active site 319224004868 catalytic site [active] 319224004869 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 319224004870 domain interface [polypeptide binding]; other site 319224004871 active site 319224004872 catalytic site [active] 319224004873 putative chaperone; Provisional; Region: PRK11678 319224004874 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 319224004875 CreA protein; Region: CreA; pfam05981 319224004876 cystathionine beta-lyase; Provisional; Region: PRK09028 319224004877 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 319224004878 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224004879 catalytic residue [active] 319224004880 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 319224004881 DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases; Region: CBM9_like_HisKa; cd09622 319224004882 putative ligand binding site [chemical binding]; other site 319224004883 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 319224004884 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 319224004885 dimer interface [polypeptide binding]; other site 319224004886 phosphorylation site [posttranslational modification] 319224004887 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 319224004888 ATP binding site [chemical binding]; other site 319224004889 Mg2+ binding site [ion binding]; other site 319224004890 G-X-G motif; other site 319224004891 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 319224004892 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 319224004893 active site 319224004894 phosphorylation site [posttranslational modification] 319224004895 intermolecular recognition site; other site 319224004896 dimerization interface [polypeptide binding]; other site 319224004897 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 319224004898 DNA binding site [nucleotide binding] 319224004899 Vault protein inter-alpha-trypsin domain; Region: VIT; cl02699 319224004900 marine proteobacterial sortase target protein; Region: marine_srt_targ; TIGR03788 319224004901 vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to...; Region: vWA_interalpha_trypsin_inhibitor; cd01461 319224004902 metal ion-dependent adhesion site (MIDAS); other site 319224004903 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved...; Region: Sortase_D_4; cd05828 319224004904 active site 319224004905 catalytic site [active] 319224004906 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224004907 metal binding site [ion binding]; metal-binding site 319224004908 active site 319224004909 I-site; other site 319224004910 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 319224004911 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 319224004912 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 319224004913 PA/protease or protease-like domain interface [polypeptide binding]; other site 319224004914 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 319224004915 metal binding site [ion binding]; metal-binding site 319224004916 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 319224004917 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224004918 Protein of unknown function, DUF; Region: DUF413; cl10479 319224004919 transcriptional regulator HdfR; Provisional; Region: PRK03601 319224004920 Helix-turn-helix domains; Region: HTH; cl00088 319224004921 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 319224004922 dimerization interface [polypeptide binding]; other site 319224004923 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 319224004924 DNA ligase; Provisional; Region: PRK09125 319224004925 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 319224004926 DNA binding site [nucleotide binding] 319224004927 active site 319224004928 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 319224004929 DNA binding site [nucleotide binding] 319224004930 Low molecular weight phosphatase family; Region: LMWPc; cd00115 319224004931 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 319224004932 active site 319224004933 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224004934 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224004935 Coenzyme A binding pocket [chemical binding]; other site 319224004936 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 319224004937 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 319224004938 GTP/Mg2+ binding site [chemical binding]; other site 319224004939 G4 box; other site 319224004940 G5 box; other site 319224004941 G1 box; other site 319224004942 Switch I region; other site 319224004943 G2 box; other site 319224004944 G3 box; other site 319224004945 Switch II region; other site 319224004946 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 319224004947 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 319224004948 bifunctional methionine sulfoxide reductase B/A protein; Provisional; Region: PRK05550 319224004949 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 319224004950 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 319224004951 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; cd00384 319224004952 dimer interface [polypeptide binding]; other site 319224004953 active site 319224004954 Schiff base residues; other site 319224004955 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 319224004956 Peptidase M50B-like; Region: Peptidase_M50B; pfam13398 319224004957 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; cl16911 319224004958 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 319224004959 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 319224004960 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 319224004961 AMP-binding enzyme; Region: AMP-binding; cl15778 319224004962 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224004963 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 319224004964 ribonuclease D; Provisional; Region: PRK10829 319224004965 catalytic site [active] 319224004966 putative active site [active] 319224004967 putative substrate binding site [chemical binding]; other site 319224004968 HRDC domain; Region: HRDC; cl02578 319224004969 Septum formation topological specificity factor MinE; Region: MinE; cl00538 319224004970 cell division inhibitor MinD; Provisional; Region: PRK10818 319224004971 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 319224004972 Switch I; other site 319224004973 Switch II; other site 319224004974 septum formation inhibitor; Reviewed; Region: minC; PRK04804 319224004975 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 319224004976 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 319224004977 YcgL domain; Region: YcgL; cl01189 319224004978 Flagellin N-methylase; Region: FliB; cl00497 319224004979 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 319224004980 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 319224004981 substrate binding site [chemical binding]; other site 319224004982 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 319224004983 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 319224004984 ATP binding site [chemical binding]; other site 319224004985 Mg++ binding site [ion binding]; other site 319224004986 motif III; other site 319224004987 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 319224004988 nucleotide binding region [chemical binding]; other site 319224004989 ATP-binding site [chemical binding]; other site 319224004990 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 319224004991 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 319224004992 AsmA family; Region: AsmA; pfam05170 319224004993 AsmA-like C-terminal region; Region: AsmA_2; cl15864 319224004994 Intracellular proteinase inhibitor; Region: BsuPI; pfam12690 319224004995 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 319224004996 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 319224004997 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224004998 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224004999 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224005000 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224005001 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 319224005002 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 319224005003 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; cl16911 319224005004 ubiquinone biosynthesis O-methyltransferase; Region: UbiG; TIGR01983 319224005005 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 319224005006 Helix-turn-helix domains; Region: HTH; cl00088 319224005007 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 319224005008 putative dimerization interface [polypeptide binding]; other site 319224005009 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 319224005010 RNA/DNA hybrid binding site [nucleotide binding]; other site 319224005011 active site 319224005012 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 319224005013 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 319224005014 active site 319224005015 catalytic site [active] 319224005016 substrate binding site [chemical binding]; other site 319224005017 TIGR03503 family protein; Region: TIGR03503 319224005018 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224005019 ligand binding site [chemical binding]; other site 319224005020 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 319224005021 outer membrane lipoprotein; Provisional; Region: PRK11023 319224005022 BON domain; Region: BON; cl02771 319224005023 BON domain; Region: BON; cl02771 319224005024 BON domain; Region: BON; cl02771 319224005025 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 319224005026 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 319224005027 ligand binding site [chemical binding]; other site 319224005028 flexible hinge region; other site 319224005029 Helix-turn-helix domains; Region: HTH; cl00088 319224005030 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 319224005031 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 319224005032 ligand binding site [chemical binding]; other site 319224005033 flexible hinge region; other site 319224005034 Helix-turn-helix domains; Region: HTH; cl00088 319224005035 BON domain; Region: BON; cl02771 319224005036 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 319224005037 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 319224005038 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 319224005039 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 319224005040 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 319224005041 active site 319224005042 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 319224005043 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 319224005044 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 319224005045 putative active site [active] 319224005046 putative dimer interface [polypeptide binding]; other site 319224005047 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 319224005048 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 319224005049 active site 319224005050 DNA binding site [nucleotide binding] 319224005051 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 319224005052 active site 319224005053 catalytic residues [active] 319224005054 metal binding site [ion binding]; metal-binding site 319224005055 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 319224005056 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 319224005057 16S rRNA methyltransferase B; Provisional; Region: PRK14902 319224005058 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 319224005059 S-adenosylmethionine binding site [chemical binding]; other site 319224005060 GAF domain; Region: GAF_2; pfam13185 319224005061 GAF domain; Region: GAF; cl15785 319224005062 PAS domain; Region: PAS_9; pfam13426 319224005063 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224005064 metal binding site [ion binding]; metal-binding site 319224005065 active site 319224005066 I-site; other site 319224005067 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 319224005068 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 319224005069 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 319224005070 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224005071 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]; Region: HisJ; COG0834 319224005072 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 319224005073 substrate binding pocket [chemical binding]; other site 319224005074 membrane-bound complex binding site; other site 319224005075 hinge residues; other site 319224005076 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 319224005077 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 319224005078 putative dimer interface [polypeptide binding]; other site 319224005079 putative anticodon binding site; other site 319224005080 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 319224005081 homodimer interface [polypeptide binding]; other site 319224005082 motif 1; other site 319224005083 motif 2; other site 319224005084 active site 319224005085 motif 3; other site 319224005086 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 319224005087 putative active site [active] 319224005088 putative CoA binding site [chemical binding]; other site 319224005089 nudix motif; other site 319224005090 metal binding site [ion binding]; metal-binding site 319224005091 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 319224005092 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 319224005093 chorismate binding enzyme; Region: Chorismate_bind; cl10555 319224005094 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 319224005095 Fumarase C-terminus; Region: Fumerase_C; cl00795 319224005096 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 319224005097 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 319224005098 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224005099 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224005100 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 319224005101 putative active site [active] 319224005102 Zn binding site [ion binding]; other site 319224005103 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 319224005104 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 319224005105 putative catalytic cysteine [active] 319224005106 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 319224005107 putative active site [active] 319224005108 metal binding site [ion binding]; metal-binding site 319224005109 MarC family integral membrane protein; Region: MarC; cl00919 319224005110 Nitrate and nitrite sensing; Region: NIT; pfam08376 319224005111 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 319224005112 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224005113 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224005114 dimer interface [polypeptide binding]; other site 319224005115 putative CheW interface [polypeptide binding]; other site 319224005116 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 319224005117 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 319224005118 putative substrate translocation pore; other site 319224005119 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 319224005120 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224005121 putative substrate translocation pore; other site 319224005122 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224005123 LysR family transcriptional regulator; Provisional; Region: PRK14997 319224005124 Helix-turn-helix domains; Region: HTH; cl00088 319224005125 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 319224005126 putative dimerization interface [polypeptide binding]; other site 319224005127 putative effector binding pocket; other site 319224005128 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 319224005129 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005130 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224005131 DEAD-like helicases superfamily; Region: DEXDc; smart00487 319224005132 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005133 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 319224005134 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 319224005135 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005136 DEAD_2; Region: DEAD_2; pfam06733 319224005137 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005138 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 319224005139 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 319224005140 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 319224005141 N-terminal plug; other site 319224005142 ligand-binding site [chemical binding]; other site 319224005143 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224005144 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224005145 dimer interface [polypeptide binding]; other site 319224005146 putative CheW interface [polypeptide binding]; other site 319224005147 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 319224005148 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 319224005149 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 319224005150 dimer interface [polypeptide binding]; other site 319224005151 motif 1; other site 319224005152 active site 319224005153 motif 2; other site 319224005154 motif 3; other site 319224005155 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 319224005156 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 319224005157 putative tRNA-binding site [nucleotide binding]; other site 319224005158 B3/4 domain; Region: B3_4; cl11458 319224005159 tRNA synthetase B5 domain; Region: B5; cl08394 319224005160 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 319224005161 dimer interface [polypeptide binding]; other site 319224005162 motif 1; other site 319224005163 motif 3; other site 319224005164 motif 2; other site 319224005165 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 319224005166 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 319224005167 IHF dimer interface [polypeptide binding]; other site 319224005168 IHF - DNA interface [nucleotide binding]; other site 319224005169 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 319224005170 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 319224005171 putative acyl-acceptor binding pocket; other site 319224005172 hydrogenase nickel incorporation protein; Provisional; Region: hypA; cl00418 319224005173 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 319224005174 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 319224005175 dimerization interface [polypeptide binding]; other site 319224005176 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 319224005177 ATP binding site [chemical binding]; other site 319224005178 Hydrogenase formation hypA family; Region: HypD; cl12072 319224005179 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 319224005180 HupF/HypC family; Region: HupF_HypC; cl00394 319224005181 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005182 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005183 G4 box; other site 319224005184 G5 box; other site 319224005185 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 319224005186 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224005187 CoA-ligase; Region: Ligase_CoA; cl02894 319224005188 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224005189 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 319224005190 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 319224005191 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 319224005192 ABC transporter; Region: ABC_tran_2; pfam12848 319224005193 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 319224005194 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 319224005195 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 319224005196 N-terminal plug; other site 319224005197 ligand-binding site [chemical binding]; other site 319224005198 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 319224005199 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 319224005200 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 319224005201 endonuclease III; Provisional; Region: PRK10702 319224005202 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 319224005203 minor groove reading motif; other site 319224005204 helix-hairpin-helix signature motif; other site 319224005205 substrate binding pocket [chemical binding]; other site 319224005206 active site 319224005207 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 319224005208 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 319224005209 FMN-binding domain; Region: FMN_bind; cl01081 319224005210 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 319224005211 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 319224005212 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 319224005213 SLBB domain; Region: SLBB; pfam10531 319224005214 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 319224005215 electron transport complex protein RnfB; Provisional; Region: PRK05113 319224005216 Putative Fe-S cluster; Region: FeS; pfam04060 319224005217 4Fe-4S binding domain; Region: Fer4; cl02805 319224005218 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 319224005219 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224005220 active site 319224005221 I-site; other site 319224005222 metal binding site [ion binding]; metal-binding site 319224005223 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 319224005224 excinuclease ABC subunit B; Provisional; Region: PRK05298 319224005225 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 319224005226 ATP binding site [chemical binding]; other site 319224005227 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 319224005228 nucleotide binding region [chemical binding]; other site 319224005229 ATP-binding site [chemical binding]; other site 319224005230 Ultra-violet resistance protein B; Region: UvrB; pfam12344 319224005231 UvrB/uvrC motif; Region: UVR; pfam02151 319224005232 Rhomboid family; Region: Rhomboid; cl11446 319224005233 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 319224005234 Ligand Binding Site [chemical binding]; other site 319224005235 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 319224005236 Ribosomal S4P (gammaproteobacterial); Region: Ribosomal_S4Pg; pfam11993 319224005237 Protein of unknown function (DUF406); Region: DUF406; cl11449 319224005238 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 319224005239 GAF domain; Region: GAF; cl15785 319224005240 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 319224005241 PAS fold; Region: PAS_3; pfam08447 319224005242 putative active site [active] 319224005243 heme pocket [chemical binding]; other site 319224005244 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224005245 metal binding site [ion binding]; metal-binding site 319224005246 active site 319224005247 I-site; other site 319224005248 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 319224005249 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 319224005250 SEC-C motif; Region: SEC-C; pfam02810 319224005251 SEC-C motif; Region: SEC-C; pfam02810 319224005252 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 319224005253 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 319224005254 Smr domain; Region: Smr; cl02619 319224005255 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11552 319224005256 Helix-turn-helix domains; Region: HTH; cl00088 319224005257 acyl-CoA dehydrogenase; Reviewed; Region: PRK13026 319224005258 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 319224005259 active site 319224005260 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 319224005261 pyruvate kinase; Provisional; Region: PRK05826 319224005262 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 319224005263 domain interfaces; other site 319224005264 active site 319224005265 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 319224005266 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 319224005267 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 319224005268 putative active site [active] 319224005269 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 319224005270 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 319224005271 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 319224005272 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 319224005273 putative active site [active] 319224005274 Dehydratase family; Region: ILVD_EDD; cl00340 319224005275 6-phosphogluconate dehydratase; Region: edd; TIGR01196 319224005276 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 319224005277 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 319224005278 active site 319224005279 intersubunit interface [polypeptide binding]; other site 319224005280 catalytic residue [active] 319224005281 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 319224005282 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224005283 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 319224005284 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224005285 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 319224005286 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 319224005287 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224005288 homodimer interface [polypeptide binding]; other site 319224005289 catalytic residue [active] 319224005290 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 319224005291 elongation factor P; Validated; Region: PRK00529 319224005292 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 319224005293 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 319224005294 RNA binding site [nucleotide binding]; other site 319224005295 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 319224005296 RNA binding site [nucleotide binding]; other site 319224005297 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 319224005298 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224005299 LexA regulated protein; Provisional; Region: PRK11675 319224005300 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 319224005301 acyl-CoA esterase; Provisional; Region: PRK10673 319224005302 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 319224005303 SeqA protein; Region: SeqA; cl11470 319224005304 phosphoglucomutase; Validated; Region: PRK07564 319224005305 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl...; Region: PGM_like3; cd05801 319224005306 active site 319224005307 substrate binding site [chemical binding]; other site 319224005308 metal binding site [ion binding]; metal-binding site 319224005309 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 319224005310 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 319224005311 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 319224005312 putative active site [active] 319224005313 Zn binding site [ion binding]; other site 319224005314 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 319224005315 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 319224005316 tetramer interface [polypeptide binding]; other site 319224005317 TPP-binding site [chemical binding]; other site 319224005318 heterodimer interface [polypeptide binding]; other site 319224005319 phosphorylation loop region [posttranslational modification] 319224005320 3-methyl-2-oxobutanate dehydrogenase; Provisional; Region: PTZ00182 319224005321 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 319224005322 alpha subunit interface [polypeptide binding]; other site 319224005323 TPP binding site [chemical binding]; other site 319224005324 heterodimer interface [polypeptide binding]; other site 319224005325 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 319224005326 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 319224005327 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 319224005328 E3 interaction surface; other site 319224005329 lipoyl attachment site [posttranslational modification]; other site 319224005330 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 319224005331 E3 interaction surface; other site 319224005332 lipoyl attachment site [posttranslational modification]; other site 319224005333 e3 binding domain; Region: E3_binding; pfam02817 319224005334 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 319224005335 Quinolinate synthetase A protein; Region: NadA; cl00420 319224005336 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224005337 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 319224005338 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224005339 Protein of unknown function (DUF2989); Region: DUF2989; pfam11207 319224005340 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 319224005341 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224005342 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224005343 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 319224005344 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 319224005345 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 319224005346 Peptidase M15; Region: Peptidase_M15_3; cl01194 319224005347 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 319224005348 5S rRNA interface [nucleotide binding]; other site 319224005349 CTC domain interface [polypeptide binding]; other site 319224005350 L16 interface [polypeptide binding]; other site 319224005351 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 319224005352 Family of unknown function (DUF490); Region: DUF490; pfam04357 319224005353 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 319224005354 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224005355 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224005356 Surface antigen; Region: Bac_surface_Ag; cl03097 319224005357 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 319224005358 catalytic nucleophile [active] 319224005359 FOG: CBS domain [General function prediction only]; Region: COG0517 319224005360 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_16; cd04629 319224005361 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 319224005362 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 319224005363 ATP binding site [chemical binding]; other site 319224005364 putative Mg++ binding site [ion binding]; other site 319224005365 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 319224005366 nucleotide binding region [chemical binding]; other site 319224005367 ATP-binding site [chemical binding]; other site 319224005368 Helicase associated domain (HA2); Region: HA2; cl04503 319224005369 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 319224005370 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 319224005371 Periplasmic nitrate reductase protein NapE; Region: NapE; cl01848 319224005372 NapD protein; Region: NapD; cl01163 319224005373 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 319224005374 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 319224005375 [4Fe-4S] binding site [ion binding]; other site 319224005376 molybdopterin cofactor binding site; other site 319224005377 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 319224005378 molybdopterin cofactor binding site; other site 319224005379 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 319224005380 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 319224005381 Protein of unknown function (DUF419); Region: DUF419; cl15265 319224005382 Uncharacterized conserved protein [Function unknown]; Region: COG2850 319224005383 JmjC domain, hydroxylase; Region: JmjC; cl15814 319224005384 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 319224005385 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 319224005386 transmembrane helices; other site 319224005387 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224005388 Helix-turn-helix domain; Region: HTH_18; pfam12833 319224005389 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224005390 YCII-related domain; Region: YCII; cl00999 319224005391 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 319224005392 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 319224005393 putative RNA binding site [nucleotide binding]; other site 319224005394 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; cl16911 319224005395 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 319224005396 Helix-turn-helix domain; Region: HTH_18; pfam12833 319224005397 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224005398 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 319224005399 Ligand Binding Site [chemical binding]; other site 319224005400 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; cl16911 319224005401 PAS fold; Region: PAS_4; pfam08448 319224005402 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 319224005403 putative active site [active] 319224005404 heme pocket [chemical binding]; other site 319224005405 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 319224005406 PAS fold; Region: PAS_3; pfam08447 319224005407 putative active site [active] 319224005408 heme pocket [chemical binding]; other site 319224005409 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 319224005410 PAS fold; Region: PAS_3; pfam08447 319224005411 putative active site [active] 319224005412 heme pocket [chemical binding]; other site 319224005413 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224005414 metal binding site [ion binding]; metal-binding site 319224005415 active site 319224005416 I-site; other site 319224005417 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 319224005418 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_27; cd04686 319224005419 nudix motif; other site 319224005420 DTW domain; Region: DTW; cl01221 319224005421 Haemolysin-III related; Region: HlyIII; cl03831 319224005422 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 319224005423 ThiC-associated domain; Region: ThiC-associated; pfam13667 319224005424 ThiC family; Region: ThiC; cl08031 319224005425 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 319224005426 ATP binding site [chemical binding]; other site 319224005427 substrate binding site [chemical binding]; other site 319224005428 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 319224005429 thiamine phosphate binding site [chemical binding]; other site 319224005430 active site 319224005431 pyrophosphate binding site [ion binding]; other site 319224005432 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 319224005433 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 319224005434 ATP binding site [chemical binding]; other site 319224005435 substrate interface [chemical binding]; other site 319224005436 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 319224005437 thiS-thiF/thiG interaction site; other site 319224005438 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 319224005439 ThiS interaction site; other site 319224005440 putative active site [active] 319224005441 tetramer interface [polypeptide binding]; other site 319224005442 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 319224005443 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 319224005444 FeS/SAM binding site; other site 319224005445 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 319224005446 SprA-related family; Region: SprA-related; pfam12118 319224005447 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224005448 Helix-turn-helix domains; Region: HTH; cl00088 319224005449 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 319224005450 dimerization interface [polypeptide binding]; other site 319224005451 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 319224005452 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 319224005453 S-adenosylmethionine binding site [chemical binding]; other site 319224005454 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 319224005455 S-adenosylmethionine binding site [chemical binding]; other site 319224005456 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 319224005457 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224005458 substrate binding pocket [chemical binding]; other site 319224005459 membrane-bound complex binding site; other site 319224005460 hinge residues; other site 319224005461 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224005462 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 319224005463 substrate binding pocket [chemical binding]; other site 319224005464 membrane-bound complex binding site; other site 319224005465 hinge residues; other site 319224005466 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 319224005467 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224005468 substrate binding pocket [chemical binding]; other site 319224005469 membrane-bound complex binding site; other site 319224005470 hinge residues; other site 319224005471 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224005472 metal binding site [ion binding]; metal-binding site 319224005473 active site 319224005474 I-site; other site 319224005475 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 319224005476 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 319224005477 dimer interface [polypeptide binding]; other site 319224005478 anticodon binding site; other site 319224005479 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 319224005480 homodimer interface [polypeptide binding]; other site 319224005481 motif 1; other site 319224005482 active site 319224005483 motif 2; other site 319224005484 GAD domain; Region: GAD; pfam02938 319224005485 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 319224005486 active site 319224005487 motif 3; other site 319224005488 Transcriptional regulator; Region: Transcrip_reg; cl00361 319224005489 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 319224005490 active site 319224005491 putative DNA-binding cleft [nucleotide binding]; other site 319224005492 dimer interface [polypeptide binding]; other site 319224005493 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 319224005494 RuvA N terminal domain; Region: RuvA_N; pfam01330 319224005495 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 319224005496 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 319224005497 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 319224005498 Walker A motif; other site 319224005499 ATP binding site [chemical binding]; other site 319224005500 Walker B motif; other site 319224005501 arginine finger; other site 319224005502 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 319224005503 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 319224005504 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 319224005505 N-terminal plug; other site 319224005506 ligand-binding site [chemical binding]; other site 319224005507 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224005508 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 319224005509 active site 319224005510 phosphorylation site [posttranslational modification] 319224005511 intermolecular recognition site; other site 319224005512 dimerization interface [polypeptide binding]; other site 319224005513 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 319224005514 DNA binding site [nucleotide binding] 319224005515 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 319224005516 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 319224005517 putative active site [active] 319224005518 Zn binding site [ion binding]; other site 319224005519 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 319224005520 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 319224005521 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 319224005522 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224005523 homodimer interface [polypeptide binding]; other site 319224005524 catalytic residue [active] 319224005525 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 319224005526 phosphate binding site [ion binding]; other site 319224005527 putative substrate binding pocket [chemical binding]; other site 319224005528 dimer interface [polypeptide binding]; other site 319224005529 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 319224005530 Protein of unknown function (DUF2987); Region: DUF2987; pfam11205 319224005531 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 319224005532 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 319224005533 Ligand Binding Site [chemical binding]; other site 319224005534 universal stress protein UspE; Provisional; Region: PRK11175 319224005535 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 319224005536 Ligand Binding Site [chemical binding]; other site 319224005537 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 319224005538 Ligand Binding Site [chemical binding]; other site 319224005539 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 319224005540 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 319224005541 ligand binding site [chemical binding]; other site 319224005542 flexible hinge region; other site 319224005543 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 319224005544 putative switch regulator; other site 319224005545 non-specific DNA interactions [nucleotide binding]; other site 319224005546 DNA binding site [nucleotide binding] 319224005547 sequence specific DNA binding site [nucleotide binding]; other site 319224005548 putative cAMP binding site [chemical binding]; other site 319224005549 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 319224005550 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 319224005551 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 319224005552 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 319224005553 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 319224005554 metal-binding site [ion binding] 319224005555 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224005556 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224005557 FixH; Region: FixH; cl01254 319224005558 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 319224005559 Cytochrome c; Region: Cytochrom_C; cl11414 319224005560 Cytochrome c; Region: Cytochrom_C; cl11414 319224005561 Cytochrome cbb oxidase CcoQ. 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 of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 319224005562 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 319224005563 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 319224005564 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 319224005565 Low-spin heme binding site [chemical binding]; other site 319224005566 Putative water exit pathway; other site 319224005567 Binuclear center (active site) [active] 319224005568 Putative proton exit pathway; other site 319224005569 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 319224005570 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 319224005571 Helix-turn-helix domains; Region: HTH; cl00088 319224005572 putative transposase OrfB; Reviewed; Region: PHA02517 319224005573 HTH-like domain; Region: HTH_21; pfam13276 319224005574 Integrase core domain; Region: rve; cl01316 319224005575 Integrase core domain; Region: rve_3; cl15866 319224005576 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 319224005577 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 319224005578 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224005579 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224005580 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 319224005581 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 319224005582 carboxyltransferase (CT) interaction site; other site 319224005583 biotinylation site [posttranslational modification]; other site 319224005584 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 319224005585 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 319224005586 Cation efflux family; Region: Cation_efflux; cl00316 319224005587 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 319224005588 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 319224005589 DNA binding residues [nucleotide binding] 319224005590 dimer interface [polypeptide binding]; other site 319224005591 putative metal binding site [ion binding]; other site 319224005592 Cation efflux family; Region: Cation_efflux; cl00316 319224005593 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 319224005594 Bacterial Ig-like domain; Region: Big_5; cl01012 319224005595 putative metal dependent hydrolase; Provisional; Region: PRK11598 319224005596 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 319224005597 Sulfatase; Region: Sulfatase; cl10460 319224005598 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 319224005599 Sulfatase; Region: Sulfatase; cl10460 319224005600 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 319224005601 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224005602 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 319224005603 active site 319224005604 phosphorylation site [posttranslational modification] 319224005605 intermolecular recognition site; other site 319224005606 dimerization interface [polypeptide binding]; other site 319224005607 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 319224005608 DNA binding site [nucleotide binding] 319224005609 sensor protein QseC; Provisional; Region: PRK10337 319224005610 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 319224005611 dimer interface [polypeptide binding]; other site 319224005612 phosphorylation site [posttranslational modification] 319224005613 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 319224005614 ATP binding site [chemical binding]; other site 319224005615 Mg2+ binding site [ion binding]; other site 319224005616 G-X-G motif; other site 319224005617 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 319224005618 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 319224005619 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; cl00148 319224005620 primary dimer interface [polypeptide binding]; other site 319224005621 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 319224005622 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 319224005623 DNA binding site [nucleotide binding] 319224005624 dimer interface [polypeptide binding]; other site 319224005625 active site 319224005626 Int/Topo IB signature motif; other site 319224005627 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 319224005628 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 319224005629 Zn2+ binding site [ion binding]; other site 319224005630 Mg2+ binding site [ion binding]; other site 319224005631 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 319224005632 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 319224005633 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 319224005634 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 319224005635 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 319224005636 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 319224005637 catalytic residues [active] 319224005638 catalytic nucleophile [active] 319224005639 Presynaptic Site I dimer interface [polypeptide binding]; other site 319224005640 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 319224005641 Synaptic Flat tetramer interface [polypeptide binding]; other site 319224005642 Synaptic Site I dimer interface [polypeptide binding]; other site 319224005643 DNA binding site [nucleotide binding] 319224005644 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 319224005645 DNA-binding interface [nucleotide binding]; DNA binding site 319224005646 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 319224005647 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 319224005648 Ligand Binding Site [chemical binding]; other site 319224005649 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 319224005650 Ligand Binding Site [chemical binding]; other site 319224005651 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 319224005652 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224005653 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224005654 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 319224005655 putative transporter; Provisional; Region: PRK11043 319224005656 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 319224005657 putative substrate translocation pore; other site 319224005658 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 319224005659 Helix-turn-helix domains; Region: HTH; cl00088 319224005660 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 319224005661 dimerization interface [polypeptide binding]; other site 319224005662 YccA-like proteins; Region: YccA_like; cd10433 319224005663 DsrE/DsrF-like family; Region: DrsE; cl00672 319224005664 DsrE/DsrF-like family; Region: DrsE; cl00672 319224005665 DsrE/DsrF-like family; Region: DrsE; cl00672 319224005666 DsrC like protein; Region: DsrC; cl01101 319224005667 seryl-tRNA synthetase; Provisional; Region: PRK05431 319224005668 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 319224005669 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 319224005670 dimer interface [polypeptide binding]; other site 319224005671 active site 319224005672 motif 1; other site 319224005673 motif 2; other site 319224005674 motif 3; other site 319224005675 CrcB-like protein; Region: CRCB; cl09114 319224005676 recombination factor protein RarA; Reviewed; Region: PRK13342 319224005677 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 319224005678 Walker A motif; other site 319224005679 ATP binding site [chemical binding]; other site 319224005680 Walker B motif; other site 319224005681 arginine finger; other site 319224005682 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 319224005683 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 319224005684 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 319224005685 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 319224005686 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 319224005687 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224005688 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 319224005689 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 319224005690 Helix-turn-helix domains; Region: HTH; cl00088 319224005691 AsnC family; Region: AsnC_trans_reg; pfam01037 319224005692 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 319224005693 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 319224005694 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 319224005695 NAD(P) binding site [chemical binding]; other site 319224005696 thioredoxin reductase; Provisional; Region: PRK10262 319224005697 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224005698 ribosomal protein L20; Region: rpl20; CHL00068 319224005699 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 319224005700 23S rRNA binding site [nucleotide binding]; other site 319224005701 L21 binding site [polypeptide binding]; other site 319224005702 L13 binding site [polypeptide binding]; other site 319224005703 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 319224005704 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 319224005705 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 319224005706 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 319224005707 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 319224005708 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 319224005709 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 319224005710 active site 319224005711 dimer interface [polypeptide binding]; other site 319224005712 motif 1; other site 319224005713 motif 2; other site 319224005714 motif 3; other site 319224005715 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 319224005716 anticodon binding site; other site 319224005717 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 319224005718 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 319224005719 Lumazine binding domain; Region: Lum_binding; pfam00677 319224005720 Lumazine binding domain; Region: Lum_binding; pfam00677 319224005721 multidrug efflux protein; Reviewed; Region: PRK01766 319224005722 MatE; Region: MatE; cl10513 319224005723 MatE; Region: MatE; cl10513 319224005724 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 319224005725 secondary substrate binding site; other site 319224005726 primary substrate binding site; other site 319224005727 inhibition loop; other site 319224005728 dimerization interface [polypeptide binding]; other site 319224005729 DEAD-like helicases superfamily; Region: DEXDc; smart00487 319224005730 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 319224005731 ATP binding site [chemical binding]; other site 319224005732 putative Mg++ binding site [ion binding]; other site 319224005733 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 319224005734 nucleotide binding region [chemical binding]; other site 319224005735 ATP-binding site [chemical binding]; other site 319224005736 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 319224005737 TAT (twin-arginine translocation) pathway signal sequence; Region: TAT_signal; pfam10518 319224005738 DTW domain; Region: DTW; cl01221 319224005739 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224005740 multidrug resistance protein D; Provisional; Region: emrD; PRK11652 319224005741 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 319224005742 putative substrate translocation pore; other site 319224005743 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 319224005744 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 319224005745 domain interface [polypeptide binding]; other site 319224005746 putative active site [active] 319224005747 catalytic site [active] 319224005748 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 319224005749 domain interface [polypeptide binding]; other site 319224005750 putative active site [active] 319224005751 catalytic site [active] 319224005752 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 319224005753 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224005754 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 319224005755 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 319224005756 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 319224005757 active site 319224005758 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 319224005759 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 319224005760 short chain dehydrogenase; Provisional; Region: PRK07576 319224005761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224005762 NAD(P) binding site [chemical binding]; other site 319224005763 active site 319224005764 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 319224005765 active site 319224005766 dimer interface [polypeptide binding]; other site 319224005767 tetratricopeptide repeat protein; Provisional; Region: PRK11788 319224005768 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 319224005769 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 319224005770 IHF dimer interface [polypeptide binding]; other site 319224005771 IHF - DNA interface [nucleotide binding]; other site 319224005772 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 319224005773 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 319224005774 RNA binding site [nucleotide binding]; other site 319224005775 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 319224005776 RNA binding site [nucleotide binding]; other site 319224005777 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 319224005778 RNA binding site [nucleotide binding]; other site 319224005779 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 319224005780 RNA binding site [nucleotide binding]; other site 319224005781 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 319224005782 RNA binding site [nucleotide binding]; other site 319224005783 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 319224005784 RNA binding site [nucleotide binding]; other site 319224005785 cytidylate kinase; Provisional; Region: cmk; PRK00023 319224005786 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 319224005787 CMP-binding site; other site 319224005788 The sites determining sugar specificity; other site 319224005789 3-phosphoshikimate 1-carboxyvinyltransferase; Region: PLN02338 319224005790 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 319224005791 hinge; other site 319224005792 active site 319224005793 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 319224005794 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 319224005795 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224005796 homodimer interface [polypeptide binding]; other site 319224005797 catalytic residue [active] 319224005798 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 319224005799 Beta-xylosidase [Carbohydrate transport and metabolism]; Region: XynB; COG3507 319224005800 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 319224005801 substrate binding site [chemical binding]; other site 319224005802 active site 319224005803 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 319224005804 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 319224005805 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 319224005806 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; cl01155 319224005807 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; cl01155 319224005808 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 319224005809 active site 319224005810 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific...; Region: RICIN; cl15820 319224005811 Glycosyl hydrolase family 43; Region: GH43_ABN_1; cd08998 319224005812 substrate binding site [chemical binding]; other site 319224005813 active site 319224005814 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 319224005815 MFS/sugar transport protein; Region: MFS_2; pfam13347 319224005816 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 319224005817 active site 319224005818 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 319224005819 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 319224005820 dimerization interface [polypeptide binding]; other site 319224005821 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224005822 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224005823 dimer interface [polypeptide binding]; other site 319224005824 putative CheW interface [polypeptide binding]; other site 319224005825 Glycosyl hydrolase family 43; Region: GH43_1; cd08980 319224005826 active site 319224005827 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 319224005828 TM-ABC transporter signature motif; other site 319224005829 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 319224005830 TM-ABC transporter signature motif; other site 319224005831 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 319224005832 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 319224005833 Walker A/P-loop; other site 319224005834 ATP binding site [chemical binding]; other site 319224005835 Q-loop/lid; other site 319224005836 ABC transporter signature motif; other site 319224005837 Walker B; other site 319224005838 D-loop; other site 319224005839 H-loop/switch region; other site 319224005840 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 319224005841 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 319224005842 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 319224005843 putative ligand binding site [chemical binding]; other site 319224005844 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 319224005845 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 319224005846 active site 319224005847 catalytic residues [active] 319224005848 short chain dehydrogenase; Provisional; Region: PRK12939 319224005849 classical (c) SDRs; Region: SDR_c; cd05233 319224005850 NAD(P) binding site [chemical binding]; other site 319224005851 active site 319224005852 Dehydratase family; Region: ILVD_EDD; cl00340 319224005853 Glycosyl hydrolase family 43, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, alpha-L-arabinofuranosidase; Region: GH43_AXH_like; cd08990 319224005854 substrate binding site [chemical binding]; other site 319224005855 active site 319224005856 Transcriptional regulators [Transcription]; Region: FadR; COG2186 319224005857 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224005858 DNA-binding site [nucleotide binding]; DNA binding site 319224005859 FCD domain; Region: FCD; cl11656 319224005860 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 319224005861 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 319224005862 motif II; other site 319224005863 L-arabinose isomerase; Provisional; Region: PRK02929 319224005864 L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose...; Region: L-fuc_L-ara-isomerases; cl00947 319224005865 hexamer (dimer of trimers) interface [polypeptide binding]; other site 319224005866 trimer interface [polypeptide binding]; other site 319224005867 substrate binding site [chemical binding]; other site 319224005868 Mn binding site [ion binding]; other site 319224005869 L-ribulose-5-phosphate 4-epimerase; Reviewed; Region: araD; PRK08193 319224005870 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 319224005871 intersubunit interface [polypeptide binding]; other site 319224005872 active site 319224005873 Zn2+ binding site [ion binding]; other site 319224005874 ribulokinase; Provisional; Region: PRK04123 319224005875 Ribulokinases; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_RBK; cd07781 319224005876 putative N- and C-terminal domain interface [polypeptide binding]; other site 319224005877 putative active site [active] 319224005878 putative MgATP binding site [chemical binding]; other site 319224005879 catalytic site [active] 319224005880 metal binding site [ion binding]; metal-binding site 319224005881 carbohydrate binding site [chemical binding]; other site 319224005882 homodimer interface [polypeptide binding]; other site 319224005883 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 319224005884 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224005885 catalytic residue [active] 319224005886 DNA gyrase subunit A; Validated; Region: PRK05560 319224005887 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 319224005888 CAP-like domain; other site 319224005889 active site 319224005890 primary dimer interface [polypeptide binding]; other site 319224005891 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 319224005892 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 319224005893 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 319224005894 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 319224005895 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 319224005896 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 319224005897 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 319224005898 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 319224005899 S-adenosylmethionine binding site [chemical binding]; other site 319224005900 phosphoglycolate phosphatase; Provisional; Region: PRK13222 319224005901 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 319224005902 active site 319224005903 motif I; other site 319224005904 motif II; other site 319224005905 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 319224005906 ATP cone domain; Region: ATP-cone; pfam03477 319224005907 Class I ribonucleotide reductase; Region: RNR_I; cd01679 319224005908 active site 319224005909 dimer interface [polypeptide binding]; other site 319224005910 catalytic residues [active] 319224005911 effector binding site; other site 319224005912 R2 peptide binding site; other site 319224005913 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 319224005914 dimer interface [polypeptide binding]; other site 319224005915 putative radical transfer pathway; other site 319224005916 diiron center [ion binding]; other site 319224005917 tyrosyl radical; other site 319224005918 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 319224005919 catalytic loop [active] 319224005920 iron binding site [ion binding]; other site 319224005921 YCII-related domain; Region: YCII; cl00999 319224005922 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 319224005923 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 319224005924 active site 319224005925 FMN binding site [chemical binding]; other site 319224005926 2,4-decadienoyl-CoA binding site; other site 319224005927 catalytic residue [active] 319224005928 4Fe-4S cluster binding site [ion binding]; other site 319224005929 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224005930 protease 4; Provisional; Region: PRK10949 319224005931 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 319224005932 tandem repeat interface [polypeptide binding]; other site 319224005933 oligomer interface [polypeptide binding]; other site 319224005934 active site residues [active] 319224005935 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 319224005936 tandem repeat interface [polypeptide binding]; other site 319224005937 oligomer interface [polypeptide binding]; other site 319224005938 active site residues [active] 319224005939 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 319224005940 active site 319224005941 homodimer interface [polypeptide binding]; other site 319224005942 Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: MdoH; COG2943 319224005943 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 319224005944 Ligand binding site; other site 319224005945 DXD motif; other site 319224005946 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 319224005947 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 319224005948 sensor protein QseC; Provisional; Region: PRK10337 319224005949 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 319224005950 dimer interface [polypeptide binding]; other site 319224005951 phosphorylation site [posttranslational modification] 319224005952 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 319224005953 ATP binding site [chemical binding]; other site 319224005954 Mg2+ binding site [ion binding]; other site 319224005955 G-X-G motif; other site 319224005956 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 319224005957 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 319224005958 active site 319224005959 phosphorylation site [posttranslational modification] 319224005960 intermolecular recognition site; other site 319224005961 dimerization interface [polypeptide binding]; other site 319224005962 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 319224005963 DNA binding site [nucleotide binding] 319224005964 ApbE family; Region: ApbE; cl00643 319224005965 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 319224005966 Domain of unknown function (DUF4266); Region: DUF4266; pfam14086 319224005967 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 319224005968 catalytic residues [active] 319224005969 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 319224005970 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 319224005971 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 319224005972 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 319224005973 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 319224005974 putative substrate-binding site; other site 319224005975 nickel binding site [ion binding]; other site 319224005976 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 319224005977 Acylphosphatase; Region: Acylphosphatase; cl00551 319224005978 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 319224005979 HypF finger; Region: zf-HYPF; pfam07503 319224005980 HypF finger; Region: zf-HYPF; pfam07503 319224005981 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 319224005982 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 319224005983 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 319224005984 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224005985 universal stress protein UspE; Provisional; Region: PRK11175 319224005986 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 319224005987 Ligand Binding Site [chemical binding]; other site 319224005988 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 319224005989 Ligand Binding Site [chemical binding]; other site 319224005990 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224005991 metal binding site [ion binding]; metal-binding site 319224005992 active site 319224005993 I-site; other site 319224005994 putative metal dependent hydrolase; Provisional; Region: PRK11598 319224005995 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 319224005996 Sulfatase; Region: Sulfatase; cl10460 319224005997 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 319224005998 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 319224005999 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 319224006000 Helix-turn-helix domains; Region: HTH; cl00088 319224006001 Cation efflux family; Region: Cation_efflux; cl00316 319224006002 Cation efflux family; Region: Cation_efflux; cl00316 319224006003 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 319224006004 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 319224006005 dimer interface [polypeptide binding]; other site 319224006006 active site 319224006007 metal binding site [ion binding]; metal-binding site 319224006008 glutathione binding site [chemical binding]; other site 319224006009 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 319224006010 TMAO/DMSO reductase; Reviewed; Region: PRK05363 319224006011 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 319224006012 Moco binding site; other site 319224006013 metal coordination site [ion binding]; other site 319224006014 Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Region: Cenp-F_leu_zip; pfam10473 319224006015 DNA recombination protein RmuC; Provisional; Region: PRK10361 319224006016 RmuC family; Region: RmuC; pfam02646 319224006017 lytic murein transglycosylase; Provisional; Region: PRK11619 319224006018 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 319224006019 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224006020 catalytic residue [active] 319224006021 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 319224006022 MoxR-like ATPases [General function prediction only]; Region: COG0714 319224006023 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 319224006024 Walker A motif; other site 319224006025 ATP binding site [chemical binding]; other site 319224006026 Walker B motif; other site 319224006027 arginine finger; other site 319224006028 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 319224006029 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 319224006030 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 319224006031 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 319224006032 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 319224006033 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 319224006034 exodeoxyribonuclease V, beta subunit; Region: recB; TIGR00609 319224006035 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224006036 Family description; Region: UvrD_C_2; cl15862 319224006037 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 319224006038 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224006039 Family description; Region: UvrD_C_2; cl15862 319224006040 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 319224006041 active site 319224006042 catalytic site [active] 319224006043 substrate binding site [chemical binding]; other site 319224006044 Chemotaxis phosphatase CheX; Region: CheX; cl15816 319224006045 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 319224006046 Cache domain; Region: Cache_2; cl07034 319224006047 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 319224006048 dimerization interface [polypeptide binding]; other site 319224006049 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224006050 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224006051 dimer interface [polypeptide binding]; other site 319224006052 putative CheW interface [polypeptide binding]; other site 319224006053 Uncharacterized conserved protein [Function unknown]; Region: COG3603 319224006054 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 319224006055 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 319224006056 dimerization domain swap beta strand [polypeptide binding]; other site 319224006057 regulatory protein interface [polypeptide binding]; other site 319224006058 active site 319224006059 regulatory phosphorylation site [posttranslational modification]; other site 319224006060 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 319224006061 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 319224006062 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 319224006063 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 319224006064 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 319224006065 HPr interaction site; other site 319224006066 glycerol kinase (GK) interaction site [polypeptide binding]; other site 319224006067 active site 319224006068 phosphorylation site [posttranslational modification] 319224006069 Vibrio chemotaxis protein N terminus; Region: MCP_N; pfam05581 319224006070 Cache domain; Region: Cache_1; pfam02743 319224006071 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 319224006072 dimerization interface [polypeptide binding]; other site 319224006073 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224006074 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224006075 dimer interface [polypeptide binding]; other site 319224006076 putative CheW interface [polypeptide binding]; other site 319224006077 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 319224006078 ArsC family; Region: ArsC; pfam03960 319224006079 putative catalytic residues [active] 319224006080 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 319224006081 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 319224006082 metal binding site [ion binding]; metal-binding site 319224006083 dimer interface [polypeptide binding]; other site 319224006084 D-alanyl-D-alanine carboxypeptidase; Region: VanY; cl00813 319224006085 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 319224006086 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 319224006087 active site clefts [active] 319224006088 zinc binding site [ion binding]; other site 319224006089 dimer interface [polypeptide binding]; other site 319224006090 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 319224006091 Ligand binding site; other site 319224006092 oligomer interface; other site 319224006093 Protein of unknown function (DUF2897); Region: DUF2897; pfam11446 319224006094 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 319224006095 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 319224006096 active site residue [active] 319224006097 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 319224006098 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224006099 Sulfate transporter family; Region: Sulfate_transp; cl15842 319224006100 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 319224006101 LysE type translocator; Region: LysE; cl00565 319224006102 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 319224006103 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224006104 DNA-binding site [nucleotide binding]; DNA binding site 319224006105 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 319224006106 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006107 homodimer interface [polypeptide binding]; other site 319224006108 catalytic residue [active] 319224006109 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 319224006110 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 319224006111 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 319224006112 putative substrate translocation pore; other site 319224006113 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK08979 319224006114 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 319224006115 PYR/PP interface [polypeptide binding]; other site 319224006116 dimer interface [polypeptide binding]; other site 319224006117 TPP binding site [chemical binding]; other site 319224006118 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 319224006119 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 319224006120 TPP-binding site [chemical binding]; other site 319224006121 dimer interface [polypeptide binding]; other site 319224006122 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 319224006123 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 319224006124 putative valine binding site [chemical binding]; other site 319224006125 dimer interface [polypeptide binding]; other site 319224006126 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 319224006127 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 319224006128 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 319224006129 putative dimer interface [polypeptide binding]; other site 319224006130 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 319224006131 active site 319224006132 multimer interface [polypeptide binding]; other site 319224006133 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 319224006134 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 319224006135 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224006136 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 319224006137 catalytic loop [active] 319224006138 iron binding site [ion binding]; other site 319224006139 chaperone protein HscA; Provisional; Region: hscA; PRK05183 319224006140 co-chaperone HscB; Provisional; Region: hscB; PRK05014 319224006141 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 319224006142 HSP70 interaction site [polypeptide binding]; other site 319224006143 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 319224006144 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 319224006145 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 319224006146 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 319224006147 trimerization site [polypeptide binding]; other site 319224006148 active site 319224006149 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 319224006150 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 319224006151 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224006152 catalytic residue [active] 319224006153 Helix-turn-helix domains; Region: HTH; cl00088 319224006154 Rrf2 family protein; Region: rrf2_super; TIGR00738 319224006155 serine O-acetyltransferase; Region: cysE; TIGR01172 319224006156 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 319224006157 trimer interface [polypeptide binding]; other site 319224006158 active site 319224006159 substrate binding site [chemical binding]; other site 319224006160 CoA binding site [chemical binding]; other site 319224006161 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 319224006162 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 319224006163 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 319224006164 active site 319224006165 dimerization interface [polypeptide binding]; other site 319224006166 outer membrane-specific lipoprotein transporter subunit LolE; Provisional; Region: PRK11146 319224006167 FtsX-like permease family; Region: FtsX; cl15850 319224006168 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 319224006169 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 319224006170 Walker A/P-loop; other site 319224006171 ATP binding site [chemical binding]; other site 319224006172 Q-loop/lid; other site 319224006173 ABC transporter signature motif; other site 319224006174 Walker B; other site 319224006175 D-loop; other site 319224006176 H-loop/switch region; other site 319224006177 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 319224006178 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 319224006179 transcription-repair coupling factor; Provisional; Region: PRK10689 319224006180 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 319224006181 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 319224006182 ATP binding site [chemical binding]; other site 319224006183 putative Mg++ binding site [ion binding]; other site 319224006184 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 319224006185 nucleotide binding region [chemical binding]; other site 319224006186 ATP-binding site [chemical binding]; other site 319224006187 TRCF domain; Region: TRCF; cl04088 319224006188 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 319224006189 Acylphosphatase; Region: Acylphosphatase; cl00551 319224006190 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224006191 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224006192 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 319224006193 active site 319224006194 DNA binding site [nucleotide binding] 319224006195 Int/Topo IB signature motif; other site 319224006196 Salmonella virulence plasmid 65kDa B protein; Region: SpvB; pfam03534 319224006197 Family description; Region: VCBS; pfam13517 319224006198 Family description; Region: VCBS; pfam13517 319224006199 Insecticide toxin TcdB middle/N-terminal region; Region: TcdB_toxin_midN; pfam12256 319224006200 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 319224006201 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 319224006202 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 319224006203 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 319224006204 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 319224006205 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 319224006206 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 319224006207 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 319224006208 Predicted esterase [General function prediction only]; Region: COG0627 319224006209 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 319224006210 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 319224006211 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 319224006212 substrate binding site [chemical binding]; other site 319224006213 catalytic Zn binding site [ion binding]; other site 319224006214 NAD binding site [chemical binding]; other site 319224006215 structural Zn binding site [ion binding]; other site 319224006216 dimer interface [polypeptide binding]; other site 319224006217 LysR family transcriptional regulator; Provisional; Region: PRK14997 319224006218 Helix-turn-helix domains; Region: HTH; cl00088 319224006219 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 319224006220 putative effector binding pocket; other site 319224006221 putative dimerization interface [polypeptide binding]; other site 319224006222 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224006223 FAD dependent oxidoreductase; Region: DAO; pfam01266 319224006224 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; cl16911 319224006225 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 319224006226 ATP phosphoribosyltransferase; Region: HisG; cl15266 319224006227 HisG, C-terminal domain; Region: HisG_C; cl06867 319224006228 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 319224006229 histidinol dehydrogenase; Region: hisD; TIGR00069 319224006230 NAD binding site [chemical binding]; other site 319224006231 dimerization interface [polypeptide binding]; other site 319224006232 product binding site; other site 319224006233 substrate binding site [chemical binding]; other site 319224006234 zinc binding site [ion binding]; other site 319224006235 catalytic residues [active] 319224006236 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 319224006237 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 319224006238 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006239 homodimer interface [polypeptide binding]; other site 319224006240 catalytic residue [active] 319224006241 imidazole glycerol-phosphate dehydratase/histidinol phosphatase; Provisional; Region: PRK05446 319224006242 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 319224006243 active site 319224006244 motif I; other site 319224006245 motif II; other site 319224006246 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 319224006247 putative active site pocket [active] 319224006248 4-fold oligomerization interface [polypeptide binding]; other site 319224006249 metal binding residues [ion binding]; metal-binding site 319224006250 3-fold/trimer interface [polypeptide binding]; other site 319224006251 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13170 319224006252 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 319224006253 putative active site [active] 319224006254 oxyanion strand; other site 319224006255 catalytic triad [active] 319224006256 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 319224006257 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 319224006258 catalytic residues [active] 319224006259 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 319224006260 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 319224006261 substrate binding site [chemical binding]; other site 319224006262 glutamase interaction surface [polypeptide binding]; other site 319224006263 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 319224006264 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 319224006265 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 319224006266 metal binding site [ion binding]; metal-binding site 319224006267 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 319224006268 aromatic amino acid transport protein; Region: araaP; TIGR00837 319224006269 Dicarboxylate transport; Region: DctA-YdbH; cl14674 319224006270 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 319224006271 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 319224006272 alpha-galactosidase; Provisional; Region: PRK15076 319224006273 Protein of unknown function (DUF1379); Region: DUF1379; pfam07126 319224006274 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 319224006275 quinone interaction residues [chemical binding]; other site 319224006276 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 319224006277 active site 319224006278 catalytic residues [active] 319224006279 FMN binding site [chemical binding]; other site 319224006280 substrate binding site [chemical binding]; other site 319224006281 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 319224006282 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 319224006283 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 319224006284 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 319224006285 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 319224006286 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 319224006287 aminopeptidase N; Provisional; Region: pepN; PRK14015 319224006288 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 319224006289 active site 319224006290 Zn binding site [ion binding]; other site 319224006291 carboxy-terminal protease; Provisional; Region: PRK11186 319224006292 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 319224006293 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 319224006294 protein binding site [polypeptide binding]; other site 319224006295 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 319224006296 Catalytic dyad [active] 319224006297 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 319224006298 ProP expression regulator; Provisional; Region: PRK04950 319224006299 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 319224006300 GAF domain; Region: GAF; cl15785 319224006301 YebG protein; Region: YebG; cl01217 319224006302 Paraquat-inducible protein A; Region: PqiA; pfam04403 319224006303 Paraquat-inducible protein A; Region: PqiA; pfam04403 319224006304 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 319224006305 mce related protein; Region: MCE; pfam02470 319224006306 mce related protein; Region: MCE; pfam02470 319224006307 mce related protein; Region: MCE; pfam02470 319224006308 mce related protein; Region: MCE; pfam02470 319224006309 mce related protein; Region: MCE; pfam02470 319224006310 mce related protein; Region: MCE; pfam02470 319224006311 mce related protein; Region: MCE; pfam02470 319224006312 Nucleoside recognition; Region: Gate; cl00486 319224006313 Nucleoside recognition; Region: Gate; cl00486 319224006314 rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed; Region: yebU; PRK11933 319224006315 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; cl16911 319224006316 pre-rRNA processing and ribosome biogenesis; Region: Nol1_Nop2_Fmu_2; cl01283 319224006317 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 319224006318 active site 319224006319 PilZ domain; Region: PilZ; cl01260 319224006320 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 319224006321 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224006322 thymidylate kinase; Validated; Region: tmk; PRK00698 319224006323 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 319224006324 TMP-binding site; other site 319224006325 ATP-binding site [chemical binding]; other site 319224006326 YceG-like family; Region: YceG; pfam02618 319224006327 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 319224006328 dimerization interface [polypeptide binding]; other site 319224006329 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 319224006330 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006331 catalytic residue [active] 319224006332 2'-deoxycytidine 5'-triphosphate deaminase (DCD); Region: DCD; pfam06559 319224006333 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 319224006334 trimer interface [polypeptide binding]; other site 319224006335 active site 319224006336 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 319224006337 Sugar specificity; other site 319224006338 Pyrimidine base specificity; other site 319224006339 ATP-binding site [chemical binding]; other site 319224006340 antiporter inner membrane protein; Provisional; Region: PRK11670 319224006341 Domain of unknown function DUF59; Region: DUF59; cl00941 319224006342 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 319224006343 Walker A motif; other site 319224006344 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 319224006345 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 319224006346 active site 319224006347 HIGH motif; other site 319224006348 KMSKS motif; other site 319224006349 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 319224006350 tRNA binding surface [nucleotide binding]; other site 319224006351 anticodon binding site; other site 319224006352 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 319224006353 dimer interface [polypeptide binding]; other site 319224006354 putative tRNA-binding site [nucleotide binding]; other site 319224006355 Membrane transport protein; Region: Mem_trans; cl09117 319224006356 Uncharacterized conserved protein [Function unknown]; Region: COG0327 319224006357 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 319224006358 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 319224006359 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224006360 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 319224006361 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 319224006362 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224006363 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 319224006364 rRNA binding site [nucleotide binding]; other site 319224006365 predicted 30S ribosome binding site; other site 319224006366 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 319224006367 Clp amino terminal domain; Region: Clp_N; pfam02861 319224006368 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 319224006369 Walker A motif; other site 319224006370 ATP binding site [chemical binding]; other site 319224006371 Walker B motif; other site 319224006372 arginine finger; other site 319224006373 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 319224006374 Walker A motif; other site 319224006375 ATP binding site [chemical binding]; other site 319224006376 Walker B motif; other site 319224006377 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 319224006378 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 319224006379 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 319224006380 DNA-binding site [nucleotide binding]; DNA binding site 319224006381 RNA-binding motif; other site 319224006382 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 319224006383 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 319224006384 pseudouridine synthase; Region: TIGR00093 319224006385 probable active site [active] 319224006386 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 319224006387 nudix motif; other site 319224006388 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 319224006389 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 319224006390 Protein of unknown function (DUF489); Region: DUF489; cl01097 319224006391 adenylosuccinate lyase; Provisional; Region: PRK09285 319224006392 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 319224006393 tetramer interface [polypeptide binding]; other site 319224006394 active site 319224006395 Cupin superfamily protein; Region: Cupin_4; pfam08007 319224006396 JmjC domain, hydroxylase; Region: JmjC; cl15814 319224006397 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 319224006398 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 319224006399 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 319224006400 NAD binding site [chemical binding]; other site 319224006401 Phe binding site; other site 319224006402 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 319224006403 Helix-turn-helix domains; Region: HTH; cl00088 319224006404 Protein of unknown function (DUF1285); Region: DUF1285; cl01571 319224006405 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 319224006406 FAD binding domain; Region: FAD_binding_4; pfam01565 319224006407 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 319224006408 phosphoenolpyruvate synthase; Validated; Region: PRK06464 319224006409 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 319224006410 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 319224006411 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 319224006412 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 319224006413 NeuB family; Region: NeuB; cl00496 319224006414 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 319224006415 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 319224006416 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 319224006417 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 319224006418 active site 319224006419 phosphorylation site [posttranslational modification] 319224006420 intermolecular recognition site; other site 319224006421 dimerization interface [polypeptide binding]; other site 319224006422 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 319224006423 DNA binding residues [nucleotide binding] 319224006424 dimerization interface [polypeptide binding]; other site 319224006425 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 319224006426 Helix-turn-helix domains; Region: HTH; cl00088 319224006427 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 319224006428 substrate binding site [chemical binding]; other site 319224006429 dimerization interface [polypeptide binding]; other site 319224006430 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 319224006431 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 319224006432 active site 319224006433 interdomain interaction site; other site 319224006434 putative metal-binding site [ion binding]; other site 319224006435 nucleotide binding site [chemical binding]; other site 319224006436 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 319224006437 domain I; other site 319224006438 DNA binding groove [nucleotide binding] 319224006439 phosphate binding site [ion binding]; other site 319224006440 domain II; other site 319224006441 domain III; other site 319224006442 nucleotide binding site [chemical binding]; other site 319224006443 catalytic site [active] 319224006444 domain IV; other site 319224006445 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 319224006446 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 319224006447 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 319224006448 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 319224006449 Succinylarginine dihydrolase; Region: AstB; cl01511 319224006450 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 319224006451 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 319224006452 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 319224006453 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 319224006454 DNA-binding transcriptional regulator PhoP; Provisional; Region: PRK10816 319224006455 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 319224006456 active site 319224006457 phosphorylation site [posttranslational modification] 319224006458 intermolecular recognition site; other site 319224006459 dimerization interface [polypeptide binding]; other site 319224006460 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 319224006461 DNA binding site [nucleotide binding] 319224006462 sensor protein PhoQ; Provisional; Region: PRK10815 319224006463 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 319224006464 ATP binding site [chemical binding]; other site 319224006465 Mg2+ binding site [ion binding]; other site 319224006466 G-X-G motif; other site 319224006467 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 319224006468 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 319224006469 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 319224006470 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 319224006471 Zn2+ binding site [ion binding]; other site 319224006472 Mg2+ binding site [ion binding]; other site 319224006473 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 319224006474 magnesium Mg(2+) and cobalt Co(2+) transport protein (corA); Region: corA; TIGR00383 319224006475 AAA domain; Region: AAA_33; pfam13671 319224006476 NAD-dependent deacetylase; Provisional; Region: PRK00481 319224006477 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 319224006478 NAD+ binding site [chemical binding]; other site 319224006479 substrate binding site [chemical binding]; other site 319224006480 Zn binding site [ion binding]; other site 319224006481 ferric uptake regulator; Provisional; Region: fur; PRK09462 319224006482 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 319224006483 metal binding site 2 [ion binding]; metal-binding site 319224006484 putative DNA binding helix; other site 319224006485 metal binding site 1 [ion binding]; metal-binding site 319224006486 dimer interface [polypeptide binding]; other site 319224006487 structural Zn2+ binding site [ion binding]; other site 319224006488 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 319224006489 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224006490 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 319224006491 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 319224006492 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224006493 CoA-ligase; Region: Ligase_CoA; cl02894 319224006494 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 319224006495 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224006496 CoA-ligase; Region: Ligase_CoA; cl02894 319224006497 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 319224006498 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 319224006499 E3 interaction surface; other site 319224006500 lipoyl attachment site [posttranslational modification]; other site 319224006501 e3 binding domain; Region: E3_binding; pfam02817 319224006502 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 319224006503 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 319224006504 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 319224006505 TPP-binding site [chemical binding]; other site 319224006506 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 319224006507 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 319224006508 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 319224006509 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK08958 319224006510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224006511 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 319224006512 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 319224006513 SdhC subunit interface [polypeptide binding]; other site 319224006514 proximal heme binding site [chemical binding]; other site 319224006515 cardiolipin binding site; other site 319224006516 Iron-sulfur protein interface; other site 319224006517 proximal quinone binding site [chemical binding]; other site 319224006518 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 319224006519 Iron-sulfur protein interface; other site 319224006520 proximal quinone binding site [chemical binding]; other site 319224006521 SdhD (CybS) interface [polypeptide binding]; other site 319224006522 proximal heme binding site [chemical binding]; other site 319224006523 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 319224006524 dimer interface [polypeptide binding]; other site 319224006525 Citrate synthase; Region: Citrate_synt; pfam00285 319224006526 active site 319224006527 citrylCoA binding site [chemical binding]; other site 319224006528 NADH binding [chemical binding]; other site 319224006529 cationic pore residues; other site 319224006530 oxalacetate/citrate binding site [chemical binding]; other site 319224006531 coenzyme A binding site [chemical binding]; other site 319224006532 catalytic triad [active] 319224006533 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224006534 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 319224006535 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 319224006536 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 319224006537 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224006538 ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as...; Region: ASCH_yqfb_like; cd06552 319224006539 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 319224006540 MatE; Region: MatE; cl10513 319224006541 MatE; Region: MatE; cl10513 319224006542 Ion transport protein; Region: Ion_trans; pfam00520 319224006543 Ion channel; Region: Ion_trans_2; cl11596 319224006544 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 319224006545 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_4; cd07268 319224006546 putative metal binding site [ion binding]; other site 319224006547 Peptidase family M23; Region: Peptidase_M23; pfam01551 319224006548 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 319224006549 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 319224006550 Nucleoid-associated protein [General function prediction only]; Region: COG3081 319224006551 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 319224006552 Protein of unknown function (DUF1414); Region: DUF1414; cl01175 319224006553 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 319224006554 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 319224006555 Sulfatase; Region: Sulfatase; cl10460 319224006556 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 319224006557 active site 319224006558 FMN binding site [chemical binding]; other site 319224006559 substrate binding site [chemical binding]; other site 319224006560 homotetramer interface [polypeptide binding]; other site 319224006561 catalytic residue [active] 319224006562 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224006563 Helix-turn-helix domains; Region: HTH; cl00088 319224006564 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 319224006565 dimerization interface [polypeptide binding]; other site 319224006566 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 319224006567 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 319224006568 homodimer interface [polypeptide binding]; other site 319224006569 NAD binding pocket [chemical binding]; other site 319224006570 ATP binding pocket [chemical binding]; other site 319224006571 Mg binding site [ion binding]; other site 319224006572 active-site loop [active] 319224006573 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 319224006574 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 319224006575 substrate binding site [chemical binding]; other site 319224006576 ATP binding site [chemical binding]; other site 319224006577 ferrochelatase; Reviewed; Region: hemH; PRK00035 319224006578 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 319224006579 C-terminal domain interface [polypeptide binding]; other site 319224006580 active site 319224006581 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 319224006582 active site 319224006583 N-terminal domain interface [polypeptide binding]; other site 319224006584 adenylate kinase; Reviewed; Region: adk; PRK00279 319224006585 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 319224006586 AMP-binding site [chemical binding]; other site 319224006587 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 319224006588 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 319224006589 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 319224006590 heat shock protein 90; Provisional; Region: PRK05218 319224006591 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 319224006592 ATP binding site [chemical binding]; other site 319224006593 Mg2+ binding site [ion binding]; other site 319224006594 G-X-G motif; other site 319224006595 recombination protein RecR; Reviewed; Region: recR; PRK00076 319224006596 RecR protein; Region: RecR; pfam02132 319224006597 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 319224006598 putative active site [active] 319224006599 putative metal-binding site [ion binding]; other site 319224006600 tetramer interface [polypeptide binding]; other site 319224006601 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 319224006602 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14949 319224006603 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 319224006604 Walker A motif; other site 319224006605 ATP binding site [chemical binding]; other site 319224006606 Walker B motif; other site 319224006607 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224006608 arginine finger; other site 319224006609 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 319224006610 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 319224006611 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224006612 active site 319224006613 Protein of unknown function (DUF454); Region: DUF454; cl01063 319224006614 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 319224006615 Protein of unknown function (DUF692); Region: DUF692; cl01263 319224006616 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 319224006617 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 319224006618 FMN binding site [chemical binding]; other site 319224006619 active site 319224006620 catalytic residues [active] 319224006621 substrate binding site [chemical binding]; other site 319224006622 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 319224006623 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 319224006624 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 319224006625 active site 319224006626 metal binding site [ion binding]; metal-binding site 319224006627 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 319224006628 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 319224006629 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 319224006630 Protein of unknown function (DUF3389); Region: DUF3389; pfam11869 319224006631 leukotriene A-4 hydrolase/aminopeptidase; Region: leuko_A4_hydro; TIGR02411 319224006632 Peptidase M1 family contains leukotriene A4 hydrolase; Region: M1_LTA4H; cd09599 319224006633 active site 319224006634 Zn binding site [ion binding]; other site 319224006635 Leukotriene A4 hydrolase, C-terminal; Region: Leuk-A4-hydro_C; pfam09127 319224006636 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224006637 Transglycosylase SLT domain; Region: SLT_2; pfam13406 319224006638 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 319224006639 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224006640 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 319224006641 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 319224006642 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 319224006643 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 319224006644 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 319224006645 active site 319224006646 phosphorylation site [posttranslational modification] 319224006647 intermolecular recognition site; other site 319224006648 dimerization interface [polypeptide binding]; other site 319224006649 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 319224006650 S-adenosylmethionine binding site [chemical binding]; other site 319224006651 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 319224006652 RNA polymerase sigma factor; Provisional; Region: PRK12526 319224006653 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224006654 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 319224006655 DNA binding residues [nucleotide binding] 319224006656 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 319224006657 Cupin domain; Region: Cupin_2; cl09118 319224006658 putative nicotinate phosphoribosyltransferase; Provisional; Region: PRK09198 319224006659 pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general; Region: PBEF_like; cd01569 319224006660 active site 319224006661 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 319224006662 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224006663 active site 319224006664 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; cd02883 319224006665 nudix motif; other site 319224006666 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 319224006667 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 319224006668 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 319224006669 hypothetical protein; Provisional; Region: PRK11770 319224006670 Domain of unknown function (DUF307); Region: DUF307; pfam03733 319224006671 Domain of unknown function (DUF307); Region: DUF307; pfam03733 319224006672 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 319224006673 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 319224006674 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 319224006675 DNA binding residues [nucleotide binding] 319224006676 dimerization interface [polypeptide binding]; other site 319224006677 Peptidase family M48; Region: Peptidase_M48; cl12018 319224006678 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E; Region: GAT1_Peptidase_E; cd03146 319224006679 active site pocket [active] 319224006680 oxyanion hole [active] 319224006681 catalytic triad [active] 319224006682 active site nucleophile [active] 319224006683 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 319224006684 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 319224006685 Protein of unknown function (DUF3187); Region: DUF3187; pfam11383 319224006686 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224006687 Uncharacterized conserved protein (DUF2149); Region: DUF2149; cl01960 319224006688 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 319224006689 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 319224006690 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 319224006691 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 319224006692 N-terminal plug; other site 319224006693 ligand-binding site [chemical binding]; other site 319224006694 AAA domain; Region: AAA_26; pfam13500 319224006695 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224006696 Methyltransferase domain; Region: Methyltransf_31; pfam13847 319224006697 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 319224006698 S-adenosylmethionine binding site [chemical binding]; other site 319224006699 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 319224006700 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 319224006701 substrate-cofactor binding pocket; other site 319224006702 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006703 catalytic residue [active] 319224006704 biotin synthase; Provisional; Region: PRK15108 319224006705 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 319224006706 FeS/SAM binding site; other site 319224006707 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 319224006708 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated; Region: PRK07986 319224006709 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 319224006710 inhibitor-cofactor binding pocket; inhibition site 319224006711 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006712 catalytic residue [active] 319224006713 Cache domain; Region: Cache_2; cl07034 319224006714 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 319224006715 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 319224006716 dimerization interface [polypeptide binding]; other site 319224006717 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224006718 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224006719 dimer interface [polypeptide binding]; other site 319224006720 putative CheW interface [polypeptide binding]; other site 319224006721 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 319224006722 Na binding site [ion binding]; other site 319224006723 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 319224006724 PAS fold; Region: PAS_7; pfam12860 319224006725 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 319224006726 dimer interface [polypeptide binding]; other site 319224006727 phosphorylation site [posttranslational modification] 319224006728 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 319224006729 ATP binding site [chemical binding]; other site 319224006730 Mg2+ binding site [ion binding]; other site 319224006731 G-X-G motif; other site 319224006732 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 319224006733 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 319224006734 active site 319224006735 phosphorylation site [posttranslational modification] 319224006736 intermolecular recognition site; other site 319224006737 dimerization interface [polypeptide binding]; other site 319224006738 acetyl-CoA synthetase; Provisional; Region: PRK00174 319224006739 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 319224006740 AMP-binding enzyme; Region: AMP-binding; cl15778 319224006741 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224006742 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 319224006743 ATP binding site [chemical binding]; other site 319224006744 putative Mg++ binding site [ion binding]; other site 319224006745 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 319224006746 nucleotide binding region [chemical binding]; other site 319224006747 ATP-binding site [chemical binding]; other site 319224006748 Double zinc ribbon; Region: DZR; pfam12773 319224006749 Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide...; Region: GRX_family; cd02066 319224006750 GSH binding site [chemical binding]; other site 319224006751 catalytic residues [active] 319224006752 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 319224006753 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 319224006754 active site 319224006755 motif I; other site 319224006756 motif II; other site 319224006757 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224006758 Transcriptional regulators [Transcription]; Region: GntR; COG1802 319224006759 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224006760 DNA-binding site [nucleotide binding]; DNA binding site 319224006761 FCD domain; Region: FCD; cl11656 319224006762 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 319224006763 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 319224006764 dimer interface [polypeptide binding]; other site 319224006765 active site 319224006766 CoA binding pocket [chemical binding]; other site 319224006767 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 319224006768 active site 319224006769 catalytic site [active] 319224006770 substrate binding site [chemical binding]; other site 319224006771 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 319224006772 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 319224006773 ligand binding site [chemical binding]; other site 319224006774 flexible hinge region; other site 319224006775 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 319224006776 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 319224006777 metal binding triad; other site 319224006778 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 319224006779 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 319224006780 Na binding site [ion binding]; other site 319224006781 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 319224006782 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 319224006783 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 319224006784 catalytic residues [active] 319224006785 hinge region; other site 319224006786 alpha helical domain; other site 319224006787 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 319224006788 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 319224006789 putative NAD(P) binding site [chemical binding]; other site 319224006790 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 319224006791 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 319224006792 Zn2+ binding site [ion binding]; other site 319224006793 Mg2+ binding site [ion binding]; other site 319224006794 Protein of unknown function (DUF2919); Region: DUF2919; pfam11143 319224006795 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 319224006796 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 319224006797 nucleotide binding pocket [chemical binding]; other site 319224006798 K-X-D-G motif; other site 319224006799 catalytic site [active] 319224006800 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 319224006801 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 319224006802 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 319224006803 Dimer interface [polypeptide binding]; other site 319224006804 BRCT sequence motif; other site 319224006805 cell division protein ZipA; Provisional; Region: PRK03427 319224006806 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; cl12038 319224006807 FtsZ protein binding site [polypeptide binding]; other site 319224006808 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 319224006809 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 319224006810 Walker A/P-loop; other site 319224006811 ATP binding site [chemical binding]; other site 319224006812 Q-loop/lid; other site 319224006813 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 319224006814 Q-loop/lid; other site 319224006815 ABC transporter signature motif; other site 319224006816 Walker B; other site 319224006817 D-loop; other site 319224006818 H-loop/switch region; other site 319224006819 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 319224006820 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 319224006821 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 319224006822 active site 319224006823 RDD family; Region: RDD; cl00746 319224006824 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 319224006825 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 319224006826 dimer interface [polypeptide binding]; other site 319224006827 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006828 catalytic residue [active] 319224006829 C-20 methyltransferase BchU; Region: C20_methyl_CrtF; TIGR02716 319224006830 O-methyltransferase; Region: Methyltransf_2; pfam00891 319224006831 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 319224006832 gating phenylalanine in ion channel; other site 319224006833 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; cl01155 319224006834 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; cl01155 319224006835 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224006836 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 319224006837 Helix-turn-helix domains; Region: HTH; cl00088 319224006838 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 319224006839 putative dimerization interface [polypeptide binding]; other site 319224006840 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 319224006841 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 319224006842 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 319224006843 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 319224006844 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 319224006845 Pyruvate formate lyase 1; Region: PFL1; cd01678 319224006846 coenzyme A binding site [chemical binding]; other site 319224006847 active site 319224006848 catalytic residues [active] 319224006849 glycine loop; other site 319224006850 pyruvate formate lyase-activating enzyme 1; Provisional; Region: pflA; PRK11145 319224006851 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 319224006852 FeS/SAM binding site; other site 319224006853 Protein of unknown function, DUF412; Region: DUF412; cl01183 319224006854 acetate kinase; Region: ackA; TIGR00016 319224006855 Acetokinase family; Region: Acetate_kinase; cl01029 319224006856 phosphate acetyltransferase; Reviewed; Region: PRK05632 319224006857 DRTGG domain; Region: DRTGG; cl12147 319224006858 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 319224006859 S-adenosylmethionine-dependent methyltransferase; Region: Methyltrans_SAM; pfam10672 319224006860 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 319224006861 S-adenosylmethionine binding site [chemical binding]; other site 319224006862 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 319224006863 Domain of unknown function DUF20; Region: UPF0118; pfam01594 319224006864 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 319224006865 homooctamer interface [polypeptide binding]; other site 319224006866 active site 319224006867 atypical (a) SDRs, subgroup 8; Region: SDR_a8; cd05242 319224006868 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 319224006869 putative NAD(P) binding site [chemical binding]; other site 319224006870 putative active site [active] 319224006871 Sodium/glutamate symporter; Region: Glt_symporter; pfam03616 319224006872 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 319224006873 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 319224006874 FtsX-like permease family; Region: FtsX; cl15850 319224006875 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 319224006876 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 319224006877 Walker A/P-loop; other site 319224006878 ATP binding site [chemical binding]; other site 319224006879 Q-loop/lid; other site 319224006880 ABC transporter signature motif; other site 319224006881 Walker B; other site 319224006882 D-loop; other site 319224006883 H-loop/switch region; other site 319224006884 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 319224006885 active site 319224006886 catalytic triad [active] 319224006887 oxyanion hole [active] 319224006888 switch loop; other site 319224006889 Protein of unknown function (DUF3083); Region: DUF3083; pfam11281 319224006890 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 319224006891 putative inner membrane peptidase; Provisional; Region: PRK11778 319224006892 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 319224006893 tandem repeat interface [polypeptide binding]; other site 319224006894 oligomer interface [polypeptide binding]; other site 319224006895 active site residues [active] 319224006896 extracellular lipase, Pla-1/cef family; Region: lipase_Pla1_cef; TIGR03502 319224006897 Bacterial virulence factor lipase N-terminal; Region: Lipase_bact_N; pfam12262 319224006898 short chain dehydrogenase; Provisional; Region: PRK08703 319224006899 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224006900 NAD(P) binding site [chemical binding]; other site 319224006901 active site 319224006902 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 319224006903 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 319224006904 RNA binding surface [nucleotide binding]; other site 319224006905 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 319224006906 probable active site [active] 319224006907 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 319224006908 ScpA/B protein; Region: ScpA_ScpB; cl00598 319224006909 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 319224006910 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 319224006911 anthranilate synthase component I; Provisional; Region: PRK13564 319224006912 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 319224006913 chorismate binding enzyme; Region: Chorismate_bind; cl10555 319224006914 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 319224006915 glutamine binding [chemical binding]; other site 319224006916 catalytic triad [active] 319224006917 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 319224006918 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 319224006919 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 319224006920 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 319224006921 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 319224006922 active site 319224006923 ribulose/triose binding site [chemical binding]; other site 319224006924 phosphate binding site [ion binding]; other site 319224006925 substrate (anthranilate) binding pocket [chemical binding]; other site 319224006926 product (indole) binding pocket [chemical binding]; other site 319224006927 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 319224006928 active site 319224006929 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 319224006930 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 319224006931 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224006932 catalytic residue [active] 319224006933 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 319224006934 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 319224006935 substrate binding site [chemical binding]; other site 319224006936 active site 319224006937 catalytic residues [active] 319224006938 heterodimer interface [polypeptide binding]; other site 319224006939 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 319224006940 L-lysine 6-monooxygenase (NADPH-requiring); Region: K_oxygenase; pfam13434 319224006941 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 319224006942 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 319224006943 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 319224006944 IucA / IucC family; Region: IucA_IucC; pfam04183 319224006945 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 319224006946 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 319224006947 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 319224006948 N-terminal plug; other site 319224006949 ligand-binding site [chemical binding]; other site 319224006950 siderophore-iron reductase FhuF; Region: Fe_III_red_FhuF; TIGR03951 319224006951 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 319224006952 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 319224006953 Intracellular septation protein A; Region: IspA; cl01098 319224006954 YCII-related domain; Region: YCII; cl00999 319224006955 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 319224006956 putative catalytic site [active] 319224006957 putative phosphate binding site [ion binding]; other site 319224006958 active site 319224006959 metal binding site A [ion binding]; metal-binding site 319224006960 DNA binding site [nucleotide binding] 319224006961 putative AP binding site [nucleotide binding]; other site 319224006962 putative metal binding site B [ion binding]; other site 319224006963 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 319224006964 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 319224006965 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224006966 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224006967 dimer interface [polypeptide binding]; other site 319224006968 putative CheW interface [polypeptide binding]; other site 319224006969 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 319224006970 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 319224006971 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 319224006972 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 319224006973 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 319224006974 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 319224006975 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 319224006976 catalytic loop [active] 319224006977 iron binding site [ion binding]; other site 319224006978 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 319224006979 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 319224006980 Ligand binding site; other site 319224006981 metal-binding site 319224006982 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 319224006983 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 319224006984 XdhC Rossmann domain; Region: XdhC_C; pfam13478 319224006985 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 319224006986 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 319224006987 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 319224006988 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 319224006989 active sites [active] 319224006990 tetramer interface [polypeptide binding]; other site 319224006991 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224006992 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 319224006993 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]; Region: FhlA; COG3604 319224006994 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 319224006995 Walker A motif; other site 319224006996 ATP binding site [chemical binding]; other site 319224006997 Walker B motif; other site 319224006998 Helix-turn-helix domains; Region: HTH; cl00088 319224006999 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 319224007000 eyelet of channel; other site 319224007001 trimer interface [polypeptide binding]; other site 319224007002 DNA topoisomerase III; Provisional; Region: PRK07726 319224007003 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 319224007004 active site 319224007005 putative interdomain interaction site [polypeptide binding]; other site 319224007006 putative metal-binding site [ion binding]; other site 319224007007 putative nucleotide binding site [chemical binding]; other site 319224007008 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 319224007009 domain I; other site 319224007010 DNA binding groove [nucleotide binding] 319224007011 phosphate binding site [ion binding]; other site 319224007012 domain II; other site 319224007013 domain III; other site 319224007014 nucleotide binding site [chemical binding]; other site 319224007015 catalytic site [active] 319224007016 domain IV; other site 319224007017 amidophosphoribosyltransferase; Provisional; Region: PRK09246 319224007018 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 319224007019 active site 319224007020 tetramer interface [polypeptide binding]; other site 319224007021 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224007022 active site 319224007023 Colicin V production protein; Region: Colicin_V; cl00567 319224007024 cell division protein DedD; Provisional; Region: PRK11633 319224007025 Sporulation related domain; Region: SPOR; cl10051 319224007026 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 319224007027 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 319224007028 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 319224007029 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 319224007030 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 319224007031 dimerization interface 3.5A [polypeptide binding]; other site 319224007032 active site 319224007033 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 319224007034 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 319224007035 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 319224007036 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 319224007037 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007038 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224007039 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 319224007040 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007041 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 319224007042 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 319224007043 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 319224007044 dimer interface [polypeptide binding]; other site 319224007045 active site 319224007046 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 319224007047 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; cl16911 319224007048 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 319224007049 YfcL protein; Region: YfcL; pfam08891 319224007050 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 319224007051 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 319224007052 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 319224007053 putative substrate translocation pore; other site 319224007054 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 319224007055 Tetramer interface [polypeptide binding]; other site 319224007056 active site 319224007057 FMN-binding site [chemical binding]; other site 319224007058 HemK family putative methylases; Region: hemK_fam; TIGR00536 319224007059 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 319224007060 S-adenosylmethionine binding site [chemical binding]; other site 319224007061 hypothetical protein; Provisional; Region: PRK04946 319224007062 Smr domain; Region: Smr; cl02619 319224007063 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 319224007064 catalytic core [active] 319224007065 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 319224007066 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 319224007067 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224007068 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224007069 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 319224007070 Two component regulator propeller; Region: Reg_prop; pfam07494 319224007071 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 319224007072 PAS fold; Region: PAS_3; pfam08447 319224007073 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 319224007074 PAS domain; Region: PAS_9; pfam13426 319224007075 putative active site [active] 319224007076 heme pocket [chemical binding]; other site 319224007077 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224007078 metal binding site [ion binding]; metal-binding site 319224007079 active site 319224007080 I-site; other site 319224007081 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 319224007082 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 319224007083 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 319224007084 substrate binding site [chemical binding]; other site 319224007085 oxyanion hole (OAH) forming residues; other site 319224007086 trimer interface [polypeptide binding]; other site 319224007087 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007088 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 319224007089 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 319224007090 3-ketoacyl-CoA thiolase; Reviewed; Region: fadI; PRK08963 319224007091 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 319224007092 dimer interface [polypeptide binding]; other site 319224007093 active site 319224007094 MoxR-like ATPases [General function prediction only]; Region: COG0714 319224007095 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 319224007096 Walker A motif; other site 319224007097 ATP binding site [chemical binding]; other site 319224007098 Walker B motif; other site 319224007099 arginine finger; other site 319224007100 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 319224007101 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 319224007102 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 319224007103 VWA BatA type: 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...; Region: vWA_BatA_type; cd01467 319224007104 metal ion-dependent adhesion site (MIDAS); other site 319224007105 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 319224007106 metal ion-dependent adhesion site (MIDAS); other site 319224007107 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 319224007108 binding surface 319224007109 TPR motif; other site 319224007110 Tetratricopeptide repeat; Region: TPR_16; pfam13432 319224007111 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 319224007112 Oxygen tolerance; Region: BatD; pfam13584 319224007113 RNA polymerase sigma factor; Provisional; Region: PRK12517 319224007114 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224007115 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 319224007116 DNA binding residues [nucleotide binding] 319224007117 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 319224007118 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 319224007119 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 319224007120 Na binding site [ion binding]; other site 319224007121 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; cl01155 319224007122 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; cl14632 319224007123 Protein of unknown function (DUF541); Region: SIMPL; cl01077 319224007124 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224007125 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 319224007126 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 319224007127 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224007128 Protein export membrane protein; Region: SecD_SecF; cl14618 319224007129 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 319224007130 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 319224007131 active site residue [active] 319224007132 Peptidase inhibitor I9; Region: Inhibitor_I9; pfam05922 319224007133 Peptidase S8 family domain in Subtilisin proteins; Region: Peptidases_S8_Subtilisin_subset; cd07477 319224007134 active site 319224007135 catalytic residues [active] 319224007136 PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from...; Region: PA_VapT_like; cd04817 319224007137 PA/subtilisin-like domain interface [polypeptide binding]; other site 319224007138 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 319224007139 catalytic residues [active] 319224007140 Bacterial pre-peptidase C-terminal domain; Region: PPC; pfam04151 319224007141 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 319224007142 YaeQ protein; Region: YaeQ; cl01913 319224007143 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 319224007144 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007145 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 319224007146 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 319224007147 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 319224007148 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 319224007149 Protein export membrane protein; Region: SecD_SecF; cl14618 319224007150 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 319224007151 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 319224007152 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 319224007153 Protein export membrane protein; Region: SecD_SecF; cl14618 319224007154 Preprotein translocase subunit; Region: YajC; cl00806 319224007155 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 319224007156 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 319224007157 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 319224007158 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 319224007159 Protein of unknown function, DUF479; Region: DUF479; cl01203 319224007160 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224007161 active site 319224007162 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007163 Complex I intermediate-associated protein 30 (CIA30); Region: CIA30; cl15292 319224007164 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 319224007165 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 319224007166 Response regulator receiver domain; Region: Response_reg; pfam00072 319224007167 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 319224007168 active site 319224007169 phosphorylation site [posttranslational modification] 319224007170 intermolecular recognition site; other site 319224007171 dimerization interface [polypeptide binding]; other site 319224007172 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 319224007173 active site 319224007174 catalytic residues [active] 319224007175 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 319224007176 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 319224007177 ATP binding site [chemical binding]; other site 319224007178 Mg++ binding site [ion binding]; other site 319224007179 motif III; other site 319224007180 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 319224007181 nucleotide binding region [chemical binding]; other site 319224007182 ATP-binding site [chemical binding]; other site 319224007183 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 319224007184 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 319224007185 DNA binding site [nucleotide binding] 319224007186 active site 319224007187 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 319224007188 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 319224007189 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224007190 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224007191 AlkA N-terminal domain; Region: AlkA_N; cl05528 319224007192 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 319224007193 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 319224007194 minor groove reading motif; other site 319224007195 helix-hairpin-helix signature motif; other site 319224007196 substrate binding pocket [chemical binding]; other site 319224007197 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 319224007198 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224007199 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 319224007200 Walker A/P-loop; other site 319224007201 ATP binding site [chemical binding]; other site 319224007202 Q-loop/lid; other site 319224007203 ABC transporter signature motif; other site 319224007204 Walker B; other site 319224007205 D-loop; other site 319224007206 H-loop/switch region; other site 319224007207 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 319224007208 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 319224007209 active site 319224007210 HIGH motif; other site 319224007211 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 319224007212 active site 319224007213 KMSKS motif; other site 319224007214 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 319224007215 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 319224007216 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 319224007217 DctM-like transporters; Region: DctM; pfam06808 319224007218 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224007219 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 319224007220 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 319224007221 dimer interface [polypeptide binding]; other site 319224007222 phosphorylation site [posttranslational modification] 319224007223 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 319224007224 ATP binding site [chemical binding]; other site 319224007225 Mg2+ binding site [ion binding]; other site 319224007226 G-X-G motif; other site 319224007227 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 319224007228 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 319224007229 active site 319224007230 phosphorylation site [posttranslational modification] 319224007231 intermolecular recognition site; other site 319224007232 dimerization interface [polypeptide binding]; other site 319224007233 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 319224007234 Walker A motif; other site 319224007235 ATP binding site [chemical binding]; other site 319224007236 Walker B motif; other site 319224007237 arginine finger; other site 319224007238 Helix-turn-helix domains; Region: HTH; cl00088 319224007239 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 319224007240 Transglycosylase; Region: Transgly; cl07896 319224007241 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224007242 thymidine kinase; Provisional; Region: PRK04296 319224007243 decaheme c-type cytochrome, OmcA/MtrC family; Region: decahem_SO1788; TIGR03507 319224007244 dipeptidyl carboxypeptidase II; Provisional; Region: PRK10280 319224007245 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 319224007246 active site 319224007247 Zn binding site [ion binding]; other site 319224007248 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 319224007249 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 319224007250 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 319224007251 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 319224007252 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 319224007253 Ligand binding site [chemical binding]; other site 319224007254 Electron transfer flavoprotein domain; Region: ETF; pfam01012 319224007255 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 319224007256 H-NS histone family; Region: Histone_HNS; pfam00816 319224007257 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 319224007258 active site 319224007259 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 319224007260 Metallo-dependent hydrolases, subgroup C 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_C; cd01309 319224007261 active site 319224007262 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 319224007263 Metallo-dependent hydrolases, subgroup C 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_C; cd01309 319224007264 active site 319224007265 outer membrane lipoprotein; Reviewed; Region: rcsF; PRK10781 319224007266 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 319224007267 homodimer interaction site [polypeptide binding]; other site 319224007268 cofactor binding site; other site 319224007269 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 319224007270 putative CoA binding site [chemical binding]; other site 319224007271 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 319224007272 trimer interface [polypeptide binding]; other site 319224007273 active site 319224007274 substrate binding site [chemical binding]; other site 319224007275 CoA binding site [chemical binding]; other site 319224007276 prolyl-tRNA synthetase; Provisional; Region: PRK09194 319224007277 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 319224007278 dimer interface [polypeptide binding]; other site 319224007279 motif 1; other site 319224007280 active site 319224007281 motif 2; other site 319224007282 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 319224007283 putative deacylase active site [active] 319224007284 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 319224007285 active site 319224007286 motif 3; other site 319224007287 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 319224007288 anticodon binding site; other site 319224007289 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 319224007290 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 319224007291 nucleophile elbow; other site 319224007292 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 319224007293 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 319224007294 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 319224007295 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 319224007296 GIY-YIG motif/motif A; other site 319224007297 putative active site [active] 319224007298 putative metal binding site [ion binding]; other site 319224007299 GAF domain; Region: GAF_2; pfam13185 319224007300 GAF domain; Region: GAF; cl15785 319224007301 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224007302 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 319224007303 ATP binding site [chemical binding]; other site 319224007304 Mg2+ binding site [ion binding]; other site 319224007305 G-X-G motif; other site 319224007306 NlpE N-terminal domain; Region: NlpE; cl01138 319224007307 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 319224007308 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 319224007309 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 319224007310 NAD(P) binding site [chemical binding]; other site 319224007311 homodimer interface [polypeptide binding]; other site 319224007312 substrate binding site [chemical binding]; other site 319224007313 active site 319224007314 Bacterial sugar transferase; Region: Bac_transf; cl00939 319224007315 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 319224007316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007317 NAD(P) binding site [chemical binding]; other site 319224007318 active site 319224007319 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 319224007320 active site 319224007321 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_d; cd04196 319224007322 Probable Catalytic site; other site 319224007323 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 319224007324 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 319224007325 active site 319224007326 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 319224007327 active site 319224007328 MatE; Region: MatE; cl10513 319224007329 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 319224007330 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 319224007331 Cupin domain; Region: Cupin_2; cl09118 319224007332 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 319224007333 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 319224007334 NADP binding site [chemical binding]; other site 319224007335 active site 319224007336 putative substrate binding site [chemical binding]; other site 319224007337 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 319224007338 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 319224007339 substrate binding site; other site 319224007340 tetramer interface; other site 319224007341 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 319224007342 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 319224007343 NAD binding site [chemical binding]; other site 319224007344 substrate binding site [chemical binding]; other site 319224007345 homodimer interface [polypeptide binding]; other site 319224007346 active site 319224007347 Chain length determinant protein; Region: Wzz; cl15801 319224007348 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 319224007349 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 319224007350 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 319224007351 SLBB domain; Region: SLBB; pfam10531 319224007352 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 319224007353 SLBB domain; Region: SLBB; pfam10531 319224007354 SLBB domain; Region: SLBB; pfam10531 319224007355 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 319224007356 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 319224007357 transcriptional activator RfaH; Region: RfaH; TIGR01955 319224007358 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 319224007359 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 319224007360 putative substrate translocation pore; other site 319224007361 Response regulator receiver domain; Region: Response_reg; pfam00072 319224007362 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 319224007363 active site 319224007364 phosphorylation site [posttranslational modification] 319224007365 intermolecular recognition site; other site 319224007366 dimerization interface [polypeptide binding]; other site 319224007367 VacJ like lipoprotein; Region: VacJ; cl01073 319224007368 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 319224007369 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 319224007370 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 319224007371 putative CheA interaction surface; other site 319224007372 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 319224007373 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 319224007374 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 319224007375 P loop; other site 319224007376 Nucleotide binding site [chemical binding]; other site 319224007377 DTAP/Switch II; other site 319224007378 Switch I; other site 319224007379 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 319224007380 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 319224007381 active site 319224007382 phosphorylation site [posttranslational modification] 319224007383 intermolecular recognition site; other site 319224007384 CheB methylesterase; Region: CheB_methylest; pfam01339 319224007385 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 319224007386 putative binding surface; other site 319224007387 active site 319224007388 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 319224007389 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 319224007390 ATP binding site [chemical binding]; other site 319224007391 Mg2+ binding site [ion binding]; other site 319224007392 G-X-G motif; other site 319224007393 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 319224007394 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 319224007395 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 319224007396 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 319224007397 active site 319224007398 phosphorylation site [posttranslational modification] 319224007399 intermolecular recognition site; other site 319224007400 dimerization interface [polypeptide binding]; other site 319224007401 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 319224007402 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224007403 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 319224007404 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 319224007405 DNA binding residues [nucleotide binding] 319224007406 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224007407 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 319224007408 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 319224007409 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 319224007410 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224007411 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224007412 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 319224007413 FHIPEP family; Region: FHIPEP; pfam00771 319224007414 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 319224007415 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 319224007416 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 319224007417 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 319224007418 FliP family; Region: FliP; cl00593 319224007419 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 319224007420 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 319224007421 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 319224007422 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 319224007423 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 319224007424 Flagellar hook-length control protein [Cell motility and secretion]; Region: FliK; COG3144 319224007425 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 319224007426 flagellar biosynthesis chaperone; Validated; Region: fliJ; cl09161 319224007427 Flagellar FliJ protein; Region: FliJ; pfam02050 319224007428 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08972 319224007429 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 319224007430 Walker A motif/ATP binding site; other site 319224007431 Walker B motif; other site 319224007432 flagellar assembly protein H; Validated; Region: fliH; PRK05687 319224007433 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 319224007434 Flagellar assembly protein FliH; Region: FliH; pfam02108 319224007435 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 319224007436 MgtE intracellular N domain; Region: MgtE_N; cl15244 319224007437 FliG C-terminal domain; Region: FliG_C; pfam01706 319224007438 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 319224007439 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 319224007440 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 319224007441 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 319224007442 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 319224007443 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 319224007444 active site 319224007445 phosphorylation site [posttranslational modification] 319224007446 intermolecular recognition site; other site 319224007447 dimerization interface [polypeptide binding]; other site 319224007448 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 319224007449 Walker A motif; other site 319224007450 ATP binding site [chemical binding]; other site 319224007451 Walker B motif; other site 319224007452 arginine finger; other site 319224007453 Helix-turn-helix domains; Region: HTH; cl00088 319224007454 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 319224007455 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 319224007456 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 319224007457 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 319224007458 ATP binding site [chemical binding]; other site 319224007459 Mg2+ binding site [ion binding]; other site 319224007460 G-X-G motif; other site 319224007461 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 319224007462 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 319224007463 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 319224007464 Walker A motif; other site 319224007465 ATP binding site [chemical binding]; other site 319224007466 Walker B motif; other site 319224007467 arginine finger; other site 319224007468 Helix-turn-helix domains; Region: HTH; cl00088 319224007469 Flagellar protein FliS; Region: FliS; cl00654 319224007470 flagellar capping protein; Reviewed; Region: fliD; PRK08032 319224007471 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 319224007472 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 319224007473 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 319224007474 FlaG protein; Region: FlaG; cl00591 319224007475 flagellin; Provisional; Region: PRK12802 319224007476 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 319224007477 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 319224007478 flagellin; Provisional; Region: PRK12802 319224007479 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 319224007480 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 319224007481 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 319224007482 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 319224007483 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08871 319224007484 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224007485 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224007486 Rod binding protein; Region: Rod-binding; cl01626 319224007487 flagellar rod assembly protein/muramidase FlgJ; Region: flagell_FlgJ; TIGR02541 319224007488 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 319224007489 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 319224007490 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 319224007491 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 319224007492 Flagellar L-ring protein; Region: FlgH; cl00905 319224007493 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 319224007494 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224007495 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224007496 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 319224007497 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224007498 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 319224007499 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 319224007500 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224007501 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 319224007502 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 319224007503 FlgD Ig-like domain; Region: FlgD_ig; cl15790 319224007504 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12631 319224007505 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224007506 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224007507 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12625 319224007508 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224007509 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 319224007510 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 319224007511 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; cl16911 319224007512 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 319224007513 Response regulator receiver domain; Region: Response_reg; pfam00072 319224007514 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 319224007515 active site 319224007516 phosphorylation site [posttranslational modification] 319224007517 intermolecular recognition site; other site 319224007518 dimerization interface [polypeptide binding]; other site 319224007519 SAF-like; Region: SAF_2; pfam13144 319224007520 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 319224007521 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 319224007522 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 319224007523 FlgN protein; Region: FlgN; cl09176 319224007524 LPP20 lipoprotein; Region: LPP20; cl15824 319224007525 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; cl15276 319224007526 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 319224007527 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224007528 Walker A/P-loop; other site 319224007529 ATP binding site [chemical binding]; other site 319224007530 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 319224007531 active site 319224007532 metal binding site [ion binding]; metal-binding site 319224007533 RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA...; Region: RT_Bac_retron_II; cd03487 319224007534 putative active site [active] 319224007535 putative NTP binding site [chemical binding]; other site 319224007536 putative nucleic acid binding site [nucleotide binding]; other site 319224007537 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 319224007538 integrase; Provisional; Region: int; PHA02601 319224007539 active site 319224007540 DNA binding site [nucleotide binding] 319224007541 Int/Topo IB signature motif; other site 319224007542 Thiamin pyrophosphokinase, catalytic domain; Region: TPK_catalytic; cl09135 319224007543 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 319224007544 active site 319224007545 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 319224007546 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224007547 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 319224007548 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; cl16911 319224007549 LicD family; Region: LicD; cl01378 319224007550 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 319224007551 NAD(P) binding site [chemical binding]; other site 319224007552 catalytic residues [active] 319224007553 AMP-binding enzyme; Region: AMP-binding; cl15778 319224007554 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 319224007555 AMP-binding enzyme; Region: AMP-binding; cl15778 319224007556 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 319224007557 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007558 NAD(P) binding site [chemical binding]; other site 319224007559 active site 319224007560 Phosphopantetheine attachment site; Region: PP-binding; cl09936 319224007561 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 319224007562 pseudaminic acid synthase; Region: PseI; TIGR03586 319224007563 NeuB family; Region: NeuB; cl00496 319224007564 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 319224007565 NeuB binding interface [polypeptide binding]; other site 319224007566 putative substrate binding site [chemical binding]; other site 319224007567 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 319224007568 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 319224007569 ligand binding site; other site 319224007570 tetramer interface; other site 319224007571 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 319224007572 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 319224007573 inhibitor-cofactor binding pocket; inhibition site 319224007574 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224007575 catalytic residue [active] 319224007576 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 319224007577 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 319224007578 NAD(P) binding site [chemical binding]; other site 319224007579 homodimer interface [polypeptide binding]; other site 319224007580 substrate binding site [chemical binding]; other site 319224007581 active site 319224007582 Thiamin pyrophosphokinase, catalytic domain; Region: TPK_catalytic; cl09135 319224007583 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 319224007584 rhombotail lipoprotein; Region: rhombo_lipo; TIGR04179 319224007585 Protein of unknown function (DUF3308); Region: DUF3308; cl14675 319224007586 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224007587 Helix-turn-helix domains; Region: HTH; cl00088 319224007588 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224007589 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 319224007590 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 319224007591 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224007592 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 319224007593 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224007594 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224007595 dimer interface [polypeptide binding]; other site 319224007596 putative CheW interface [polypeptide binding]; other site 319224007597 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 319224007598 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 319224007599 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 319224007600 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 319224007601 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 319224007602 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 319224007603 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 319224007604 dimerization interface [polypeptide binding]; other site 319224007605 ATP binding site [chemical binding]; other site 319224007606 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 319224007607 dimerization interface [polypeptide binding]; other site 319224007608 ATP binding site [chemical binding]; other site 319224007609 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 319224007610 putative active site [active] 319224007611 catalytic triad [active] 319224007612 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 319224007613 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 319224007614 substrate binding pocket [chemical binding]; other site 319224007615 membrane-bound complex binding site; other site 319224007616 hinge residues; other site 319224007617 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 319224007618 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224007619 catalytic residue [active] 319224007620 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 319224007621 nucleoside/Zn binding site; other site 319224007622 dimer interface [polypeptide binding]; other site 319224007623 catalytic motif [active] 319224007624 GMP synthase; Reviewed; Region: guaA; PRK00074 319224007625 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 319224007626 AMP/PPi binding site [chemical binding]; other site 319224007627 candidate oxyanion hole; other site 319224007628 catalytic triad [active] 319224007629 potential glutamine specificity residues [chemical binding]; other site 319224007630 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 319224007631 ATP Binding subdomain [chemical binding]; other site 319224007632 Ligand Binding sites [chemical binding]; other site 319224007633 Dimerization subdomain; other site 319224007634 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 319224007635 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 319224007636 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 319224007637 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 319224007638 active site 319224007639 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 319224007640 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 319224007641 generic binding surface II; other site 319224007642 generic binding surface I; other site 319224007643 GTP-binding protein Der; Reviewed; Region: PRK00093 319224007644 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 319224007645 G1 box; other site 319224007646 GTP/Mg2+ binding site [chemical binding]; other site 319224007647 Switch I region; other site 319224007648 G2 box; other site 319224007649 Switch II region; other site 319224007650 G3 box; other site 319224007651 G4 box; other site 319224007652 G5 box; other site 319224007653 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 319224007654 G1 box; other site 319224007655 GTP/Mg2+ binding site [chemical binding]; other site 319224007656 Switch I region; other site 319224007657 G2 box; other site 319224007658 G3 box; other site 319224007659 Switch II region; other site 319224007660 G4 box; other site 319224007661 G5 box; other site 319224007662 outer membrane biogenesis protein BamB; Provisional; Region: PRK11138 319224007663 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 319224007664 active site 319224007665 Trp docking motif [polypeptide binding]; other site 319224007666 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 319224007667 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 319224007668 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 319224007669 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 319224007670 dimer interface [polypeptide binding]; other site 319224007671 motif 1; other site 319224007672 active site 319224007673 motif 2; other site 319224007674 motif 3; other site 319224007675 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 319224007676 anticodon binding site; other site 319224007677 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 319224007678 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 319224007679 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 319224007680 cytoskeletal protein RodZ; Provisional; Region: PRK10856 319224007681 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 319224007682 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 319224007683 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 319224007684 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 319224007685 binding surface 319224007686 TPR motif; other site 319224007687 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 319224007688 binding surface 319224007689 TPR motif; other site 319224007690 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 319224007691 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 319224007692 FeS/SAM binding site; other site 319224007693 Domain of unknown function DUF21; Region: DUF21; pfam01595 319224007694 FOG: CBS domain [General function prediction only]; Region: COG0517 319224007695 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 319224007696 NAD pyrophosphatase/5'-nucleotidase NadN; Region: nadN; TIGR01530 319224007697 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 319224007698 active site 319224007699 metal binding site [ion binding]; metal-binding site 319224007700 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 319224007701 Helix-turn-helix domains; Region: HTH; cl00088 319224007702 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 319224007703 The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; Region: PBP2_HupR; cd08431 319224007704 putative dimerization interface [polypeptide binding]; other site 319224007705 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 319224007706 Transposase; Region: DEDD_Tnp_IS110; pfam01548 319224007707 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 319224007708 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 319224007709 DoxX; Region: DoxX; cl00976 319224007710 Cupin domain; Region: Cupin_2; cl09118 319224007711 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224007712 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224007713 Coenzyme A binding pocket [chemical binding]; other site 319224007714 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224007715 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224007716 Coenzyme A binding pocket [chemical binding]; other site 319224007717 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 319224007718 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224007719 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 319224007720 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 319224007721 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 319224007722 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224007723 metal binding site [ion binding]; metal-binding site 319224007724 active site 319224007725 I-site; other site 319224007726 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 319224007727 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 319224007728 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 319224007729 tetramer interface [polypeptide binding]; other site 319224007730 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224007731 catalytic residue [active] 319224007732 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224007733 ligand binding site [chemical binding]; other site 319224007734 mechanosensitive channel MscS; Provisional; Region: PRK10334 319224007735 Conserved TM helix; Region: TM_helix; pfam05552 319224007736 Mechanosensitive ion channel; Region: MS_channel; pfam00924 319224007737 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 319224007738 dimer interface [polypeptide binding]; other site 319224007739 catalytic triad [active] 319224007740 peroxidatic and resolving cysteines [active] 319224007741 Predicted membrane protein [Function unknown]; Region: COG2860 319224007742 UPF0126 domain; Region: UPF0126; pfam03458 319224007743 UPF0126 domain; Region: UPF0126; pfam03458 319224007744 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 319224007745 translation initiation factor Sui1; Validated; Region: PRK06824 319224007746 Homologs of eIF1/SUI1 including Escherichia coli YciH; Region: YciH_like; cd11567 319224007747 putative rRNA binding site [nucleotide binding]; other site 319224007748 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 319224007749 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 319224007750 ferrochelatase; Reviewed; Region: hemH; PRK00035 319224007751 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 319224007752 active site 319224007753 C-terminal domain interface [polypeptide binding]; other site 319224007754 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 319224007755 active site 319224007756 N-terminal domain interface [polypeptide binding]; other site 319224007757 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 319224007758 catalytic residues [active] 319224007759 dimer interface [polypeptide binding]; other site 319224007760 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 319224007761 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224007762 Walker A motif; other site 319224007763 ATP binding site [chemical binding]; other site 319224007764 Walker B motif; other site 319224007765 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 319224007766 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 319224007767 Walker A motif; other site 319224007768 ATP binding site [chemical binding]; other site 319224007769 Walker B motif; other site 319224007770 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 319224007771 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 319224007772 catalytic residue [active] 319224007773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007774 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 319224007775 YGGT family; Region: YGGT; cl00508 319224007776 YGGT family; Region: YGGT; cl00508 319224007777 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 319224007778 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 319224007779 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 319224007780 active site 319224007781 dimerization interface [polypeptide binding]; other site 319224007782 HemN family oxidoreductase; Provisional; Region: PRK05660 319224007783 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 319224007784 FeS/SAM binding site; other site 319224007785 HemN C-terminal domain; Region: HemN_C; pfam06969 319224007786 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 319224007787 Helix-turn-helix domains; Region: HTH; cl00088 319224007788 LysR family transcriptional regulator; Provisional; Region: PRK14997 319224007789 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 319224007790 putative effector binding pocket; other site 319224007791 dimerization interface [polypeptide binding]; other site 319224007792 Protein of unknown function (DUF2884); Region: DUF2884; cl08135 319224007793 Glutaminase; Region: Glutaminase; cl00907 319224007794 Protein with unknown function (DUF469); Region: DUF469; cl01237 319224007795 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; cl16911 319224007796 adenine DNA glycosylase; Provisional; Region: PRK10880 319224007797 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 319224007798 minor groove reading motif; other site 319224007799 helix-hairpin-helix signature motif; other site 319224007800 substrate binding pocket [chemical binding]; other site 319224007801 active site 319224007802 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 319224007803 DNA binding and oxoG recognition site [nucleotide binding] 319224007804 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 319224007805 YceI-like domain; Region: YceI; cl01001 319224007806 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 319224007807 Protein of unknown function (DUF3634); Region: DUF3634; pfam12321 319224007808 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 319224007809 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 319224007810 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 319224007811 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 319224007812 S-adenosylmethionine binding site [chemical binding]; other site 319224007813 Uncharacterized conserved protein [Function unknown]; Region: COG3496 319224007814 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 319224007815 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 319224007816 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007817 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007818 NAD(P) binding site [chemical binding]; other site 319224007819 active site 319224007820 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 319224007821 DNA photolyase; Region: DNA_photolyase; pfam00875 319224007822 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 319224007823 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 319224007824 transcriptional regulator MirA; Provisional; Region: PRK15043 319224007825 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 319224007826 DNA binding residues [nucleotide binding] 319224007827 Protein of unknown function (DUF523); Region: DUF523; cl00733 319224007828 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 319224007829 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 319224007830 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 319224007831 DEAD-like helicases superfamily; Region: DEXDc; smart00487 319224007832 ATP binding site [chemical binding]; other site 319224007833 Mg++ binding site [ion binding]; other site 319224007834 motif III; other site 319224007835 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 319224007836 nucleotide binding region [chemical binding]; other site 319224007837 ATP-binding site [chemical binding]; other site 319224007838 AAA domain; Region: AAA_32; pfam13654 319224007839 lon-related putative ATP-dependent protease; Region: lon_rel; TIGR00764 319224007840 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 319224007841 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 319224007842 FMN binding site [chemical binding]; other site 319224007843 active site 319224007844 substrate binding site [chemical binding]; other site 319224007845 catalytic residue [active] 319224007846 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224007847 Helix-turn-helix domains; Region: HTH; cl00088 319224007848 Protein of unknown function (DUF2375); Region: DUF2375; cl09781 319224007849 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224007850 dimer interface [polypeptide binding]; other site 319224007851 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 319224007852 putative CheW interface [polypeptide binding]; other site 319224007853 Transcriptional regulator; Region: Transcrip_reg; cl00361 319224007854 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 319224007855 30S subunit binding site; other site 319224007856 PAS domain; Region: PAS_9; pfam13426 319224007857 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 319224007858 putative active site [active] 319224007859 heme pocket [chemical binding]; other site 319224007860 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224007861 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224007862 dimer interface [polypeptide binding]; other site 319224007863 putative CheW interface [polypeptide binding]; other site 319224007864 Protein of unknown function (DUF3649); Region: DUF3649; pfam12365 319224007865 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 319224007866 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 319224007867 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 319224007868 Protein of unknown function (DUF3325); Region: DUF3325; pfam11804 319224007869 OsmC-like protein; Region: OsmC; cl00767 319224007870 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]; Region: COG4946 319224007871 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224007872 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224007873 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 319224007874 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 319224007875 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 319224007876 protein binding site [polypeptide binding]; other site 319224007877 Tricorn protease; serine protease family S41; Region: Peptidase_S41_TRI; cd07562 319224007878 Domain interface; other site 319224007879 Peptide binding site; other site 319224007880 Active site tetrad [active] 319224007881 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 319224007882 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224007883 substrate binding pocket [chemical binding]; other site 319224007884 membrane-bound complex binding site; other site 319224007885 hinge residues; other site 319224007886 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 319224007887 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 319224007888 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 319224007889 catalytic residue [active] 319224007890 homoserine kinase; Provisional; Region: PRK01212 319224007891 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 319224007892 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 319224007893 bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional; Region: thrA; PRK09436 319224007894 AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli...; Region: AAK_AK-HSDH; cd04257 319224007895 putative catalytic residues [active] 319224007896 putative nucleotide binding site [chemical binding]; other site 319224007897 putative aspartate binding site [chemical binding]; other site 319224007898 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA-like_1; cd04921 319224007899 dimer interface [polypeptide binding]; other site 319224007900 putative threonine allosteric regulatory site; other site 319224007901 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH); Region: ACT_AKi-HSDH-ThrA_2; cd04922 319224007902 putative threonine allosteric regulatory site; other site 319224007903 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224007904 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 319224007905 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224007906 Helix-turn-helix domains; Region: HTH; cl00088 319224007907 Cytochrome C'; Region: Cytochrom_C_2; cl01610 319224007908 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 319224007909 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 319224007910 30S subunit binding site; other site 319224007911 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 319224007912 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 319224007913 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 319224007914 HIGH motif; other site 319224007915 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 319224007916 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 319224007917 active site 319224007918 KMSKS motif; other site 319224007919 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 319224007920 tRNA binding surface [nucleotide binding]; other site 319224007921 anticodon binding site; other site 319224007922 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 319224007923 Global regulator protein family; Region: CsrA; cl00670 319224007924 aspartate kinase; Reviewed; Region: PRK06635 319224007925 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 319224007926 putative nucleotide binding site [chemical binding]; other site 319224007927 putative catalytic residues [active] 319224007928 putative Mg ion binding site [ion binding]; other site 319224007929 putative aspartate binding site [chemical binding]; other site 319224007930 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 319224007931 putative allosteric regulatory residue; other site 319224007932 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 319224007933 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 319224007934 motif 1; other site 319224007935 active site 319224007936 motif 2; other site 319224007937 motif 3; other site 319224007938 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 319224007939 DHHA1 domain; Region: DHHA1; pfam02272 319224007940 RecX family; Region: RecX; cl00936 319224007941 recombinase A; Provisional; Region: recA; PRK09354 319224007942 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 319224007943 hexamer interface [polypeptide binding]; other site 319224007944 Walker A motif; other site 319224007945 ATP binding site [chemical binding]; other site 319224007946 Walker B motif; other site 319224007947 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 319224007948 MutS domain I; Region: MutS_I; pfam01624 319224007949 MutS domain II; Region: MutS_II; pfam05188 319224007950 MutS family domain IV; Region: MutS_IV; pfam05190 319224007951 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 319224007952 Walker A/P-loop; other site 319224007953 ATP binding site [chemical binding]; other site 319224007954 Q-loop/lid; other site 319224007955 ABC transporter signature motif; other site 319224007956 Walker B; other site 319224007957 D-loop; other site 319224007958 H-loop/switch region; other site 319224007959 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 319224007960 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 319224007961 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224007962 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 319224007963 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 319224007964 DNA binding residues [nucleotide binding] 319224007965 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 319224007966 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224007967 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 319224007968 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; cl16911 319224007969 Survival protein SurE; Region: SurE; cl00448 319224007970 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 319224007971 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 319224007972 Permutation of conserved domain; other site 319224007973 active site 319224007974 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 319224007975 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 319224007976 homotrimer interaction site [polypeptide binding]; other site 319224007977 zinc binding site [ion binding]; other site 319224007978 CDP-binding sites; other site 319224007979 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 319224007980 substrate binding site; other site 319224007981 dimer interface; other site 319224007982 Septum formation initiator; Region: DivIC; cl11433 319224007983 enolase; Provisional; Region: eno; PRK00077 319224007984 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 319224007985 dimer interface [polypeptide binding]; other site 319224007986 metal binding site [ion binding]; metal-binding site 319224007987 substrate binding pocket [chemical binding]; other site 319224007988 CTP synthetase; Validated; Region: pyrG; PRK05380 319224007989 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 319224007990 Catalytic site [active] 319224007991 active site 319224007992 UTP binding site [chemical binding]; other site 319224007993 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 319224007994 active site 319224007995 putative oxyanion hole; other site 319224007996 catalytic triad [active] 319224007997 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 319224007998 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 319224007999 homodimer interface [polypeptide binding]; other site 319224008000 metal binding site [ion binding]; metal-binding site 319224008001 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs'; Region: NTP-PPase_MazG_Cterm; cd11529 319224008002 homodimer interface [polypeptide binding]; other site 319224008003 active site 319224008004 putative chemical substrate binding site [chemical binding]; other site 319224008005 metal binding site [ion binding]; metal-binding site 319224008006 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 319224008007 agmatine deiminase; Region: agmatine_aguA; TIGR03380 319224008008 amidase; Validated; Region: PRK06565 319224008009 Amidase; Region: Amidase; cl11426 319224008010 Amidase; Region: Amidase; cl11426 319224008011 methionine synthase; Provisional; Region: PRK01207 319224008012 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 319224008013 substrate binding site [chemical binding]; other site 319224008014 THF binding site; other site 319224008015 zinc-binding site [ion binding]; other site 319224008016 Domain of unknown function (DUF1852); Region: DUF1852; pfam08908 319224008017 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 319224008018 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008019 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008020 Family description; Region: UvrD_C_2; cl15862 319224008021 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 319224008022 putative active site [active] 319224008023 Protein of unknown function (DUF3320); Region: DUF3320; pfam11784 319224008024 (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional; Region: relA; PRK10872 319224008025 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224008026 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 319224008027 synthetase active site [active] 319224008028 NTP binding site [chemical binding]; other site 319224008029 metal binding site [ion binding]; metal-binding site 319224008030 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 319224008031 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 319224008032 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 319224008033 TRAM domain; Region: TRAM; cl01282 319224008034 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 319224008035 S-adenosylmethionine binding site [chemical binding]; other site 319224008036 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 319224008037 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 319224008038 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 319224008039 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 319224008040 dimer interface [polypeptide binding]; other site 319224008041 phosphorylation site [posttranslational modification] 319224008042 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 319224008043 ATP binding site [chemical binding]; other site 319224008044 Mg2+ binding site [ion binding]; other site 319224008045 G-X-G motif; other site 319224008046 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 319224008047 active site 319224008048 phosphorylation site [posttranslational modification] 319224008049 intermolecular recognition site; other site 319224008050 dimerization interface [polypeptide binding]; other site 319224008051 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 319224008052 Protein of unknown function (DUF416); Region: DUF416; cl01166 319224008053 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224008054 Helix-turn-helix domains; Region: HTH; cl00088 319224008055 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 319224008056 putative effector binding pocket; other site 319224008057 dimerization interface [polypeptide binding]; other site 319224008058 Membrane transport protein; Region: Mem_trans; cl09117 319224008059 recombination and repair protein; Provisional; Region: PRK10869 319224008060 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 319224008061 Walker A/P-loop; other site 319224008062 ATP binding site [chemical binding]; other site 319224008063 Q-loop/lid; other site 319224008064 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 319224008065 ABC transporter signature motif; other site 319224008066 Walker B; other site 319224008067 D-loop; other site 319224008068 H-loop/switch region; other site 319224008069 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 319224008070 tetramer interfaces [polypeptide binding]; other site 319224008071 binuclear metal-binding site [ion binding]; other site 319224008072 thiamine monophosphate kinase; Provisional; Region: PRK05731 319224008073 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 319224008074 ATP binding site [chemical binding]; other site 319224008075 dimerization interface [polypeptide binding]; other site 319224008076 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 319224008077 putative RNA binding site [nucleotide binding]; other site 319224008078 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 319224008079 homopentamer interface [polypeptide binding]; other site 319224008080 active site 319224008081 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 319224008082 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 319224008083 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 319224008084 dimerization interface [polypeptide binding]; other site 319224008085 active site 319224008086 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 319224008087 Lumazine binding domain; Region: Lum_binding; pfam00677 319224008088 Lumazine binding domain; Region: Lum_binding; pfam00677 319224008089 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 319224008090 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 319224008091 catalytic motif [active] 319224008092 Zn binding site [ion binding]; other site 319224008093 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 319224008094 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 319224008095 ATP cone domain; Region: ATP-cone; pfam03477 319224008096 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 319224008097 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 319224008098 dimer interface [polypeptide binding]; other site 319224008099 active site 319224008100 glycine-pyridoxal phosphate binding site [chemical binding]; other site 319224008101 folate binding site [chemical binding]; other site 319224008102 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 319224008103 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 319224008104 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 319224008105 ABC transporter; Region: ABC_tran_2; pfam12848 319224008106 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 319224008107 transcriptional regulator; Provisional; Region: PRK10632 319224008108 Helix-turn-helix domains; Region: HTH; cl00088 319224008109 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 319224008110 putative effector binding pocket; other site 319224008111 dimerization interface [polypeptide binding]; other site 319224008112 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 319224008113 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 319224008114 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 319224008115 catalytic residues [active] 319224008116 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 319224008117 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224008118 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 319224008119 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 319224008120 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224008121 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 319224008122 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 319224008123 putative substrate translocation pore; other site 319224008124 Cupin domain; Region: Cupin_2; cl09118 319224008125 Helix-turn-helix domain; Region: HTH_18; pfam12833 319224008126 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224008127 LabA_like proteins; Region: LabA_like/DUF88; cl10034 319224008128 putative metal binding site [ion binding]; other site 319224008129 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 319224008130 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224008131 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 319224008132 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 319224008133 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224008134 Helix-turn-helix domains; Region: HTH; cl00088 319224008135 OsmC-like protein; Region: OsmC; cl00767 319224008136 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224008137 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224008138 Helix-turn-helix domains; Region: HTH; cl00088 319224008139 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 319224008140 dimerization interface [polypeptide binding]; other site 319224008141 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 319224008142 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 319224008143 GDP-binding site [chemical binding]; other site 319224008144 ACT binding site; other site 319224008145 IMP binding site; other site 319224008146 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 319224008147 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 319224008148 active site 319224008149 phosphorylation site [posttranslational modification] 319224008150 intermolecular recognition site; other site 319224008151 dimerization interface [polypeptide binding]; other site 319224008152 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 319224008153 active site 319224008154 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224008155 metal binding site [ion binding]; metal-binding site 319224008156 active site 319224008157 I-site; other site 319224008158 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 319224008159 HDOD domain; Region: HDOD; pfam08668 319224008160 putative protease; Provisional; Region: PRK15452 319224008161 Peptidase family U32; Region: Peptidase_U32; cl03113 319224008162 ferredoxin; Validated; Region: PRK07118 319224008163 SCP-2 sterol transfer family; Region: SCP2; cl01225 319224008164 Peptidase family U32; Region: Peptidase_U32; cl03113 319224008165 Peptidase family U32; Region: Peptidase_U32; cl03113 319224008166 Predicted membrane protein [Function unknown]; Region: COG3371 319224008167 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 319224008168 Nucleoside recognition; Region: Gate; cl00486 319224008169 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 319224008170 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 319224008171 putative active site [active] 319224008172 putative metal binding site [ion binding]; other site 319224008173 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224008174 putative acyl-acceptor binding pocket; other site 319224008175 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224008176 FOG: CBS domain [General function prediction only]; Region: COG0517 319224008177 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_24; cd04637 319224008178 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 319224008179 PilZ domain; Region: PilZ; cl01260 319224008180 DNA repair protein RadA; Provisional; Region: PRK11823 319224008181 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 319224008182 Walker A motif/ATP binding site; other site 319224008183 ATP binding site [chemical binding]; other site 319224008184 Walker B motif; other site 319224008185 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 319224008186 PilZ domain; Region: PilZ; cl01260 319224008187 PilZ domain; Region: PilZ; cl01260 319224008188 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 319224008189 phosphoserine phosphatase SerB; Region: serB; TIGR00338 319224008190 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 319224008191 motif II; other site 319224008192 Bacterial virulence factor haemolysin; Region: SMP_2; cl11479 319224008193 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 319224008194 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 319224008195 Sulfatase; Region: Sulfatase; cl10460 319224008196 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 319224008197 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 319224008198 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 319224008199 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 319224008200 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 319224008201 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 319224008202 intersubunit interface [polypeptide binding]; other site 319224008203 active site 319224008204 catalytic residue [active] 319224008205 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 319224008206 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 319224008207 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 319224008208 Nucleoside recognition; Region: Gate; cl00486 319224008209 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 319224008210 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 319224008211 active site 319224008212 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 319224008213 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 319224008214 G1 box; other site 319224008215 putative GEF interaction site [polypeptide binding]; other site 319224008216 GTP/Mg2+ binding site [chemical binding]; other site 319224008217 Switch I region; other site 319224008218 G2 box; other site 319224008219 G3 box; other site 319224008220 Switch II region; other site 319224008221 G4 box; other site 319224008222 G5 box; other site 319224008223 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 319224008224 lipoprotein NlpI; Provisional; Region: PRK11189 319224008225 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 319224008226 binding surface 319224008227 TPR motif; other site 319224008228 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 319224008229 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 319224008230 RNase E interface [polypeptide binding]; other site 319224008231 trimer interface [polypeptide binding]; other site 319224008232 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 319224008233 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 319224008234 RNase E interface [polypeptide binding]; other site 319224008235 trimer interface [polypeptide binding]; other site 319224008236 active site 319224008237 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 319224008238 putative nucleic acid binding region [nucleotide binding]; other site 319224008239 G-X-X-G motif; other site 319224008240 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 319224008241 RNA binding site [nucleotide binding]; other site 319224008242 domain interface; other site 319224008243 biofilm formation regulator HmsP; Provisional; Region: PRK11829 319224008244 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224008245 metal binding site [ion binding]; metal-binding site 319224008246 active site 319224008247 I-site; other site 319224008248 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 319224008249 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 319224008250 16S/18S rRNA binding site [nucleotide binding]; other site 319224008251 S13e-L30e interaction site [polypeptide binding]; other site 319224008252 25S rRNA binding site [nucleotide binding]; other site 319224008253 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 319224008254 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 319224008255 RNA binding site [nucleotide binding]; other site 319224008256 active site 319224008257 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 319224008258 Ribosome-binding factor A; Region: RBFA; cl00542 319224008259 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 319224008260 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 319224008261 translation initiation factor IF-2; Region: IF-2; TIGR00487 319224008262 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 319224008263 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 319224008264 G1 box; other site 319224008265 putative GEF interaction site [polypeptide binding]; other site 319224008266 GTP/Mg2+ binding site [chemical binding]; other site 319224008267 Switch I region; other site 319224008268 G2 box; other site 319224008269 G3 box; other site 319224008270 Switch II region; other site 319224008271 G4 box; other site 319224008272 G5 box; other site 319224008273 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 319224008274 Translation-initiation factor 2; Region: IF-2; pfam11987 319224008275 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 319224008276 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 319224008277 NusA N-terminal domain; Region: NusA_N; pfam08529 319224008278 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 319224008279 RNA binding site [nucleotide binding]; other site 319224008280 homodimer interface [polypeptide binding]; other site 319224008281 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 319224008282 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 319224008283 G-X-X-G motif; other site 319224008284 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 319224008285 ribosome maturation protein RimP; Reviewed; Region: PRK00092 319224008286 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 319224008287 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 319224008288 Sm1 motif; other site 319224008289 D1 - D2 interaction site; other site 319224008290 D3 - B interaction site; other site 319224008291 Hfq - Hfq interaction site; other site 319224008292 RNA binding pocket [nucleotide binding]; other site 319224008293 Sm2 motif; other site 319224008294 Preprotein translocase SecG subunit; Region: SecG; cl09123 319224008295 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 319224008296 substrate binding site [chemical binding]; other site 319224008297 dimer interface [polypeptide binding]; other site 319224008298 catalytic triad [active] 319224008299 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 319224008300 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 319224008301 active site 319224008302 substrate binding site [chemical binding]; other site 319224008303 metal binding site [ion binding]; metal-binding site 319224008304 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 319224008305 dihydropteroate synthase; Region: DHPS; TIGR01496 319224008306 substrate binding pocket [chemical binding]; other site 319224008307 dimer interface [polypeptide binding]; other site 319224008308 inhibitor binding site; inhibition site 319224008309 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 319224008310 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 319224008311 Walker A motif; other site 319224008312 ATP binding site [chemical binding]; other site 319224008313 Walker B motif; other site 319224008314 arginine finger; other site 319224008315 Peptidase family M41; Region: Peptidase_M41; pfam01434 319224008316 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 319224008317 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 319224008318 S-adenosylmethionine binding site [chemical binding]; other site 319224008319 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 319224008320 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13021 319224008321 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 319224008322 Protein export membrane protein; Region: SecD_SecF; cl14618 319224008323 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK12933 319224008324 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 319224008325 Protein export membrane protein; Region: SecD_SecF; cl14618 319224008326 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 319224008327 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 319224008328 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 319224008329 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 319224008330 FlgD Ig-like domain; Region: FlgD_ig; cl15790 319224008331 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 319224008332 GTP-binding protein YchF; Reviewed; Region: PRK09601 319224008333 YchF GTPase; Region: YchF; cd01900 319224008334 G1 box; other site 319224008335 GTP/Mg2+ binding site [chemical binding]; other site 319224008336 Switch I region; other site 319224008337 G2 box; other site 319224008338 Switch II region; other site 319224008339 G3 box; other site 319224008340 G4 box; other site 319224008341 G5 box; other site 319224008342 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 319224008343 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 319224008344 putative active site [active] 319224008345 catalytic residue [active] 319224008346 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224008347 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional; Region: PRK08849 319224008348 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 319224008349 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 319224008350 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 319224008351 FeS/SAM binding site; other site 319224008352 TRAM domain; Region: TRAM; cl01282 319224008353 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 319224008354 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008355 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 319224008356 magnesium/cobalt efflux protein CorC; Provisional; Region: PRK15094 319224008357 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 319224008358 Transporter associated domain; Region: CorC_HlyC; cl08393 319224008359 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 319224008360 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 319224008361 putative active site [active] 319224008362 catalytic triad [active] 319224008363 putative dimer interface [polypeptide binding]; other site 319224008364 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; cl16911 319224008365 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 319224008366 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 319224008367 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 319224008368 HIGH motif; other site 319224008369 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 319224008370 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 319224008371 active site 319224008372 KMSKS motif; other site 319224008373 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 319224008374 tRNA binding surface [nucleotide binding]; other site 319224008375 Lipopolysaccharide-assembly; Region: LptE; cl01125 319224008376 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 319224008377 DNA polymerase III, delta subunit; Region: holA; TIGR01128 319224008378 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 319224008379 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 319224008380 active site 319224008381 (T/H)XGH motif; other site 319224008382 Oligomerisation domain; Region: Oligomerisation; cl00519 319224008383 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 319224008384 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 319224008385 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 319224008386 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 319224008387 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224008388 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 319224008389 Transglycosylase SLT domain; Region: SLT_2; pfam13406 319224008390 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 319224008391 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224008392 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 319224008393 Sporulation related domain; Region: SPOR; cl10051 319224008394 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 319224008395 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224008396 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 319224008397 Protein of unknown function (DUF493); Region: DUF493; cl01102 319224008398 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 319224008399 lipoyl synthase; Provisional; Region: PRK05481 319224008400 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 319224008401 FeS/SAM binding site; other site 319224008402 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 319224008403 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224008404 Coenzyme A binding pocket [chemical binding]; other site 319224008405 DNA polymerase III psi subunit; Region: DNA_III_psi; cl11436 319224008406 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 319224008407 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 319224008408 dimerization interface [polypeptide binding]; other site 319224008409 DPS ferroxidase diiron center [ion binding]; other site 319224008410 ion pore; other site 319224008411 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 319224008412 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224008413 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 319224008414 N-terminal plug; other site 319224008415 ligand-binding site [chemical binding]; other site 319224008416 Integrase core domain; Region: rve; cl01316 319224008417 Integrase core domain; Region: rve; cl01316 319224008418 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 319224008419 binding surface 319224008420 TPR motif; other site 319224008421 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 319224008422 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 319224008423 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 319224008424 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 319224008425 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 319224008426 active site 319224008427 metal binding site [ion binding]; metal-binding site 319224008428 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 319224008429 active site 319224008430 Int/Topo IB signature motif; other site 319224008431 catalytic residues [active] 319224008432 DNA binding site [nucleotide binding] 319224008433 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 319224008434 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 319224008435 active site 319224008436 catalytic residues [active] 319224008437 Int/Topo IB signature motif; other site 319224008438 DNA binding site [nucleotide binding] 319224008439 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008440 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 319224008441 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 319224008442 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 319224008443 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 319224008444 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 319224008445 active site 319224008446 DNA binding site [nucleotide binding] 319224008447 Int/Topo IB signature motif; other site 319224008448 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 319224008449 integrase; Provisional; Region: PRK09692 319224008450 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 319224008451 active site 319224008452 Int/Topo IB signature motif; other site 319224008453 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 319224008454 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 319224008455 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 319224008456 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 319224008457 HsdM N-terminal domain; Region: HsdM_N; pfam12161 319224008458 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 319224008459 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; cl16911 319224008460 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 319224008461 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224008462 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224008463 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional; Region: PRK11331 319224008464 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008465 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional; Region: PRK11331 319224008466 McrBC 5-methylcytosine restriction system component; Region: McrBC; cl01737 319224008467 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 319224008468 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 319224008469 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008470 ATP binding site [chemical binding]; other site 319224008471 putative Mg++ binding site [ion binding]; other site 319224008472 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 319224008473 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 319224008474 non-specific DNA binding site [nucleotide binding]; other site 319224008475 salt bridge; other site 319224008476 sequence-specific DNA binding site [nucleotide binding]; other site 319224008477 EcsC protein family; Region: EcsC; pfam12787 319224008478 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 319224008479 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 319224008480 HipA-like N-terminal domain; Region: HipA_N; pfam07805 319224008481 HipA-like C-terminal domain; Region: HipA_C; pfam07804 319224008482 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 319224008483 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 319224008484 hypothetical protein; Provisional; Region: yieM; PRK10997 319224008485 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 319224008486 metal ion-dependent adhesion site (MIDAS); other site 319224008487 regulatory ATPase RavA; Provisional; Region: PRK13531 319224008488 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 319224008489 Walker A motif; other site 319224008490 ATP binding site [chemical binding]; other site 319224008491 Walker B motif; other site 319224008492 arginine finger; other site 319224008493 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 319224008494 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 319224008495 Walker A motif; other site 319224008496 ATP binding site [chemical binding]; other site 319224008497 Walker B motif; other site 319224008498 arginine finger; other site 319224008499 Helix-turn-helix domains; Region: HTH; cl00088 319224008500 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 319224008501 S-adenosylmethionine binding site [chemical binding]; other site 319224008502 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; cl00083 319224008503 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family; Region: SWIM_PBPRA1643; TIGR04102 319224008504 SEC-C motif; Region: SEC-C; pfam02810 319224008505 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 319224008506 catalytic site [active] 319224008507 putative active site [active] 319224008508 putative substrate binding site [chemical binding]; other site 319224008509 Protein of unknown function (DUF808); Region: DUF808; cl01002 319224008510 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 319224008511 tetramer (dimer of dimers) interface [polypeptide binding]; other site 319224008512 active site 319224008513 dimer interface [polypeptide binding]; other site 319224008514 23S rRNA m(5)C1962 methyltransferase; Provisional; Region: PRK15128 319224008515 PUA domain; Region: PUA; cl00607 319224008516 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 319224008517 putative RNA binding site [nucleotide binding]; other site 319224008518 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 319224008519 S-adenosylmethionine binding site [chemical binding]; other site 319224008520 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 319224008521 putative metal binding site [ion binding]; other site 319224008522 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 319224008523 putative catalytic site [active] 319224008524 putative phosphate binding site [ion binding]; other site 319224008525 putative metal binding site [ion binding]; other site 319224008526 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 319224008527 MgtE intracellular N domain; Region: MgtE_N; cl15244 319224008528 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 319224008529 Divalent cation transporter; Region: MgtE; cl00786 319224008530 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224008531 dimer interface [polypeptide binding]; other site 319224008532 putative CheW interface [polypeptide binding]; other site 319224008533 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 319224008534 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224008535 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 319224008536 substrate binding pocket [chemical binding]; other site 319224008537 membrane-bound complex binding site; other site 319224008538 hinge residues; other site 319224008539 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 319224008540 active site 319224008541 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 319224008542 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 319224008543 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224008544 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 319224008545 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 319224008546 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224008547 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 319224008548 IMP binding site; other site 319224008549 dimer interface [polypeptide binding]; other site 319224008550 interdomain contacts; other site 319224008551 partial ornithine binding site; other site 319224008552 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 319224008553 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 319224008554 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 319224008555 catalytic site [active] 319224008556 subunit interface [polypeptide binding]; other site 319224008557 dihydrodipicolinate reductase; Provisional; Region: PRK00048 319224008558 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224008559 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 319224008560 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 319224008561 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 319224008562 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224008563 Peptidase family M48; Region: Peptidase_M48; cl12018 319224008564 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 319224008565 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008566 ATP binding site [chemical binding]; other site 319224008567 putative Mg++ binding site [ion binding]; other site 319224008568 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 319224008569 nucleotide binding region [chemical binding]; other site 319224008570 ATP-binding site [chemical binding]; other site 319224008571 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 319224008572 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 319224008573 dimer interface [polypeptide binding]; other site 319224008574 active site 319224008575 metal binding site [ion binding]; metal-binding site 319224008576 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 319224008577 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 319224008578 NAD(P) binding site [chemical binding]; other site 319224008579 catalytic residues [active] 319224008580 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 319224008581 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 319224008582 cobalamin binding residues [chemical binding]; other site 319224008583 putative BtuC binding residues; other site 319224008584 dimer interface [polypeptide binding]; other site 319224008585 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 319224008586 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224008587 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224008588 Coenzyme A binding pocket [chemical binding]; other site 319224008589 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224008590 Protein of unknown function (DUF2931); Region: DUF2931; pfam11153 319224008591 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224008592 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008593 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 319224008594 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 319224008595 homodimer interface [polypeptide binding]; other site 319224008596 Walker A motif; other site 319224008597 ATP binding site [chemical binding]; other site 319224008598 hydroxycobalamin binding site [chemical binding]; other site 319224008599 Walker B motif; other site 319224008600 cobyric acid synthase; Provisional; Region: PRK00784 319224008601 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008602 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008603 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 319224008604 catalytic triad [active] 319224008605 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 319224008606 homotrimer interface [polypeptide binding]; other site 319224008607 Walker A motif; other site 319224008608 GTP binding site [chemical binding]; other site 319224008609 Walker B motif; other site 319224008610 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 319224008611 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 319224008612 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 319224008613 putative dimer interface [polypeptide binding]; other site 319224008614 active site pocket [active] 319224008615 putative cataytic base [active] 319224008616 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 319224008617 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 319224008618 ABC-ATPase subunit interface; other site 319224008619 dimer interface [polypeptide binding]; other site 319224008620 putative PBP binding regions; other site 319224008621 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 319224008622 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 319224008623 Walker A/P-loop; other site 319224008624 ATP binding site [chemical binding]; other site 319224008625 Q-loop/lid; other site 319224008626 ABC transporter signature motif; other site 319224008627 Walker B; other site 319224008628 D-loop; other site 319224008629 H-loop/switch region; other site 319224008630 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 319224008631 catalytic core [active] 319224008632 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 319224008633 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 319224008634 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 319224008635 substrate binding pocket [chemical binding]; other site 319224008636 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 319224008637 B12 binding site [chemical binding]; other site 319224008638 cobalt ligand [ion binding]; other site 319224008639 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 319224008640 Protein of unknown function DUF262; Region: DUF262; cl14890 319224008641 PAS domain; Region: PAS_9; pfam13426 319224008642 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 319224008643 PAS domain; Region: PAS_9; pfam13426 319224008644 putative active site [active] 319224008645 heme pocket [chemical binding]; other site 319224008646 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224008647 dimer interface [polypeptide binding]; other site 319224008648 putative CheW interface [polypeptide binding]; other site 319224008649 chaperone protein DnaJ; Provisional; Region: PRK10767 319224008650 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 319224008651 HSP70 interaction site [polypeptide binding]; other site 319224008652 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 319224008653 substrate binding site [polypeptide binding]; other site 319224008654 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 319224008655 Zn binding sites [ion binding]; other site 319224008656 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 319224008657 dimer interface [polypeptide binding]; other site 319224008658 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 319224008659 aromatic amino acid exporter; Provisional; Region: PRK11689 319224008660 EamA-like transporter family; Region: EamA; cl01037 319224008661 EamA-like transporter family; Region: EamA; cl01037 319224008662 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 319224008663 putative deacylase active site [active] 319224008664 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 319224008665 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 319224008666 putative catalytic cysteine [active] 319224008667 gamma-glutamyl kinase; Provisional; Region: PRK05429 319224008668 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 319224008669 nucleotide binding site [chemical binding]; other site 319224008670 homotetrameric interface [polypeptide binding]; other site 319224008671 putative phosphate binding site [ion binding]; other site 319224008672 putative allosteric binding site; other site 319224008673 PUA domain; Region: PUA; cl00607 319224008674 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 319224008675 Uncharacterized protein conserved in bacteria (DUF2131); Region: DUF2131; cl11547 319224008676 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 319224008677 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224008678 substrate binding pocket [chemical binding]; other site 319224008679 membrane-bound complex binding site; other site 319224008680 hinge residues; other site 319224008681 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 319224008682 Ligand Binding Site [chemical binding]; other site 319224008683 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 319224008684 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 319224008685 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 319224008686 NAD(P) binding site [chemical binding]; other site 319224008687 catalytic residues [active] 319224008688 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224008689 Helix-turn-helix domains; Region: HTH; cl00088 319224008690 TolB amino-terminal domain; Region: TolB_N; cl00639 319224008691 Type VIII secretion system (T8SS), CsgF protein; Region: CsgF; cl08082 319224008692 Curli assembly protein CsgE; Region: CsgE; cl08115 319224008693 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 319224008694 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 319224008695 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 319224008696 ATP binding site [chemical binding]; other site 319224008697 Mg2+ binding site [ion binding]; other site 319224008698 G-X-G motif; other site 319224008699 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 319224008700 FtsX-like permease family; Region: FtsX; cl15850 319224008701 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 319224008702 FtsX-like permease family; Region: FtsX; cl15850 319224008703 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 319224008704 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 319224008705 Walker A/P-loop; other site 319224008706 ATP binding site [chemical binding]; other site 319224008707 Q-loop/lid; other site 319224008708 ABC transporter signature motif; other site 319224008709 Walker B; other site 319224008710 D-loop; other site 319224008711 H-loop/switch region; other site 319224008712 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224008713 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 319224008714 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 319224008715 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 319224008716 active site 319224008717 substrate binding pocket [chemical binding]; other site 319224008718 dimer interface [polypeptide binding]; other site 319224008719 Protein of unknown function (DUF3144); Region: DUF3144; pfam11342 319224008720 FRG domain; Region: FRG; cl07460 319224008721 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 319224008722 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224008723 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 319224008724 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224008725 Coenzyme A binding pocket [chemical binding]; other site 319224008726 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 319224008727 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224008728 DNA-binding site [nucleotide binding]; DNA binding site 319224008729 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 319224008730 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224008731 homodimer interface [polypeptide binding]; other site 319224008732 catalytic residue [active] 319224008733 MAPEG family; Region: MAPEG; cl09190 319224008734 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 319224008735 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 319224008736 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 319224008737 CoenzymeA binding site [chemical binding]; other site 319224008738 subunit interaction site [polypeptide binding]; other site 319224008739 PHB binding site; other site 319224008740 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 319224008741 Lamin Tail Domain; Region: LTD; pfam00932 319224008742 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 319224008743 generic binding surface II; other site 319224008744 generic binding surface I; other site 319224008745 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 319224008746 putative catalytic site [active] 319224008747 putative metal binding site [ion binding]; other site 319224008748 putative phosphate binding site [ion binding]; other site 319224008749 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK10902 319224008750 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 319224008751 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224008752 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 319224008753 structural tetrad; other site 319224008754 SlyX; Region: SlyX; cl01090 319224008755 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 319224008756 active site 319224008757 catalytic residues [active] 319224008758 metal binding site [ion binding]; metal-binding site 319224008759 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 319224008760 TolB amino-terminal domain; Region: TolB_N; cl00639 319224008761 aminopeptidase N, Streptomyces lividans type; Region: pepN_strep_liv; TIGR02412 319224008762 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_3; cd09602 319224008763 Zn binding site [ion binding]; other site 319224008764 Cache domain; Region: Cache_1; pfam02743 319224008765 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 319224008766 dimerization interface [polypeptide binding]; other site 319224008767 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224008768 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224008769 dimer interface [polypeptide binding]; other site 319224008770 putative CheW interface [polypeptide binding]; other site 319224008771 PAS domain S-box; Region: sensory_box; TIGR00229 319224008772 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 319224008773 putative active site [active] 319224008774 heme pocket [chemical binding]; other site 319224008775 GAF domain; Region: GAF_2; pfam13185 319224008776 GAF domain; Region: GAF; cl15785 319224008777 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224008778 metal binding site [ion binding]; metal-binding site 319224008779 active site 319224008780 I-site; other site 319224008781 Protein of unknown function DUF72; Region: DUF72; cl00777 319224008782 Phosphate transporter family; Region: PHO4; cl00396 319224008783 Phosphate transporter family; Region: PHO4; cl00396 319224008784 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 319224008785 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 319224008786 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 319224008787 Carbon starvation protein CstA; Region: CstA; pfam02554 319224008788 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 319224008789 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 319224008790 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224008791 LrgB-like family; Region: LrgB; cl00596 319224008792 LrgA family; Region: LrgA; cl00608 319224008793 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008794 G4 box; other site 319224008795 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224008796 Helix-turn-helix domains; Region: HTH; cl00088 319224008797 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 319224008798 putative dimerization interface [polypeptide binding]; other site 319224008799 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 319224008800 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 319224008801 substrate binding pocket [chemical binding]; other site 319224008802 membrane-bound complex binding site; other site 319224008803 hinge residues; other site 319224008804 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 319224008805 dimer interface [polypeptide binding]; other site 319224008806 conserved gate region; other site 319224008807 putative PBP binding loops; other site 319224008808 ABC-ATPase subunit interface; other site 319224008809 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 319224008810 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 319224008811 Walker A/P-loop; other site 319224008812 ATP binding site [chemical binding]; other site 319224008813 Q-loop/lid; other site 319224008814 ABC transporter signature motif; other site 319224008815 Walker B; other site 319224008816 D-loop; other site 319224008817 H-loop/switch region; other site 319224008818 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; cl14632 319224008819 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 319224008820 dimer interface [polypeptide binding]; other site 319224008821 FMN binding site [chemical binding]; other site 319224008822 DNA-J related protein; Region: DNAJ_related; pfam12339 319224008823 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 319224008824 HSP70 interaction site [polypeptide binding]; other site 319224008825 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 319224008826 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 319224008827 catalytic residues [active] 319224008828 hinge region; other site 319224008829 alpha helical domain; other site 319224008830 GlyGly-CTERM domain; Region: GlyGly_CTERM; TIGR03501 319224008831 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224008832 Protein of unknown function (DUF2806); Region: DUF2806; cl12560 319224008833 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 319224008834 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 319224008835 ligand-binding site [chemical binding]; other site 319224008836 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 319224008837 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 319224008838 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 319224008839 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 319224008840 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 319224008841 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 319224008842 CysD dimerization site [polypeptide binding]; other site 319224008843 G1 box; other site 319224008844 putative GEF interaction site [polypeptide binding]; other site 319224008845 GTP/Mg2+ binding site [chemical binding]; other site 319224008846 Switch I region; other site 319224008847 G2 box; other site 319224008848 G3 box; other site 319224008849 Switch II region; other site 319224008850 G4 box; other site 319224008851 G5 box; other site 319224008852 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 319224008853 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 319224008854 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 319224008855 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 319224008856 Active Sites [active] 319224008857 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 319224008858 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 319224008859 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 319224008860 dimerization interface [polypeptide binding]; other site 319224008861 substrate binding site [chemical binding]; other site 319224008862 active site 319224008863 calcium binding site [ion binding]; other site 319224008864 D-alanyl-D-alanine endopeptidase; Provisional; Region: pbpG; PRK11669 319224008865 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224008866 Protein of unknown function (DUF2846); Region: DUF2846; pfam11008 319224008867 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 319224008868 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 319224008869 dimer interface [polypeptide binding]; other site 319224008870 putative anticodon binding site; other site 319224008871 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 319224008872 motif 1; other site 319224008873 active site 319224008874 motif 2; other site 319224008875 motif 3; other site 319224008876 peptide chain release factor 2; Validated; Region: prfB; PRK00578 319224008877 RF-1 domain; Region: RF-1; cl02875 319224008878 RF-1 domain; Region: RF-1; cl02875 319224008879 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 319224008880 putative NADPH-dependent glutamate synthase small subunit; Provisional; Region: PRK12814 319224008881 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224008882 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224008883 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 319224008884 4Fe-4S binding domain; Region: Fer4; cl02805 319224008885 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 319224008886 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 319224008887 [4Fe-4S] binding site [ion binding]; other site 319224008888 molybdopterin cofactor binding site; other site 319224008889 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 319224008890 molybdopterin cofactor binding site; other site 319224008891 Cache domain; Region: Cache_2; cl07034 319224008892 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 319224008893 dimerization interface [polypeptide binding]; other site 319224008894 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224008895 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224008896 dimer interface [polypeptide binding]; other site 319224008897 putative CheW interface [polypeptide binding]; other site 319224008898 Chromate transporter; Region: Chromate_transp; pfam02417 319224008899 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 319224008900 Chromate transporter; Region: Chromate_transp; pfam02417 319224008901 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 319224008902 23S rRNA methyluridine methyltransferase; Reviewed; Region: rumB; PRK03522 319224008903 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; cl16911 319224008904 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GlpA; COG0578 319224008905 Helix-turn-helix domains; Region: HTH; cl00088 319224008906 OsmC-like protein; Region: OsmC; cl00767 319224008907 Predicted ATPase [General function prediction only]; Region: COG3903 319224008908 Transglycosylase; Region: Transgly; cl07896 319224008909 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 319224008910 Active Sites [active] 319224008911 sulfite reductase subunit beta; Provisional; Region: PRK13504 319224008912 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 319224008913 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 319224008914 sulfite reductase [NADPH] flavoprotein, alpha-component; Region: cysJ; TIGR01931 319224008915 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224008916 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; cd06199 319224008917 FAD binding pocket [chemical binding]; other site 319224008918 FAD binding motif [chemical binding]; other site 319224008919 catalytic residues [active] 319224008920 NAD binding pocket [chemical binding]; other site 319224008921 phosphate binding motif [ion binding]; other site 319224008922 beta-alpha-beta structure motif; other site 319224008923 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 319224008924 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 319224008925 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224008926 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 319224008927 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 319224008928 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 319224008929 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224008930 Helix-turn-helix domains; Region: HTH; cl00088 319224008931 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 319224008932 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 319224008933 putative ribose interaction site [chemical binding]; other site 319224008934 putative ADP binding site [chemical binding]; other site 319224008935 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 319224008936 active site 319224008937 HIGH motif; other site 319224008938 nucleotide binding site [chemical binding]; other site 319224008939 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 319224008940 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 319224008941 putative acyl-acceptor binding pocket; other site 319224008942 potassium/proton antiporter; Reviewed; Region: PRK05326 319224008943 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 319224008944 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 319224008945 Transporter associated domain; Region: CorC_HlyC; cl08393 319224008946 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 319224008947 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 319224008948 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 319224008949 GAF domain; Region: GAF; cl15785 319224008950 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 319224008951 Walker A motif; other site 319224008952 ATP binding site [chemical binding]; other site 319224008953 Walker B motif; other site 319224008954 arginine finger; other site 319224008955 L,D-transpeptidase; Provisional; Region: PRK10260 319224008956 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224008957 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 319224008958 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_4; cd06231 319224008959 putative active site [active] 319224008960 Zn binding site [ion binding]; other site 319224008961 Predicted ATPase [General function prediction only]; Region: COG1485 319224008962 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224008963 Walker A/P-loop; other site 319224008964 ATP binding site [chemical binding]; other site 319224008965 Q-loop/lid; other site 319224008966 Walker B; other site 319224008967 D-loop; other site 319224008968 H-loop/switch region; other site 319224008969 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 319224008970 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 319224008971 active site 319224008972 phosphorylation site [posttranslational modification] 319224008973 intermolecular recognition site; other site 319224008974 dimerization interface [polypeptide binding]; other site 319224008975 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 319224008976 DNA binding site [nucleotide binding] 319224008977 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 319224008978 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 319224008979 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 319224008980 Ligand Binding Site [chemical binding]; other site 319224008981 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 319224008982 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 319224008983 dimer interface [polypeptide binding]; other site 319224008984 phosphorylation site [posttranslational modification] 319224008985 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 319224008986 ATP binding site [chemical binding]; other site 319224008987 Mg2+ binding site [ion binding]; other site 319224008988 G-X-G motif; other site 319224008989 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 319224008990 K+-transporting ATPase, c chain; Region: KdpC; cl00944 319224008991 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 319224008992 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224008993 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224008994 Potassium-transporting ATPase A subunit; Region: KdpA; cl00903 319224008995 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 319224008996 Helix-turn-helix domains; Region: HTH; cl00088 319224008997 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 319224008998 dimerization interface [polypeptide binding]; other site 319224008999 Domain of unknown function (DUF897); Region: DUF897; cl01312 319224009000 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 319224009001 GAF domain; Region: GAF; cl15785 319224009002 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009003 metal binding site [ion binding]; metal-binding site 319224009004 active site 319224009005 I-site; other site 319224009006 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 319224009007 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 319224009008 metal binding triad; other site 319224009009 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 319224009010 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 319224009011 metal binding triad; other site 319224009012 spermidine synthase; Provisional; Region: PRK03612 319224009013 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; cl16911 319224009014 Uncharacterized protein conserved in bacteria (DUF2170); Region: DUF2170; cl01551 319224009015 PspA/IM30 family; Region: PspA_IM30; pfam04012 319224009016 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 319224009017 Ion channel; Region: Ion_trans_2; cl11596 319224009018 Uncharacterized conserved protein [Function unknown]; Region: COG3025 319224009019 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 319224009020 putative active site [active] 319224009021 putative metal binding residues [ion binding]; other site 319224009022 signature motif; other site 319224009023 putative triphosphate binding site [ion binding]; other site 319224009024 Protein of unknown function DUF47; Region: PhoU_div; pfam01865 319224009025 Phosphate transporter family; Region: PHO4; cl00396 319224009026 Phosphate transporter family; Region: PHO4; cl00396 319224009027 Bacterial SH3 domain; Region: SH3_3; cl02551 319224009028 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 319224009029 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 319224009030 Proline dehydrogenase; Region: Pro_dh; cl03282 319224009031 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 319224009032 Glutamate binding site [chemical binding]; other site 319224009033 NAD binding site [chemical binding]; other site 319224009034 catalytic residues [active] 319224009035 Protein of unknown function, DUF599; Region: DUF599; cl01575 319224009036 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 319224009037 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 319224009038 putative active site [active] 319224009039 putative metal binding residues [ion binding]; other site 319224009040 signature motif; other site 319224009041 putative triphosphate binding site [ion binding]; other site 319224009042 dimer interface [polypeptide binding]; other site 319224009043 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11160 319224009044 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224009045 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009046 Walker A/P-loop; other site 319224009047 ATP binding site [chemical binding]; other site 319224009048 Q-loop/lid; other site 319224009049 ABC transporter signature motif; other site 319224009050 Walker B; other site 319224009051 D-loop; other site 319224009052 H-loop/switch region; other site 319224009053 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed; Region: PRK11174 319224009054 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224009055 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009056 Walker A/P-loop; other site 319224009057 ATP binding site [chemical binding]; other site 319224009058 Q-loop/lid; other site 319224009059 ABC transporter signature motif; other site 319224009060 Walker B; other site 319224009061 D-loop; other site 319224009062 H-loop/switch region; other site 319224009063 Protein of unknown function (DUF3626); Region: DUF3626; pfam12294 319224009064 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 319224009065 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 319224009066 ATP binding site [chemical binding]; other site 319224009067 Mg++ binding site [ion binding]; other site 319224009068 motif III; other site 319224009069 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 319224009070 nucleotide binding region [chemical binding]; other site 319224009071 ATP-binding site [chemical binding]; other site 319224009072 PAS domain; Region: PAS_9; pfam13426 319224009073 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 319224009074 putative active site [active] 319224009075 heme pocket [chemical binding]; other site 319224009076 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224009077 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224009078 dimer interface [polypeptide binding]; other site 319224009079 putative CheW interface [polypeptide binding]; other site 319224009080 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 319224009081 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 319224009082 ATP binding site [chemical binding]; other site 319224009083 Mg++ binding site [ion binding]; other site 319224009084 motif III; other site 319224009085 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 319224009086 nucleotide binding region [chemical binding]; other site 319224009087 ATP-binding site [chemical binding]; other site 319224009088 DbpA RNA binding domain; Region: DbpA; pfam03880 319224009089 Pirin-related protein [General function prediction only]; Region: COG1741 319224009090 Cupin domain; Region: Cupin_2; cl09118 319224009091 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 319224009092 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224009093 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 319224009094 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 319224009095 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009096 Walker A/P-loop; other site 319224009097 ATP binding site [chemical binding]; other site 319224009098 Q-loop/lid; other site 319224009099 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 319224009100 ABC transporter; Region: ABC_tran_2; pfam12848 319224009101 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 319224009102 Protein of unknown function (DUF2390); Region: DUF2390; cl02376 319224009103 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 319224009104 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 319224009105 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 319224009106 putative hydrolase; Provisional; Region: PRK10985 319224009107 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 319224009108 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009109 active site 319224009110 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 319224009111 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224009112 Coenzyme A binding pocket [chemical binding]; other site 319224009113 aminopeptidase B; Provisional; Region: PRK05015 319224009114 Peptidase; Region: DUF3663; pfam12404 319224009115 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 319224009116 interface (dimer of trimers) [polypeptide binding]; other site 319224009117 Substrate-binding/catalytic site; other site 319224009118 Zn-binding sites [ion binding]; other site 319224009119 Sugar fermentation stimulation protein; Region: SfsA; cl00647 319224009120 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 319224009121 tRNA synthetases class I (E and Q), catalytic domain; Region: tRNA-synt_1c; pfam00749 319224009122 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 319224009123 active site 319224009124 HIGH motif; other site 319224009125 nucleotide binding site [chemical binding]; other site 319224009126 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 319224009127 active site 319224009128 KMSKS motif; other site 319224009129 poly(A) polymerase; Region: pcnB; TIGR01942 319224009130 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 319224009131 active site 319224009132 NTP binding site [chemical binding]; other site 319224009133 metal binding triad [ion binding]; metal-binding site 319224009134 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 319224009135 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 319224009136 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 319224009137 catalytic center binding site [active] 319224009138 ATP binding site [chemical binding]; other site 319224009139 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 319224009140 oligomerization interface [polypeptide binding]; other site 319224009141 active site 319224009142 metal binding site [ion binding]; metal-binding site 319224009143 Pantoate-beta-alanine ligase; Region: PanC; cd00560 319224009144 pantoate--beta-alanine ligase; Region: panC; TIGR00018 319224009145 active site 319224009146 ATP-binding site [chemical binding]; other site 319224009147 pantoate-binding site; other site 319224009148 HXXH motif; other site 319224009149 Curlin associated repeat; Region: Curlin_rpt; pfam07012 319224009150 Curlin associated repeat; Region: Curlin_rpt; pfam07012 319224009151 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 319224009152 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 319224009153 major curlin subunit; Provisional; Region: csgA; PRK10051 319224009154 Curlin associated repeat; Region: Curlin_rpt; pfam07012 319224009155 curlin minor subunit CsgB; Provisional; Region: csgB; PRK10101 319224009156 Curlin associated repeat; Region: Curlin_rpt; pfam07012 319224009157 Curlin associated repeat; Region: Curlin_rpt; pfam07012 319224009158 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 319224009159 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 319224009160 DNA binding residues [nucleotide binding] 319224009161 dimerization interface [polypeptide binding]; other site 319224009162 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 319224009163 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 319224009164 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224009165 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 319224009166 L-serine binding site [chemical binding]; other site 319224009167 ACT domain interface; other site 319224009168 putative global regulator; Reviewed; Region: PRK09559 319224009169 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 319224009170 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 319224009171 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 319224009172 active site 319224009173 phosphorylation site [posttranslational modification] 319224009174 intermolecular recognition site; other site 319224009175 dimerization interface [polypeptide binding]; other site 319224009176 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 319224009177 Zn2+ binding site [ion binding]; other site 319224009178 Mg2+ binding site [ion binding]; other site 319224009179 PAS domain; Region: PAS_9; pfam13426 319224009180 PAS domain S-box; Region: sensory_box; TIGR00229 319224009181 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 319224009182 putative active site [active] 319224009183 heme pocket [chemical binding]; other site 319224009184 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 319224009185 PAS fold; Region: PAS_3; pfam08447 319224009186 putative active site [active] 319224009187 heme pocket [chemical binding]; other site 319224009188 PAS fold; Region: PAS_3; pfam08447 319224009189 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 319224009190 PAS domain S-box; Region: sensory_box; TIGR00229 319224009191 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 319224009192 putative active site [active] 319224009193 heme pocket [chemical binding]; other site 319224009194 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 319224009195 dimer interface [polypeptide binding]; other site 319224009196 phosphorylation site [posttranslational modification] 319224009197 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 319224009198 ATP binding site [chemical binding]; other site 319224009199 Mg2+ binding site [ion binding]; other site 319224009200 G-X-G motif; other site 319224009201 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009202 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 319224009203 active site 319224009204 phosphorylation site [posttranslational modification] 319224009205 intermolecular recognition site; other site 319224009206 dimerization interface [polypeptide binding]; other site 319224009207 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 319224009208 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009209 active site 319224009210 phosphorylation site [posttranslational modification] 319224009211 intermolecular recognition site; other site 319224009212 dimerization interface [polypeptide binding]; other site 319224009213 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 319224009214 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 319224009215 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 319224009216 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 319224009217 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 319224009218 Walker A/P-loop; other site 319224009219 ATP binding site [chemical binding]; other site 319224009220 Q-loop/lid; other site 319224009221 ABC transporter signature motif; other site 319224009222 Walker B; other site 319224009223 D-loop; other site 319224009224 H-loop/switch region; other site 319224009225 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 319224009226 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 319224009227 FtsX-like permease family; Region: FtsX; cl15850 319224009228 Hydroxyneurosporene synthase (CrtC); Region: CrtC; cl12101 319224009229 NapD protein; Region: NapD; cl01163 319224009230 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 319224009231 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 319224009232 [4Fe-4S] binding site [ion binding]; other site 319224009233 molybdopterin cofactor binding site; other site 319224009234 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 319224009235 molybdopterin cofactor binding site; other site 319224009236 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 319224009237 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 319224009238 4Fe-4S binding domain; Region: Fer4_5; pfam12801 319224009239 4Fe-4S binding domain; Region: Fer4_5; pfam12801 319224009240 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 319224009241 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224009242 Helix-turn-helix domains; Region: HTH; cl00088 319224009243 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 319224009244 putative dimerization interface [polypeptide binding]; other site 319224009245 elongation factor G; Reviewed; Region: PRK00007 319224009246 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 319224009247 G1 box; other site 319224009248 putative GEF interaction site [polypeptide binding]; other site 319224009249 GTP/Mg2+ binding site [chemical binding]; other site 319224009250 Switch I region; other site 319224009251 G2 box; other site 319224009252 G3 box; other site 319224009253 Switch II region; other site 319224009254 G4 box; other site 319224009255 G5 box; other site 319224009256 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 319224009257 Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily...; Region: EFG_like_IV; cl02789 319224009258 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 319224009259 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 319224009260 Acetyl-CoA carboxylase beta subunit [Lipid metabolism]; Region: AccD; COG0777 319224009261 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 319224009262 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 319224009263 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224009264 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 319224009265 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 319224009266 carboxyltransferase (CT) interaction site; other site 319224009267 biotinylation site [posttranslational modification]; other site 319224009268 LysR family transcriptional regulator; Provisional; Region: PRK14997 319224009269 Helix-turn-helix domains; Region: HTH; cl00088 319224009270 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 319224009271 putative effector binding pocket; other site 319224009272 dimerization interface [polypeptide binding]; other site 319224009273 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224009274 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cl00237 319224009275 putative substrate binding pocket [chemical binding]; other site 319224009276 AC domain interface; other site 319224009277 catalytic triad [active] 319224009278 AB domain interface; other site 319224009279 interchain disulfide; other site 319224009280 hypothetical protein; Provisional; Region: PRK04860 319224009281 SprT homologues; Region: SprT; cl01182 319224009282 DNA-specific endonuclease I; Provisional; Region: PRK15137 319224009283 Endonuclease I; Region: Endonuclease_1; cl01003 319224009284 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 319224009285 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 319224009286 glutathione synthetase; Provisional; Region: PRK05246 319224009287 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 319224009288 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224009289 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 319224009290 dimer interface [polypeptide binding]; other site 319224009291 Alkaline phosphatase homologues; Region: alkPPc; smart00098 319224009292 active site 319224009293 16S ribosomal RNA m2G1207 methyltransferase; Provisional; Region: rsmC; PRK09489 319224009294 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 319224009295 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 319224009296 S-adenosylmethionine binding site [chemical binding]; other site 319224009297 Protein of unknown function (DUF342); Region: DUF342; pfam03961 319224009298 protein structure with unknown function; Region: DUF4144; pfam13642 319224009299 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_2; cd06160 319224009300 active site 319224009301 putative substrate binding region [chemical binding]; other site 319224009302 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009303 metal binding site [ion binding]; metal-binding site 319224009304 active site 319224009305 I-site; other site 319224009306 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 319224009307 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 319224009308 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 319224009309 Walker A/P-loop; other site 319224009310 ATP binding site [chemical binding]; other site 319224009311 Q-loop/lid; other site 319224009312 ABC transporter signature motif; other site 319224009313 Walker B; other site 319224009314 D-loop; other site 319224009315 H-loop/switch region; other site 319224009316 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 319224009317 FtsX-like permease family; Region: FtsX; cl15850 319224009318 macrolide transporter subunit MacA; Provisional; Region: PRK11578 319224009319 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 319224009320 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 319224009321 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 319224009322 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 319224009323 THF binding site; other site 319224009324 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 319224009325 substrate binding site [chemical binding]; other site 319224009326 THF binding site; other site 319224009327 zinc-binding site [ion binding]; other site 319224009328 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224009329 Helix-turn-helix domains; Region: HTH; cl00088 319224009330 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 319224009331 putative dimerization interface [polypeptide binding]; other site 319224009332 HDOD domain; Region: HDOD; pfam08668 319224009333 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224009334 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 319224009335 N-terminal plug; other site 319224009336 ligand-binding site [chemical binding]; other site 319224009337 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 319224009338 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 319224009339 active site 319224009340 tetramer interface [polypeptide binding]; other site 319224009341 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 319224009342 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 319224009343 substrate binding site [chemical binding]; other site 319224009344 dimer interface [polypeptide binding]; other site 319224009345 ATP binding site [chemical binding]; other site 319224009346 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224009347 Protein of unknown function (DUF3103); Region: DUF3103; pfam11301 319224009348 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 319224009349 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 319224009350 active site 319224009351 PhoD-like phosphatase; Region: PhoD; pfam09423 319224009352 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 319224009353 putative active site [active] 319224009354 putative metal binding site [ion binding]; other site 319224009355 PhoD-like phosphatase; Region: PhoD; pfam09423 319224009356 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 319224009357 FOG: CBS domain [General function prediction only]; Region: COG0517 319224009358 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 319224009359 Domain of unknown function (DUF4274); Region: DUF4274; pfam14096 319224009360 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 319224009361 MatE; Region: MatE; cl10513 319224009362 MatE; Region: MatE; cl10513 319224009363 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 319224009364 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 319224009365 substrate binding pocket [chemical binding]; other site 319224009366 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 319224009367 Cupin superfamily (DUF985); Region: Cupin_5; cl01418 319224009368 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 319224009369 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 319224009370 N-terminal plug; other site 319224009371 ligand-binding site [chemical binding]; other site 319224009372 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224009373 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 319224009374 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 319224009375 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224009376 TIGR03549 family protein; Region: TIGR03549 319224009377 OsmC-like protein; Region: OsmC; cl00767 319224009378 bacteriocin biosynthesis docking scaffold, SagD family; Region: docking_ocin; cl09146 319224009379 Cache domain; Region: Cache_2; cl07034 319224009380 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 319224009381 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 319224009382 dimerization interface [polypeptide binding]; other site 319224009383 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224009384 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224009385 dimer interface [polypeptide binding]; other site 319224009386 putative CheW interface [polypeptide binding]; other site 319224009387 Ribosome recycling factor; Region: RRF_GI; pfam12614 319224009388 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 319224009389 Predicted ATP-binding protein involved in virulence [General function prediction only]; Region: COG3950 319224009390 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009391 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009392 Walker A motif; other site 319224009393 Walker A/P-loop; other site 319224009394 ATP binding site [chemical binding]; other site 319224009395 ATP binding site [chemical binding]; other site 319224009396 glycine dehydrogenase; Provisional; Region: PRK05367 319224009397 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 319224009398 tetramer interface [polypeptide binding]; other site 319224009399 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224009400 catalytic residue [active] 319224009401 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 319224009402 tetramer interface [polypeptide binding]; other site 319224009403 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224009404 catalytic residue [active] 319224009405 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 319224009406 lipoyl attachment site [posttranslational modification]; other site 319224009407 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 319224009408 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 319224009409 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224009410 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 319224009411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224009412 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 319224009413 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 319224009414 Cell division protein ZapA; Region: ZapA; cl01146 319224009415 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 319224009416 dihydromonapterin reductase; Provisional; Region: PRK06483 319224009417 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224009418 NAD(P) binding site [chemical binding]; other site 319224009419 active site 319224009420 Protein of unknown function, DUF393; Region: DUF393; cl01136 319224009421 malate dehydrogenase; Provisional; Region: PRK05086 319224009422 Glyoxysomal and mitochondrial malate dehydrogenases; Region: MDH_glyoxysomal_mitochondrial; cd01337 319224009423 NAD binding site [chemical binding]; other site 319224009424 dimerization interface [polypeptide binding]; other site 319224009425 Substrate binding site [chemical binding]; other site 319224009426 arginine repressor; Provisional; Region: PRK05066 319224009427 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 319224009428 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 319224009429 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 319224009430 NADH(P)-binding; Region: NAD_binding_10; pfam13460 319224009431 NAD binding site [chemical binding]; other site 319224009432 substrate binding site [chemical binding]; other site 319224009433 putative active site [active] 319224009434 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224009435 Helix-turn-helix domains; Region: HTH; cl00088 319224009436 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 319224009437 putative effector binding pocket; other site 319224009438 dimerization interface [polypeptide binding]; other site 319224009439 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 319224009440 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 319224009441 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 319224009442 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 319224009443 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 319224009444 Walker A/P-loop; other site 319224009445 ATP binding site [chemical binding]; other site 319224009446 Q-loop/lid; other site 319224009447 ABC transporter signature motif; other site 319224009448 Walker B; other site 319224009449 D-loop; other site 319224009450 H-loop/switch region; other site 319224009451 TOBE domain; Region: TOBE_2; cl01440 319224009452 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 319224009453 dimer interface [polypeptide binding]; other site 319224009454 conserved gate region; other site 319224009455 putative PBP binding loops; other site 319224009456 ABC-ATPase subunit interface; other site 319224009457 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 319224009458 dimer interface [polypeptide binding]; other site 319224009459 conserved gate region; other site 319224009460 putative PBP binding loops; other site 319224009461 ABC-ATPase subunit interface; other site 319224009462 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 319224009463 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 319224009464 putative glutathione S-transferase; Provisional; Region: PRK10357 319224009465 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 319224009466 putative C-terminal domain interface [polypeptide binding]; other site 319224009467 putative GSH binding site (G-site) [chemical binding]; other site 319224009468 putative dimer interface [polypeptide binding]; other site 319224009469 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 319224009470 substrate binding pocket (H-site) [chemical binding]; other site 319224009471 N-terminal domain interface [polypeptide binding]; other site 319224009472 ferredoxin-NADP reductase; Provisional; Region: PRK10926 319224009473 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 319224009474 FAD binding pocket [chemical binding]; other site 319224009475 FAD binding motif [chemical binding]; other site 319224009476 phosphate binding motif [ion binding]; other site 319224009477 beta-alpha-beta structure motif; other site 319224009478 NAD binding pocket [chemical binding]; other site 319224009479 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cd07040 319224009480 catalytic core [active] 319224009481 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 319224009482 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 319224009483 active site 319224009484 FMN binding site [chemical binding]; other site 319224009485 substrate binding site [chemical binding]; other site 319224009486 3Fe-4S cluster binding site [ion binding]; other site 319224009487 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224009488 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 319224009489 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009490 Walker A/P-loop; other site 319224009491 ATP binding site [chemical binding]; other site 319224009492 Q-loop/lid; other site 319224009493 ABC transporter signature motif; other site 319224009494 Walker B; other site 319224009495 D-loop; other site 319224009496 H-loop/switch region; other site 319224009497 NeuB family; Region: NeuB; cl00496 319224009498 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 319224009499 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 319224009500 Nitrogen regulatory protein P-II; Region: P-II; cl00412 319224009501 Nitrogen regulatory protein P-II; Region: P-II; smart00938 319224009502 Isochorismatase family; Region: Isochorismatase; pfam00857 319224009503 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 319224009504 catalytic triad [active] 319224009505 dimer interface [polypeptide binding]; other site 319224009506 conserved cis-peptide bond; other site 319224009507 Protein of unknown function (DUF2999); Region: DUF2999; pfam11212 319224009508 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 319224009509 heme-binding site [chemical binding]; other site 319224009510 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009511 metal binding site [ion binding]; metal-binding site 319224009512 active site 319224009513 I-site; other site 319224009514 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 319224009515 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 319224009516 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 319224009517 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 319224009518 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 319224009519 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 319224009520 DsbD alpha interface [polypeptide binding]; other site 319224009521 catalytic residues [active] 319224009522 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 319224009523 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 319224009524 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224009525 galactokinase; Provisional; Region: PRK05101 319224009526 Galactokinase galactose-binding signature; Region: GalKase_gal_bdg; pfam10509 319224009527 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 319224009528 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 319224009529 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 319224009530 active site 319224009531 catalytic residues [active] 319224009532 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 319224009533 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 319224009534 NAD(P) binding site [chemical binding]; other site 319224009535 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224009536 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224009537 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 319224009538 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 319224009539 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224009540 active site 319224009541 ATP binding site [chemical binding]; other site 319224009542 substrate binding site [chemical binding]; other site 319224009543 serine/threonine kinase US3; Provisional; Region: PHA03209 319224009544 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 319224009545 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 319224009546 N-acetyl-D-glucosamine binding site [chemical binding]; other site 319224009547 catalytic residue [active] 319224009548 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224009549 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224009550 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 319224009551 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009552 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009553 Family description; Region: UvrD_C_2; cl15862 319224009554 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224009555 Coenzyme A binding pocket [chemical binding]; other site 319224009556 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 319224009557 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 319224009558 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 319224009559 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224009560 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 319224009561 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224009562 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 319224009563 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 319224009564 polycystin cation channel protein; Region: PCC; TIGR00864 319224009565 polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is...; Region: PKD; cd00146 319224009566 Protein of unknown function (DUF1566); Region: DUF1566; pfam07603 319224009567 sensory histidine kinase AtoS; Provisional; Region: PRK11360 319224009568 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009569 metal binding site [ion binding]; metal-binding site 319224009570 active site 319224009571 I-site; other site 319224009572 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009573 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 319224009574 active site 319224009575 phosphorylation site [posttranslational modification] 319224009576 intermolecular recognition site; other site 319224009577 dimerization interface [polypeptide binding]; other site 319224009578 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 319224009579 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 319224009580 Stringent starvation protein B; Region: SspB; cl01120 319224009581 stringent starvation protein A; Provisional; Region: sspA; PRK09481 319224009582 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 319224009583 C-terminal domain interface [polypeptide binding]; other site 319224009584 putative GSH binding site (G-site) [chemical binding]; other site 319224009585 dimer interface [polypeptide binding]; other site 319224009586 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 319224009587 dimer interface [polypeptide binding]; other site 319224009588 N-terminal domain interface [polypeptide binding]; other site 319224009589 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 319224009590 cytochrome b; Provisional; Region: CYTB; MTH00145 319224009591 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 319224009592 Qi binding site; other site 319224009593 intrachain domain interface; other site 319224009594 interchain domain interface [polypeptide binding]; other site 319224009595 heme bH binding site [chemical binding]; other site 319224009596 heme bL binding site [chemical binding]; other site 319224009597 Qo binding site; other site 319224009598 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; cd00290 319224009599 interchain domain interface [polypeptide binding]; other site 319224009600 intrachain domain interface; other site 319224009601 Qi binding site; other site 319224009602 Qo binding site; other site 319224009603 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 319224009604 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 319224009605 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 319224009606 [2Fe-2S] cluster binding site [ion binding]; other site 319224009607 HflC protein; Region: hflC; TIGR01932 319224009608 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 319224009609 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 319224009610 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 319224009611 HflK protein; Region: hflK; TIGR01933 319224009612 GTPase HflX; Provisional; Region: PRK11058 319224009613 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 319224009614 HflX GTPase family; Region: HflX; cd01878 319224009615 G1 box; other site 319224009616 GTP/Mg2+ binding site [chemical binding]; other site 319224009617 Switch I region; other site 319224009618 G2 box; other site 319224009619 G3 box; other site 319224009620 Switch II region; other site 319224009621 G4 box; other site 319224009622 G5 box; other site 319224009623 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 319224009624 Sm1 motif; other site 319224009625 intra - hexamer interaction site; other site 319224009626 inter - hexamer interaction site [polypeptide binding]; other site 319224009627 nucleotide binding pocket [chemical binding]; other site 319224009628 Sm2 motif; other site 319224009629 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009630 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 319224009631 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 319224009632 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 319224009633 ATP binding site [chemical binding]; other site 319224009634 Mg2+ binding site [ion binding]; other site 319224009635 G-X-G motif; other site 319224009636 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 319224009637 ATP binding site [chemical binding]; other site 319224009638 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 319224009639 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 319224009640 AMIN domain; Region: AMIN; pfam11741 319224009641 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 319224009642 active site 319224009643 metal binding site [ion binding]; metal-binding site 319224009644 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 319224009645 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 319224009646 putative carbohydrate kinase; Provisional; Region: PRK10565 319224009647 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 319224009648 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 319224009649 putative substrate binding site [chemical binding]; other site 319224009650 putative ATP binding site [chemical binding]; other site 319224009651 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 319224009652 dinuclear metal binding motif [ion binding]; other site 319224009653 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 319224009654 catalytic site [active] 319224009655 putative active site [active] 319224009656 putative substrate binding site [chemical binding]; other site 319224009657 dimer interface [polypeptide binding]; other site 319224009658 GTPase RsgA; Reviewed; Region: PRK12288 319224009659 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 319224009660 RNA binding site [nucleotide binding]; other site 319224009661 homodimer interface [polypeptide binding]; other site 319224009662 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 319224009663 GTPase/Zn-binding domain interface [polypeptide binding]; other site 319224009664 GTP/Mg2+ binding site [chemical binding]; other site 319224009665 G4 box; other site 319224009666 G5 box; other site 319224009667 G1 box; other site 319224009668 Switch I region; other site 319224009669 G2 box; other site 319224009670 G3 box; other site 319224009671 Switch II region; other site 319224009672 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 319224009673 EamA-like transporter family; Region: EamA; cl01037 319224009674 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 319224009675 putative mechanosensitive channel protein; Provisional; Region: PRK10929 319224009676 Mechanosensitive ion channel inner membrane domain 1; Region: MscS_TM; pfam12794 319224009677 Mechanosensitive ion channel; Region: MS_channel; pfam00924 319224009678 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 319224009679 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 319224009680 active site 319224009681 catalytic site [active] 319224009682 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 319224009683 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 319224009684 PAS fold; Region: PAS_3; pfam08447 319224009685 putative active site [active] 319224009686 heme pocket [chemical binding]; other site 319224009687 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224009688 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224009689 dimer interface [polypeptide binding]; other site 319224009690 putative CheW interface [polypeptide binding]; other site 319224009691 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 319224009692 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; cl16911 319224009693 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...; Region: metallo-dependent_hydrolases; cl00281 319224009694 Protein kinase domain; Region: Pkinase; pfam00069 319224009695 Catalytic domain of Protein Kinases; Region: PKc; cd00180 319224009696 active site 319224009697 ATP binding site [chemical binding]; other site 319224009698 substrate binding site [chemical binding]; other site 319224009699 activation loop (A-loop); other site 319224009700 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 319224009701 active site 319224009702 Cache domain; Region: Cache_1; pfam02743 319224009703 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 319224009704 PAS fold; Region: PAS_4; pfam08448 319224009705 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 319224009706 putative active site [active] 319224009707 heme pocket [chemical binding]; other site 319224009708 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 319224009709 PAS fold; Region: PAS_3; pfam08447 319224009710 putative active site [active] 319224009711 heme pocket [chemical binding]; other site 319224009712 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 319224009713 dimer interface [polypeptide binding]; other site 319224009714 phosphorylation site [posttranslational modification] 319224009715 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 319224009716 ATP binding site [chemical binding]; other site 319224009717 Mg2+ binding site [ion binding]; other site 319224009718 G-X-G motif; other site 319224009719 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 319224009720 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009721 active site 319224009722 phosphorylation site [posttranslational modification] 319224009723 intermolecular recognition site; other site 319224009724 dimerization interface [polypeptide binding]; other site 319224009725 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009726 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 319224009727 active site 319224009728 phosphorylation site [posttranslational modification] 319224009729 intermolecular recognition site; other site 319224009730 dimerization interface [polypeptide binding]; other site 319224009731 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 319224009732 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 319224009733 putative active site [active] 319224009734 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009735 ATP-dependent helicase HepA; Validated; Region: PRK04914 319224009736 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 319224009737 ATP binding site [chemical binding]; other site 319224009738 putative Mg++ binding site [ion binding]; other site 319224009739 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 319224009740 nucleotide binding region [chemical binding]; other site 319224009741 ATP-binding site [chemical binding]; other site 319224009742 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 319224009743 enoyl-CoA hydratase; Provisional; Region: PRK07509 319224009744 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 319224009745 substrate binding site [chemical binding]; other site 319224009746 oxyanion hole (OAH) forming residues; other site 319224009747 trimer interface [polypeptide binding]; other site 319224009748 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009749 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 319224009750 active site 319224009751 phosphorylation site [posttranslational modification] 319224009752 intermolecular recognition site; other site 319224009753 dimerization interface [polypeptide binding]; other site 319224009754 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 319224009755 PAS domain; Region: PAS_9; pfam13426 319224009756 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009757 metal binding site [ion binding]; metal-binding site 319224009758 active site 319224009759 I-site; other site 319224009760 RNase E inhibitor protein; Provisional; Region: PRK11191 319224009761 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 319224009762 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional; Region: PRK15018 319224009763 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 319224009764 putative acyl-acceptor binding pocket; other site 319224009765 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 319224009766 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 319224009767 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 319224009768 putative ligand binding site [chemical binding]; other site 319224009769 Formate--tetrahydrofolate ligase; Region: FTHFS; pfam01268 319224009770 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 319224009771 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 319224009772 active site 2 [active] 319224009773 active site 1 [active] 319224009774 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 319224009775 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 319224009776 S-adenosylmethionine binding site [chemical binding]; other site 319224009777 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3735 319224009778 TraB family; Region: TraB; cl12050 319224009779 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 319224009780 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 319224009781 FOG: CBS domain [General function prediction only]; Region: COG0517 319224009782 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009783 metal binding site [ion binding]; metal-binding site 319224009784 active site 319224009785 I-site; other site 319224009786 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 319224009787 Protein of unknown function (DUF4240); Region: DUF4240; pfam14024 319224009788 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009789 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 319224009790 active site 319224009791 phosphorylation site [posttranslational modification] 319224009792 intermolecular recognition site; other site 319224009793 dimerization interface [polypeptide binding]; other site 319224009794 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 319224009795 Response regulator receiver domain; Region: Response_reg; pfam00072 319224009796 active site 319224009797 phosphorylation site [posttranslational modification] 319224009798 intermolecular recognition site; other site 319224009799 dimerization interface [polypeptide binding]; other site 319224009800 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 319224009801 IHF dimer interface [polypeptide binding]; other site 319224009802 IHF - DNA interface [nucleotide binding]; other site 319224009803 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 319224009804 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 319224009805 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224009806 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 319224009807 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 319224009808 active site 319224009809 phosphorylation site [posttranslational modification] 319224009810 intermolecular recognition site; other site 319224009811 dimerization interface [polypeptide binding]; other site 319224009812 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009813 metal binding site [ion binding]; metal-binding site 319224009814 active site 319224009815 I-site; other site 319224009816 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 319224009817 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 319224009818 active site 319224009819 phosphorylation site [posttranslational modification] 319224009820 intermolecular recognition site; other site 319224009821 CHASE domain; Region: CHASE; cl01369 319224009822 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 319224009823 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 319224009824 putative active site [active] 319224009825 heme pocket [chemical binding]; other site 319224009826 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 319224009827 dimer interface [polypeptide binding]; other site 319224009828 phosphorylation site [posttranslational modification] 319224009829 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 319224009830 ATP binding site [chemical binding]; other site 319224009831 Mg2+ binding site [ion binding]; other site 319224009832 G-X-G motif; other site 319224009833 conserved hypothetical protein; Region: QEGLA; TIGR02421 319224009834 Domain of unknown function (DUF1704); Region: DUF1704; cl06858 319224009835 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 319224009836 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 319224009837 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 319224009838 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 319224009839 Beta-Casp domain; Region: Beta-Casp; cl12567 319224009840 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 319224009841 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 319224009842 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224009843 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 319224009844 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224009845 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 319224009846 Coenzyme A binding pocket [chemical binding]; other site 319224009847 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 319224009848 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 319224009849 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 319224009850 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 319224009851 Protein export membrane protein; Region: SecD_SecF; cl14618 319224009852 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 319224009853 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224009854 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 319224009855 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 319224009856 Protein of unknown function (DUF3012); Region: DUF3012; pfam11216 319224009857 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 319224009858 RF-1 domain; Region: RF-1; cl02875 319224009859 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 319224009860 active site 319224009861 trimer interface [polypeptide binding]; other site 319224009862 dimer interface [polypeptide binding]; other site 319224009863 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224009864 NAD(P) binding site [chemical binding]; other site 319224009865 active site 319224009866 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 319224009867 FMN reductase; Validated; Region: fre; PRK08051 319224009868 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 319224009869 FAD binding pocket [chemical binding]; other site 319224009870 FAD binding motif [chemical binding]; other site 319224009871 phosphate binding motif [ion binding]; other site 319224009872 beta-alpha-beta structure motif; other site 319224009873 NAD binding pocket [chemical binding]; other site 319224009874 Flavin Reductases; Region: FlaRed; cl00801 319224009875 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 319224009876 DNA binding site [nucleotide binding] 319224009877 ABC-2 type transporter; Region: ABC2_membrane; cl11417 319224009878 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 319224009879 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 319224009880 Walker A/P-loop; other site 319224009881 ATP binding site [chemical binding]; other site 319224009882 Q-loop/lid; other site 319224009883 ABC transporter signature motif; other site 319224009884 Walker B; other site 319224009885 D-loop; other site 319224009886 H-loop/switch region; other site 319224009887 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 319224009888 NosL; Region: NosL; cl01769 319224009889 formate-dependent nitrite reductase complex subunit NrfG; Provisional; Region: PRK10370 319224009890 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 319224009891 binding surface 319224009892 TPR motif; other site 319224009893 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 319224009894 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 319224009895 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224009896 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 319224009897 active site residue [active] 319224009898 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 319224009899 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 319224009900 Cytochrome C biogenesis protein; Region: CcmH; cl01179 319224009901 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 319224009902 catalytic residues [active] 319224009903 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 319224009904 metal binding site [ion binding]; metal-binding site 319224009905 TfoX N-terminal domain; Region: TfoX_N; cl01167 319224009906 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 319224009907 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 319224009908 Nitronate monooxygenase; Region: NMO; pfam03060 319224009909 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 319224009910 FMN binding site [chemical binding]; other site 319224009911 substrate binding site [chemical binding]; other site 319224009912 putative catalytic residue [active] 319224009913 UbiA prenyltransferase family; Region: UbiA; cl00337 319224009914 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 319224009915 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009916 Family description; Region: UvrD_C_2; cl15862 319224009917 ERCC4-like helicases [DNA replication, recombination, and repair]; Region: MPH1; COG1111 319224009918 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 319224009919 ATP binding site [chemical binding]; other site 319224009920 putative Mg++ binding site [ion binding]; other site 319224009921 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 319224009922 nucleotide binding region [chemical binding]; other site 319224009923 ATP-binding site [chemical binding]; other site 319224009924 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; cl16911 319224009925 Methyltransferase domain; Region: Methyltransf_31; pfam13847 319224009926 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_21; cd04680 319224009927 nudix motif; other site 319224009928 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 319224009929 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224009930 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 319224009931 NMT1-like family; Region: NMT1_2; cl15260 319224009932 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 319224009933 DctM-like transporters; Region: DctM; pfam06808 319224009934 Domain of unknown function (DUF1850); Region: DUF1850; cl01950 319224009935 Transcriptional regulators [Transcription]; Region: FadR; COG2186 319224009936 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224009937 DNA-binding site [nucleotide binding]; DNA binding site 319224009938 FCD domain; Region: FCD; cl11656 319224009939 outer membrane porin, OprD family; Region: OprD; pfam03573 319224009940 Tannase and feruloyl esterase; Region: Tannase; pfam07519 319224009941 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 319224009942 chaperone protein DnaJ; Provisional; Region: PRK14298 319224009943 PAS fold; Region: PAS_3; pfam08447 319224009944 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 319224009945 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009946 metal binding site [ion binding]; metal-binding site 319224009947 active site 319224009948 I-site; other site 319224009949 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 319224009950 thioredoxin 2; Provisional; Region: PRK10996 319224009951 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 319224009952 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 319224009953 catalytic residues [active] 319224009954 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 319224009955 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 319224009956 transmembrane helices; other site 319224009957 putative MFS family transporter protein; Provisional; Region: PRK03633 319224009958 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 319224009959 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 319224009960 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 319224009961 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 319224009962 Predicted permease; Region: DUF318; pfam03773 319224009963 Predicted permease; Region: DUF318; pfam03773 319224009964 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 319224009965 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 319224009966 DNA binding residues [nucleotide binding] 319224009967 dimer interface [polypeptide binding]; other site 319224009968 metal binding site [ion binding]; metal-binding site 319224009969 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 319224009970 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 319224009971 purine monophosphate binding site [chemical binding]; other site 319224009972 dimer interface [polypeptide binding]; other site 319224009973 putative catalytic residues [active] 319224009974 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 319224009975 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 319224009976 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 319224009977 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 319224009978 ATP-grasp domain; Region: ATP-grasp_4; cl03087 319224009979 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 319224009980 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs; Region: 11beta-HSD1_like_SDR_c; cd05332 319224009981 short chain dehydrogenase; Provisional; Region: PRK06181 319224009982 NADP binding site [chemical binding]; other site 319224009983 homodimer interface [polypeptide binding]; other site 319224009984 substrate binding site [chemical binding]; other site 319224009985 active site 319224009986 PAS fold; Region: PAS_4; pfam08448 319224009987 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 319224009988 putative active site [active] 319224009989 heme pocket [chemical binding]; other site 319224009990 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224009991 metal binding site [ion binding]; metal-binding site 319224009992 active site 319224009993 I-site; other site 319224009994 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 319224009995 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 319224009996 substrate binding site [chemical binding]; other site 319224009997 active site 319224009998 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 319224009999 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 319224010000 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 319224010001 substrate binding site [chemical binding]; other site 319224010002 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 319224010003 substrate binding site [chemical binding]; other site 319224010004 ligand binding site [chemical binding]; other site 319224010005 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 319224010006 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 319224010007 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 319224010008 motif II; other site 319224010009 Protein of unknown function (DUF2845); Region: DUF2845; pfam11006 319224010010 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 319224010011 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 319224010012 active site 319224010013 Zn binding site [ion binding]; other site 319224010014 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 319224010015 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 319224010016 active site 319224010017 nucleophile elbow; other site 319224010018 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 319224010019 Surface antigen; Region: Bac_surface_Ag; cl03097 319224010020 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 319224010021 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224010022 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 319224010023 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 319224010024 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 319224010025 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 319224010026 E3 interaction surface; other site 319224010027 lipoyl attachment site [posttranslational modification]; other site 319224010028 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 319224010029 E3 interaction surface; other site 319224010030 lipoyl attachment site [posttranslational modification]; other site 319224010031 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 319224010032 E3 interaction surface; other site 319224010033 lipoyl attachment site [posttranslational modification]; other site 319224010034 e3 binding domain; Region: E3_binding; pfam02817 319224010035 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 319224010036 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 319224010037 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 319224010038 dimer interface [polypeptide binding]; other site 319224010039 TPP-binding site [chemical binding]; other site 319224010040 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 319224010041 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224010042 DNA-binding site [nucleotide binding]; DNA binding site 319224010043 FCD domain; Region: FCD; cl11656 319224010044 CobD/Cbib protein; Region: CobD_Cbib; cl00561 319224010045 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 319224010046 amidase catalytic site [active] 319224010047 Zn binding residues [ion binding]; other site 319224010048 substrate binding site [chemical binding]; other site 319224010049 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 319224010050 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 319224010051 dimerization interface [polypeptide binding]; other site 319224010052 active site 319224010053 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 319224010054 Pilin (bacterial filament); Region: Pilin; pfam00114 319224010055 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 319224010056 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 319224010057 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 319224010058 Walker A motif; other site 319224010059 ATP binding site [chemical binding]; other site 319224010060 Walker B motif; other site 319224010061 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 319224010062 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 319224010063 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 319224010064 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 319224010065 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 319224010066 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 319224010067 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 319224010068 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 319224010069 CoA-binding site [chemical binding]; other site 319224010070 ATP-binding [chemical binding]; other site 319224010071 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 319224010072 Domain of unknown function (DUF329); Region: DUF329; cl01144 319224010073 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 319224010074 active site 319224010075 8-oxo-dGMP binding site [chemical binding]; other site 319224010076 nudix motif; other site 319224010077 metal binding site [ion binding]; metal-binding site 319224010078 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 319224010079 catalytic residues [active] 319224010080 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 319224010081 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 319224010082 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 319224010083 ATP binding site [chemical binding]; other site 319224010084 Mg++ binding site [ion binding]; other site 319224010085 motif III; other site 319224010086 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 319224010087 nucleotide binding region [chemical binding]; other site 319224010088 ATP-binding site [chemical binding]; other site 319224010089 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 319224010090 catalytic residues [active] 319224010091 transcription termination factor Rho; Provisional; Region: rho; PRK09376 319224010092 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 319224010093 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 319224010094 RNA binding site [nucleotide binding]; other site 319224010095 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 319224010096 multimer interface [polypeptide binding]; other site 319224010097 Walker A motif; other site 319224010098 ATP binding site [chemical binding]; other site 319224010099 Walker B motif; other site 319224010100 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224010101 Helix-turn-helix domains; Region: HTH; cl00088 319224010102 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 319224010103 putative effector binding pocket; other site 319224010104 dimerization interface [polypeptide binding]; other site 319224010105 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 319224010106 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 319224010107 putative NAD(P) binding site [chemical binding]; other site 319224010108 dimer interface [polypeptide binding]; other site 319224010109 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 319224010110 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 319224010111 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 319224010112 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 319224010113 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224010114 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 319224010115 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 319224010116 Iron-sulfur protein interface; other site 319224010117 proximal heme binding site [chemical binding]; other site 319224010118 distal heme binding site [chemical binding]; other site 319224010119 dimer interface [polypeptide binding]; other site 319224010120 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13554 319224010121 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 319224010122 Iron-sulfur protein interface; other site 319224010123 proximal heme binding site [chemical binding]; other site 319224010124 distal heme binding site [chemical binding]; other site 319224010125 dimer interface [polypeptide binding]; other site 319224010126 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 319224010127 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; cl16911 319224010128 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 319224010129 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 319224010130 FMN binding site [chemical binding]; other site 319224010131 active site 319224010132 catalytic residues [active] 319224010133 substrate binding site [chemical binding]; other site 319224010134 Helix-turn-helix domains; Region: HTH; cl00088 319224010135 PilZ domain; Region: PilZ; cl01260 319224010136 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 319224010137 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 319224010138 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 319224010139 ligand binding site [chemical binding]; other site 319224010140 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 319224010141 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 319224010142 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 319224010143 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 319224010144 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 319224010145 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 319224010146 DNA binding residues [nucleotide binding] 319224010147 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 319224010148 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 319224010149 Flagellar protein FliS; Region: FliS; cl00654 319224010150 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 319224010151 flagellar capping protein; Reviewed; Region: fliD; PRK08032 319224010152 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 319224010153 flagellin; Provisional; Region: PRK12802 319224010154 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 319224010155 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 319224010156 flagellin; Provisional; Region: PRK12802 319224010157 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 319224010158 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 319224010159 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 319224010160 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 319224010161 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07191 319224010162 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224010163 Rod binding protein; Region: Rod-binding; cl01626 319224010164 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 319224010165 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 319224010166 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 319224010167 Flagellar L-ring protein; Region: FlgH; cl00905 319224010168 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 319224010169 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224010170 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224010171 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 319224010172 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224010173 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224010174 flagellar hook protein FlgE; Validated; Region: flgE; PRK06803 319224010175 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224010176 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 319224010177 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224010178 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 319224010179 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 319224010180 FlgD Ig-like domain; Region: FlgD_ig; cl15790 319224010181 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK06802 319224010182 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 319224010183 Flagella basal body rod protein; Region: Flg_bb_rod; cl16922 319224010184 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK12685 319224010185 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 319224010186 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 319224010187 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 319224010188 FlgN protein; Region: FlgN; cl09176 319224010189 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 319224010190 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 319224010191 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224010192 Walker A motif; other site 319224010193 ATP binding site [chemical binding]; other site 319224010194 Walker B motif; other site 319224010195 flagellar assembly protein H; Provisional; Region: fliH; PRK13386 319224010196 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 319224010197 Flagellar assembly protein FliH; Region: FliH; pfam02108 319224010198 flagellar motor switch protein G; Reviewed; Region: fliG; PRK07194 319224010199 FliG C-terminal domain; Region: FliG_C; pfam01706 319224010200 flagellar MS-ring protein; Reviewed; Region: fliF; PRK07193 319224010201 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 319224010202 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 319224010203 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 319224010204 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 319224010205 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 319224010206 Walker A motif; other site 319224010207 ATP binding site [chemical binding]; other site 319224010208 Walker B motif; other site 319224010209 arginine finger; other site 319224010210 Helix-turn-helix domains; Region: HTH; cl00088 319224010211 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 319224010212 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 319224010213 FliP family; Region: FliP; cl00593 319224010214 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 319224010215 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 319224010216 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 319224010217 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 319224010218 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 319224010219 FHIPEP family; Region: FHIPEP; pfam00771 319224010220 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224010221 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 319224010222 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 319224010223 Nucleoside recognition; Region: Gate; cl00486 319224010224 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 319224010225 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 319224010226 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 319224010227 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 319224010228 ligand binding site [chemical binding]; other site 319224010229 flexible hinge region; other site 319224010230 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 319224010231 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 319224010232 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224010233 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 319224010234 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 319224010235 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 319224010236 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 319224010237 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 319224010238 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 319224010239 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224010240 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 319224010241 EamA-like transporter family; Region: EamA; cl01037 319224010242 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 319224010243 EamA-like transporter family; Region: EamA; cl01037 319224010244 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 319224010245 Helix-turn-helix domains; Region: HTH; cl00088 319224010246 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 319224010247 substrate binding pocket [chemical binding]; other site 319224010248 dimerization interface [polypeptide binding]; other site 319224010249 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 319224010250 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 319224010251 active site 319224010252 nucleophile elbow; other site 319224010253 transcriptional regulator; Provisional; Region: PRK10632 319224010254 Helix-turn-helix domains; Region: HTH; cl00088 319224010255 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 319224010256 putative effector binding pocket; other site 319224010257 dimerization interface [polypeptide binding]; other site 319224010258 enterobactin receptor protein; Provisional; Region: PRK13483 319224010259 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 319224010260 N-terminal plug; other site 319224010261 ligand-binding site [chemical binding]; other site 319224010262 Domain of unknown function (DUF4424); Region: DUF4424; pfam14415 319224010263 Predicted nuclease (RecB family) [General function prediction only]; Region: COG2251 319224010264 coproporphyrinogen III oxidase; Provisional; Region: PRK08629 319224010265 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 319224010266 FeS/SAM binding site; other site 319224010267 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 319224010268 Membrane transport protein; Region: Mem_trans; cl09117 319224010269 RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA...; Region: RRM; cd00590 319224010270 RNA/DNA binding site [nucleotide binding]; other site 319224010271 RRM dimerization site [polypeptide binding]; other site 319224010272 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 319224010273 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; cl16911 319224010274 tRNA (uracil-5-)-methyltransferase; Region: trmA_only; TIGR02143 319224010275 Transposase, Mutator family; Region: Transposase_mut; pfam00872 319224010276 Protein of unknown function (DUF3296); Region: DUF3296; pfam11726 319224010277 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 319224010278 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 319224010279 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 319224010280 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 319224010281 active site 319224010282 DNA binding site [nucleotide binding] 319224010283 Int/Topo IB signature motif; other site 319224010284 Protein of unknown function (DUF2787); Region: DUF2787; pfam10980 319224010285 YagB/YeeU/YfjZ family; Region: YagB_YeeU_YfjZ; pfam06154 319224010286 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 319224010287 MPN+ (JAMM) motif; other site 319224010288 Zinc-binding site [ion binding]; other site 319224010289 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 319224010290 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 319224010291 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 319224010292 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 319224010293 ATP binding site [chemical binding]; other site 319224010294 putative Mg++ binding site [ion binding]; other site 319224010295 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 319224010296 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 319224010297 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224010298 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224010299 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 319224010300 ADP-ribose binding site [chemical binding]; other site 319224010301 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 319224010302 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 319224010303 NADP binding site [chemical binding]; other site 319224010304 dimer interface [polypeptide binding]; other site 319224010305 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224010306 Transcriptional regulator [Transcription]; Region: LysR; COG0583 319224010307 Helix-turn-helix domains; Region: HTH; cl00088 319224010308 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 319224010309 dimerization interface [polypeptide binding]; other site 319224010310 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 319224010311 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cd08168 319224010312 heme-binding residues [chemical binding]; other site 319224010313 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 319224010314 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224010315 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 319224010316 non-specific DNA binding site [nucleotide binding]; other site 319224010317 salt bridge; other site 319224010318 sequence-specific DNA binding site [nucleotide binding]; other site 319224010319 integrase; Provisional; Region: PRK09692 319224010320 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 319224010321 active site 319224010322 Int/Topo IB signature motif; other site 319224010323 DNA-binding transcriptional repressor FabR; Provisional; Region: PRK11202 319224010324 Helix-turn-helix domains; Region: HTH; cl00088 319224010325 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 319224010326 Fatty acid desaturase; Region: FA_desaturase; pfam00487 319224010327 Di-iron ligands [ion binding]; other site 319224010328 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 319224010329 selenophosphate synthetase; Provisional; Region: PRK00943 319224010330 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 319224010331 dimerization interface [polypeptide binding]; other site 319224010332 putative ATP binding site [chemical binding]; other site 319224010333 Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB; Region: RHOD_YbbB; cd01520 319224010334 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 319224010335 active site residue [active] 319224010336 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 319224010337 putative substrate translocation pore; other site 319224010338 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 319224010339 putative acyl-acceptor binding pocket; other site 319224010340 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 319224010341 Helix-turn-helix domains; Region: HTH; cl00088 319224010342 WHG domain; Region: WHG; pfam13305 319224010343 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 319224010344 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224010345 Coenzyme A binding pocket [chemical binding]; other site 319224010346 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 319224010347 active site 319224010348 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 319224010349 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 319224010350 dimer interface [polypeptide binding]; other site 319224010351 ADP-ribose binding site [chemical binding]; other site 319224010352 active site 319224010353 nudix motif; other site 319224010354 metal binding site [ion binding]; metal-binding site 319224010355 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; cl00065 319224010356 Cadherin repeat-like domain; Region: CA_like; cl15786 319224010357 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 319224010358 Ca2+ binding site [ion binding]; other site 319224010359 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 319224010360 Cadherin repeat-like domain; Region: CA_like; cl15786 319224010361 Ca2+ binding site [ion binding]; other site 319224010362 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; cl01155 319224010363 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 319224010364 Phage Tail Collar Domain; Region: Collar; pfam07484 319224010365 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 319224010366 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 319224010367 Cupin domain; Region: Cupin_2; cl09118 319224010368 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 319224010369 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 319224010370 motif II; other site 319224010371 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 319224010372 Type II secretion system (T2SS), protein M; Region: T2SM; cl01222 319224010373 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 319224010374 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 319224010375 GspL periplasmic domain; Region: GspL_C; cl14909 319224010376 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 319224010377 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224010378 type II secretion system protein J; Region: gspJ; TIGR01711 319224010379 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 319224010380 type II secretion system protein I; Region: gspI; TIGR01707 319224010381 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 319224010382 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 319224010383 Type II transport protein GspH; Region: GspH; pfam12019 319224010384 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 319224010385 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 319224010386 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 319224010387 type II secretion system protein F; Region: GspF; TIGR02120 319224010388 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 319224010389 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 319224010390 type II secretion system protein E; Region: type_II_gspE; TIGR02533 319224010391 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 319224010392 Walker A motif; other site 319224010393 ATP binding site [chemical binding]; other site 319224010394 Walker B motif; other site 319224010395 type II secretion system protein D; Region: type_II_gspD; TIGR02517 319224010396 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 319224010397 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 319224010398 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 319224010399 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 319224010400 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 319224010401 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 319224010402 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 319224010403 RNA binding surface [nucleotide binding]; other site 319224010404 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 319224010405 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 319224010406 dimerization interface [polypeptide binding]; other site 319224010407 domain crossover interface; other site 319224010408 redox-dependent activation switch; other site 319224010409 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 319224010410 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 319224010411 active site 319224010412 substrate-binding site [chemical binding]; other site 319224010413 metal-binding site [ion binding] 319224010414 ATP binding site [chemical binding]; other site 319224010415 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 319224010416 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 319224010417 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 319224010418 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; cl15774 319224010419 Divergent AAA domain; Region: AAA_4; pfam04326 319224010420 HupE / UreJ protein; Region: HupE_UreJ; cl01011 319224010421 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 319224010422 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 319224010423 motif II; other site 319224010424 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 319224010425 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 319224010426 active site 319224010427 Int/Topo IB signature motif; other site 319224010428 GAF domain; Region: GAF; cl15785 319224010429 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 319224010430 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 319224010431 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 319224010432 diaminopimelate decarboxylase; Region: lysA; TIGR01048 319224010433 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 319224010434 active site 319224010435 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 319224010436 substrate binding site [chemical binding]; other site 319224010437 catalytic residues [active] 319224010438 dimer interface [polypeptide binding]; other site 319224010439 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 319224010440 putative iron binding site [ion binding]; other site 319224010441 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 319224010442 adenylate cyclase; Provisional; Region: cyaA; PRK09450 319224010443 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 319224010444 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 319224010445 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 319224010446 domain interfaces; other site 319224010447 active site 319224010448 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 319224010449 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 319224010450 active site 319224010451 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 319224010452 hemY protein; Region: hemY_coli; TIGR00540 319224010453 HemY protein N-terminus; Region: HemY_N; pfam07219 319224010454 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 319224010455 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 319224010456 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 319224010457 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 319224010458 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 319224010459 ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two...; Region: ABCC_bacteriocin_exporters; cd03245 319224010460 Walker A/P-loop; other site 319224010461 ATP binding site [chemical binding]; other site 319224010462 Q-loop/lid; other site 319224010463 ABC transporter signature motif; other site 319224010464 Walker B; other site 319224010465 D-loop; other site 319224010466 H-loop/switch region; other site 319224010467 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 319224010468 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 319224010469 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 319224010470 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 319224010471 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 319224010472 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 319224010473 ligand binding site [chemical binding]; other site 319224010474 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 319224010475 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 319224010476 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 319224010477 dimerization interface [polypeptide binding]; other site 319224010478 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224010479 metal binding site [ion binding]; metal-binding site 319224010480 active site 319224010481 I-site; other site 319224010482 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 319224010483 GAF domain; Region: GAF_2; pfam13185 319224010484 GAF domain; Region: GAF; cl15785 319224010485 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 319224010486 GAF domain; Region: GAF_2; pfam13185 319224010487 GAF domain; Region: GAF; cl15785 319224010488 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224010489 metal binding site [ion binding]; metal-binding site 319224010490 active site 319224010491 I-site; other site 319224010492 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 319224010493 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 319224010494 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224010495 Family description; Region: UvrD_C_2; cl15862 319224010496 Membrane fusogenic activity; Region: BMFP; cl01115 319224010497 NnrS protein; Region: NnrS; cl01258 319224010498 Cytochrome c552; Region: Cytochrom_C552; pfam02335 319224010499 Inner membrane protein CreD; Region: CreD; cl01844 319224010500 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 319224010501 Tim44-like domain; Region: Tim44; cl09208 319224010502 Domain of unknown function (DUF4303); Region: DUF4303; pfam14136 319224010503 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 319224010504 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 319224010505 homodimer interface [polypeptide binding]; other site 319224010506 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224010507 catalytic residue [active] 319224010508 threonine dehydratase; Reviewed; Region: PRK09224 319224010509 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 319224010510 tetramer interface [polypeptide binding]; other site 319224010511 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224010512 catalytic residue [active] 319224010513 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 319224010514 putative Ile/Val binding site [chemical binding]; other site 319224010515 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 319224010516 putative Ile/Val binding site [chemical binding]; other site 319224010517 Dehydratase family; Region: ILVD_EDD; cl00340 319224010518 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 319224010519 acetolactate synthase 2 catalytic subunit; Reviewed; Region: PRK08978 319224010520 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 319224010521 PYR/PP interface [polypeptide binding]; other site 319224010522 dimer interface [polypeptide binding]; other site 319224010523 TPP binding site [chemical binding]; other site 319224010524 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 319224010525 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 319224010526 TPP-binding site [chemical binding]; other site 319224010527 dimer interface [polypeptide binding]; other site 319224010528 ketol-acid reductoisomerase; Validated; Region: PRK05225 319224010529 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224010530 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 319224010531 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 319224010532 Helix-turn-helix domains; Region: HTH; cl00088 319224010533 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 319224010534 The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic bindin; Region: PBP2_IlvY; cd08430 319224010535 putative dimerization interface [polypeptide binding]; other site 319224010536 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 319224010537 Domain of unknown function DUF21; Region: DUF21; pfam01595 319224010538 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 319224010539 Transporter associated domain; Region: CorC_HlyC; cl08393 319224010540 Flagellin N-methylase; Region: FliB; cl00497 319224010541 Hef nuclease; Provisional; Region: PRK13766 319224010542 ERCC4 domain; Region: ERCC4; cl10594 319224010543 dUMP phosphatase; Provisional; Region: PRK09449 319224010544 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 319224010545 motif II; other site 319224010546 transcriptional regulator; Provisional; Region: PRK10632 319224010547 Helix-turn-helix domains; Region: HTH; cl00088 319224010548 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 319224010549 putative effector binding pocket; other site 319224010550 dimerization interface [polypeptide binding]; other site 319224010551 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 319224010552 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 319224010553 non-specific DNA binding site [nucleotide binding]; other site 319224010554 salt bridge; other site 319224010555 sequence-specific DNA binding site [nucleotide binding]; other site 319224010556 Fic family protein [Function unknown]; Region: COG3177 319224010557 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 319224010558 Fic/DOC family; Region: Fic; cl00960 319224010559 Helix-turn-helix domains; Region: HTH; cl00088 319224010560 putative DNA binding site [nucleotide binding]; other site 319224010561 putative Zn2+ binding site [ion binding]; other site 319224010562 Sulfotransferase family; Region: Sulfotransfer_3; cl14559 319224010563 Phosphotransferase enzyme family; Region: APH; pfam01636 319224010564 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224010565 substrate binding site [chemical binding]; other site 319224010566 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 319224010567 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 319224010568 active site 319224010569 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 319224010570 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 319224010571 catalytic site [active] 319224010572 G-X2-G-X-G-K; other site 319224010573 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 319224010574 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 319224010575 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 319224010576 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 319224010577 synthetase active site [active] 319224010578 NTP binding site [chemical binding]; other site 319224010579 metal binding site [ion binding]; metal-binding site 319224010580 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 319224010581 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 319224010582 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 319224010583 homotrimer interaction site [polypeptide binding]; other site 319224010584 putative active site [active] 319224010585 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 319224010586 AMP-binding enzyme; Region: AMP-binding; cl15778 319224010587 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 319224010588 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 319224010589 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 319224010590 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 319224010591 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 319224010592 N-terminal plug; other site 319224010593 ligand-binding site [chemical binding]; other site 319224010594 Domain of unknown function (DUF1963); Region: DUF1963; cl01600 319224010595 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 319224010596 E-class dimer interface [polypeptide binding]; other site 319224010597 P-class dimer interface [polypeptide binding]; other site 319224010598 active site 319224010599 Cu2+ binding site [ion binding]; other site 319224010600 Zn2+ binding site [ion binding]; other site 319224010601 Mg chelatase-related protein; Region: TIGR00368 319224010602 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 319224010603 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 319224010604 Walker A motif; other site 319224010605 ATP binding site [chemical binding]; other site 319224010606 Walker B motif; other site 319224010607 arginine finger; other site 319224010608 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 319224010609 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 319224010610 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 319224010611 putative acyl-acceptor binding pocket; other site 319224010612 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 319224010613 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 319224010614 putative acyl-acceptor binding pocket; other site 319224010615 Protein of unknown function (DUF523); Region: DUF523; cl00733 319224010616 Transcriptional regulators [Transcription]; Region: GntR; COG1802 319224010617 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 319224010618 DNA-binding site [nucleotide binding]; DNA binding site 319224010619 FCD domain; Region: FCD; cl11656 319224010620 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 319224010621 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 319224010622 tetramer interface [polypeptide binding]; other site 319224010623 active site 319224010624 Mg2+/Mn2+ binding site [ion binding]; other site 319224010625 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 319224010626 dimer interface [polypeptide binding]; other site 319224010627 Citrate synthase; Region: Citrate_synt; pfam00285 319224010628 active site 319224010629 citrylCoA binding site [chemical binding]; other site 319224010630 oxalacetate/citrate binding site [chemical binding]; other site 319224010631 coenzyme A binding site [chemical binding]; other site 319224010632 catalytic triad [active] 319224010633 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 319224010634 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 319224010635 substrate binding site [chemical binding]; other site 319224010636 ligand binding site [chemical binding]; other site 319224010637 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 319224010638 substrate binding site [chemical binding]; other site 319224010639 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 319224010640 PrpF protein; Region: PrpF; pfam04303 319224010641 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 319224010642 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 319224010643 PAS fold; Region: PAS_3; pfam08447 319224010644 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 319224010645 PAS domain; Region: PAS_9; pfam13426 319224010646 putative active site [active] 319224010647 heme pocket [chemical binding]; other site 319224010648 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224010649 metal binding site [ion binding]; metal-binding site 319224010650 active site 319224010651 I-site; other site 319224010652 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 319224010653 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 319224010654 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 319224010655 homodimer interface [polypeptide binding]; other site 319224010656 substrate-cofactor binding pocket; other site 319224010657 catalytic residue [active] 319224010658 Modulator of Rho-dependent transcription termination (ROF); Region: ROF; cl09210 319224010659 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 319224010660 homotrimer interaction site [polypeptide binding]; other site 319224010661 putative active site [active] 319224010662 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 319224010663 Protein of unknown function (DUF1107); Region: DUF1107; pfam06526 319224010664 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 319224010665 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 319224010666 catalytic residues [active] 319224010667 hinge region; other site 319224010668 alpha helical domain; other site 319224010669 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224010670 active site 319224010671 ATP binding site [chemical binding]; other site 319224010672 Protein of unknown function (DUF3630); Region: DUF3630; pfam12305 319224010673 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 319224010674 ribonuclease E; Reviewed; Region: rne; PRK10811 319224010675 DsrE/DsrF-like family; Region: DrsE; cl00672 319224010676 Nitrous oxide-stimulated promoter; Region: YgbA_NO; cl08119 319224010677 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 319224010678 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 319224010679 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 319224010680 putative ligand binding residues [chemical binding]; other site 319224010681 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 319224010682 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 319224010683 Walker A/P-loop; other site 319224010684 ATP binding site [chemical binding]; other site 319224010685 Q-loop/lid; other site 319224010686 ABC transporter signature motif; other site 319224010687 Walker B; other site 319224010688 D-loop; other site 319224010689 H-loop/switch region; other site 319224010690 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 319224010691 ABC-ATPase subunit interface; other site 319224010692 dimer interface [polypeptide binding]; other site 319224010693 putative PBP binding regions; other site 319224010694 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 319224010695 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 319224010696 ABC-ATPase subunit interface; other site 319224010697 dimer interface [polypeptide binding]; other site 319224010698 putative PBP binding regions; other site 319224010699 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224010700 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 319224010701 N-terminal plug; other site 319224010702 ligand-binding site [chemical binding]; other site 319224010703 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 319224010704 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a...; Region: ABCC_MRP_Like; cd03228 319224010705 Walker A/P-loop; other site 319224010706 ATP binding site [chemical binding]; other site 319224010707 Q-loop/lid; other site 319224010708 ABC transporter signature motif; other site 319224010709 Walker B; other site 319224010710 D-loop; other site 319224010711 H-loop/switch region; other site 319224010712 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 319224010713 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224010714 Walker A/P-loop; other site 319224010715 ATP binding site [chemical binding]; other site 319224010716 Q-loop/lid; other site 319224010717 ABC transporter signature motif; other site 319224010718 Walker B; other site 319224010719 D-loop; other site 319224010720 H-loop/switch region; other site 319224010721 OpgC protein; Region: OpgC_C; cl00792 319224010722 Acyltransferase family; Region: Acyl_transf_3; pfam01757 319224010723 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 319224010724 Protein of unknown function (DUF2618); Region: DUF2618; pfam10940 319224010725 ornithine decarboxylase; Provisional; Region: PRK13578 319224010726 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 319224010727 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 319224010728 homodimer interface [polypeptide binding]; other site 319224010729 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224010730 catalytic residue [active] 319224010731 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 319224010732 putrescine transporter; Provisional; Region: potE; PRK10655 319224010733 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 319224010734 trimer interface [polypeptide binding]; other site 319224010735 eyelet of channel; other site 319224010736 hypothetical protein; Provisional; Region: PRK01254 319224010737 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 319224010738 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 319224010739 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 319224010740 MAPEG family; Region: MAPEG; cl09190 319224010741 Uncharacterized conserved protein [Function unknown]; Region: COG2966 319224010742 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 319224010743 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 319224010744 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 319224010745 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 319224010746 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 319224010747 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 319224010748 conserved cys residue [active] 319224010749 Helix-turn-helix domains; Region: HTH; cl00088 319224010750 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 319224010751 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 319224010752 Putative lipoprotein [General function prediction only]; Region: LppC; COG3107 319224010753 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 319224010754 putative ligand binding site [chemical binding]; other site 319224010755 Restriction endonuclease; Region: Mrr_cat; cl00516 319224010756 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 319224010757 dimer interface [polypeptide binding]; other site 319224010758 active site 319224010759 BON domain; Region: BON; cl02771 319224010760 BON domain; Region: BON; cl02771 319224010761 EamA-like transporter family; Region: EamA; cl01037 319224010762 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 319224010763 EamA-like transporter family; Region: EamA; cl01037 319224010764 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 319224010765 Helix-turn-helix domains; Region: HTH; cl00088 319224010766 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 319224010767 dimerization interface [polypeptide binding]; other site 319224010768 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 319224010769 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 319224010770 active site 319224010771 HIGH motif; other site 319224010772 dimer interface [polypeptide binding]; other site 319224010773 KMSKS motif; other site 319224010774 phosphoglycolate phosphatase; Provisional; Region: PRK13222 319224010775 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 319224010776 motif II; other site 319224010777 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 319224010778 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 319224010779 substrate binding site [chemical binding]; other site 319224010780 hexamer interface [polypeptide binding]; other site 319224010781 metal binding site [ion binding]; metal-binding site 319224010782 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 319224010783 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; cl16911 319224010784 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224010785 AAA domain; Region: AAA_22; pfam13401 319224010786 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 319224010787 active site 319224010788 dimer interface [polypeptide binding]; other site 319224010789 metal binding site [ion binding]; metal-binding site 319224010790 shikimate kinase; Reviewed; Region: aroK; PRK00131 319224010791 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 319224010792 ADP binding site [chemical binding]; other site 319224010793 magnesium binding site [ion binding]; other site 319224010794 putative shikimate binding site; other site 319224010795 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 319224010796 Secretin and TonB N terminus short domain; Region: STN; cl06624 319224010797 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 319224010798 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 319224010799 Pilus assembly protein, PilP; Region: PilP; pfam04351 319224010800 Pilus assembly protein, PilO; Region: PilO; cl01234 319224010801 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 319224010802 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 319224010803 Cell division protein FtsA; Region: FtsA; cl11496 319224010804 Competence protein A; Region: Competence_A; pfam11104 319224010805 Cell division protein FtsA; Region: FtsA; cl11496 319224010806 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 319224010807 Transglycosylase; Region: Transgly; cl07896 319224010808 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 319224010809 argininosuccinate lyase; Provisional; Region: PRK04833 319224010810 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 319224010811 active sites [active] 319224010812 tetramer interface [polypeptide binding]; other site 319224010813 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 319224010814 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 319224010815 ANP binding site [chemical binding]; other site 319224010816 Substrate Binding Site II [chemical binding]; other site 319224010817 Substrate Binding Site I [chemical binding]; other site 319224010818 ornithine carbamoyltransferase; Provisional; Region: PRK14805 319224010819 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 319224010820 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224010821 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 319224010822 nucleotide binding site [chemical binding]; other site 319224010823 substrate binding site [chemical binding]; other site 319224010824 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 319224010825 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224010826 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224010827 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 319224010828 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 319224010829 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 319224010830 competence damage-inducible protein A; Provisional; Region: PRK00549 319224010831 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 319224010832 putative MPT binding site; other site 319224010833 Competence-damaged protein; Region: CinA; cl00666 319224010834 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 319224010835 catalytic residues [active] 319224010836 Cytochrome C biogenesis protein; Region: CcmH; cl01179 319224010837 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 319224010838 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 319224010839 catalytic residues [active] 319224010840 central insert; other site 319224010841 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 319224010842 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 319224010843 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 319224010844 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 319224010845 binding surface 319224010846 TPR motif; other site 319224010847 Cytochrome c; Region: Cytochrom_C; cl11414 319224010848 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 319224010849 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 319224010850 Walker A/P-loop; other site 319224010851 ATP binding site [chemical binding]; other site 319224010852 Q-loop/lid; other site 319224010853 ABC transporter signature motif; other site 319224010854 Walker B; other site 319224010855 D-loop; other site 319224010856 H-loop/switch region; other site 319224010857 CcmB protein; Region: CcmB; cl01016 319224010858 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 319224010859 Heme exporter protein D (CcmD); Region: CcmD; cl11475 319224010860 CcmE; Region: CcmE; cl00994 319224010861 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 319224010862 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 319224010863 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 319224010864 alphaNTD homodimer interface [polypeptide binding]; other site 319224010865 alphaNTD - beta interaction site [polypeptide binding]; other site 319224010866 alphaNTD - beta' interaction site [polypeptide binding]; other site 319224010867 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 319224010868 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 319224010869 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 319224010870 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 319224010871 RNA binding surface [nucleotide binding]; other site 319224010872 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 319224010873 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 319224010874 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 319224010875 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 319224010876 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 319224010877 SecY translocase; Region: SecY; pfam00344 319224010878 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 319224010879 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 319224010880 23S rRNA binding site [nucleotide binding]; other site 319224010881 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 319224010882 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 319224010883 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 319224010884 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 319224010885 5S rRNA interface [nucleotide binding]; other site 319224010886 L5 interface [polypeptide binding]; other site 319224010887 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 319224010888 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 319224010889 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 319224010890 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 319224010891 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 319224010892 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 319224010893 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 319224010894 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 319224010895 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 319224010896 KOW motif; Region: KOW; cl00354 319224010897 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 319224010898 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 319224010899 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 319224010900 23S rRNA interface [nucleotide binding]; other site 319224010901 putative translocon interaction site; other site 319224010902 signal recognition particle (SRP54) interaction site; other site 319224010903 L23 interface [polypeptide binding]; other site 319224010904 trigger factor interaction site; other site 319224010905 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 319224010906 23S rRNA interface [nucleotide binding]; other site 319224010907 5S rRNA interface [nucleotide binding]; other site 319224010908 putative antibiotic binding site [chemical binding]; other site 319224010909 L25 interface [polypeptide binding]; other site 319224010910 L27 interface [polypeptide binding]; other site 319224010911 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 319224010912 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 319224010913 G-X-X-G motif; other site 319224010914 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 319224010915 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 319224010916 putative translocon binding site; other site 319224010917 protein-rRNA interface [nucleotide binding]; other site 319224010918 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 319224010919 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 319224010920 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 319224010921 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 319224010922 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 319224010923 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 319224010924 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 319224010925 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 319224010926 elongation factor Tu; Reviewed; Region: PRK00049 319224010927 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 319224010928 G1 box; other site 319224010929 GEF interaction site [polypeptide binding]; other site 319224010930 GTP/Mg2+ binding site [chemical binding]; other site 319224010931 Switch I region; other site 319224010932 G2 box; other site 319224010933 G3 box; other site 319224010934 Switch II region; other site 319224010935 G4 box; other site 319224010936 G5 box; other site 319224010937 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 319224010938 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 319224010939 Antibiotic Binding Site [chemical binding]; other site 319224010940 elongation factor G; Reviewed; Region: PRK00007 319224010941 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 319224010942 G1 box; other site 319224010943 putative GEF interaction site [polypeptide binding]; other site 319224010944 GTP/Mg2+ binding site [chemical binding]; other site 319224010945 Switch I region; other site 319224010946 G2 box; other site 319224010947 G3 box; other site 319224010948 Switch II region; other site 319224010949 G4 box; other site 319224010950 G5 box; other site 319224010951 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 319224010952 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 319224010953 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 319224010954 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 319224010955 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 319224010956 S17 interaction site [polypeptide binding]; other site 319224010957 S8 interaction site; other site 319224010958 16S rRNA interaction site [nucleotide binding]; other site 319224010959 streptomycin interaction site [chemical binding]; other site 319224010960 23S rRNA interaction site [nucleotide binding]; other site 319224010961 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 319224010962 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 319224010963 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 319224010964 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 319224010965 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 319224010966 DNA-directed RNA polymerase, beta'' subunit; Region: rpoC2_cyan; TIGR02388 319224010967 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 319224010968 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 319224010969 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 319224010970 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 319224010971 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 319224010972 DNA binding site [nucleotide binding] 319224010973 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 319224010974 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 319224010975 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 319224010976 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 319224010977 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 319224010978 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 319224010979 RPB11 interaction site [polypeptide binding]; other site 319224010980 RPB12 interaction site [polypeptide binding]; other site 319224010981 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 319224010982 RPB3 interaction site [polypeptide binding]; other site 319224010983 RPB1 interaction site [polypeptide binding]; other site 319224010984 RPB11 interaction site [polypeptide binding]; other site 319224010985 RPB10 interaction site [polypeptide binding]; other site 319224010986 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 319224010987 core dimer interface [polypeptide binding]; other site 319224010988 peripheral dimer interface [polypeptide binding]; other site 319224010989 L10 interface [polypeptide binding]; other site 319224010990 L11 interface [polypeptide binding]; other site 319224010991 putative EF-Tu interaction site [polypeptide binding]; other site 319224010992 putative EF-G interaction site [polypeptide binding]; other site 319224010993 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 319224010994 23S rRNA interface [nucleotide binding]; other site 319224010995 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 319224010996 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 319224010997 mRNA/rRNA interface [nucleotide binding]; other site 319224010998 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 319224010999 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 319224011000 23S rRNA interface [nucleotide binding]; other site 319224011001 L7/L12 interface [polypeptide binding]; other site 319224011002 putative thiostrepton binding site; other site 319224011003 L25 interface [polypeptide binding]; other site 319224011004 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 319224011005 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 319224011006 putative homodimer interface [polypeptide binding]; other site 319224011007 KOW motif; Region: KOW; cl00354 319224011008 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 319224011009 elongation factor Tu; Reviewed; Region: PRK00049 319224011010 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 319224011011 G1 box; other site 319224011012 GEF interaction site [polypeptide binding]; other site 319224011013 GTP/Mg2+ binding site [chemical binding]; other site 319224011014 Switch I region; other site 319224011015 G2 box; other site 319224011016 G3 box; other site 319224011017 Switch II region; other site 319224011018 G4 box; other site 319224011019 G5 box; other site 319224011020 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 319224011021 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 319224011022 Antibiotic Binding Site [chemical binding]; other site 319224011023 pantothenate kinase; Provisional; Region: PRK05439 319224011024 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 319224011025 ATP-binding site [chemical binding]; other site 319224011026 CoA-binding site [chemical binding]; other site 319224011027 Mg2+-binding site [ion binding]; other site 319224011028 Helix-turn-helix domains; Region: HTH; cl00088 319224011029 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 319224011030 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 319224011031 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 319224011032 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 319224011033 FAD binding domain; Region: FAD_binding_4; pfam01565 319224011034 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 319224011035 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 319224011036 B1 nucleotide binding pocket [chemical binding]; other site 319224011037 B2 nucleotide binding pocket [chemical binding]; other site 319224011038 CAS motifs; other site 319224011039 active site 319224011040 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 319224011041 aromatic amino acid transport protein; Region: araaP; TIGR00837 319224011042 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 319224011043 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 319224011044 putative acyl-acceptor binding pocket; other site 319224011045 LexA repressor; Validated; Region: PRK00215 319224011046 Helix-turn-helix domains; Region: HTH; cl00088 319224011047 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 319224011048 Catalytic site [active] 319224011049 Cell division inhibitor SulA; Region: SulA; cl01880 319224011050 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 319224011051 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 319224011052 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224011053 Cytochrome c; Region: Cytochrom_C; cl11414 319224011054 Cytochrome c; Region: Cytochrom_C; cl11414 319224011055 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 319224011056 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 319224011057 Subunit I/III interface [polypeptide binding]; other site 319224011058 D-pathway; other site 319224011059 Subunit I/VIIc interface [polypeptide binding]; other site 319224011060 Subunit I/IV interface [polypeptide binding]; other site 319224011061 Subunit I/II interface [polypeptide binding]; other site 319224011062 Low-spin heme (heme a) binding site [chemical binding]; other site 319224011063 Subunit I/VIIa interface [polypeptide binding]; other site 319224011064 Subunit I/VIa interface [polypeptide binding]; other site 319224011065 Dimer interface; other site 319224011066 Putative water exit pathway; other site 319224011067 Binuclear center (heme a3/CuB) [ion binding]; other site 319224011068 K-pathway; other site 319224011069 Subunit I/Vb interface [polypeptide binding]; other site 319224011070 Putative proton exit pathway; other site 319224011071 Subunit I/VIb interface; other site 319224011072 Subunit I/VIc interface [polypeptide binding]; other site 319224011073 Electron transfer pathway; other site 319224011074 Subunit I/VIIIb interface [polypeptide binding]; other site 319224011075 Subunit I/VIIb interface [polypeptide binding]; other site 319224011076 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 319224011077 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 319224011078 Subunit III/VIIa interface [polypeptide binding]; other site 319224011079 Phospholipid binding site [chemical binding]; other site 319224011080 Subunit I/III interface [polypeptide binding]; other site 319224011081 Subunit III/VIb interface [polypeptide binding]; other site 319224011082 Subunit III/VIa interface; other site 319224011083 Subunit III/Vb interface [polypeptide binding]; other site 319224011084 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 319224011085 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 319224011086 UbiA prenyltransferase family; Region: UbiA; cl00337 319224011087 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 319224011088 Cu(I) binding site [ion binding]; other site 319224011089 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 319224011090 putative active site [active] 319224011091 putative metal binding site [ion binding]; other site 319224011092 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 319224011093 MatE; Region: MatE; cl10513 319224011094 MatE; Region: MatE; cl10513 319224011095 RES domain; Region: RES; cl02411 319224011096 Fe/S biogenesis protein NfuA; Provisional; Region: PRK11190 319224011097 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 319224011098 NifU-like domain; Region: NifU; cl00484 319224011099 FMN-binding domain; Region: FMN_bind; cl01081 319224011100 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 319224011101 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224011102 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224011103 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 319224011104 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224011105 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 319224011106 dimer interface [polypeptide binding]; other site 319224011107 phosphorylation site [posttranslational modification] 319224011108 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 319224011109 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224011110 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 319224011111 active site 319224011112 phosphorylation site [posttranslational modification] 319224011113 intermolecular recognition site; other site 319224011114 dimerization interface [polypeptide binding]; other site 319224011115 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 319224011116 DNA binding site [nucleotide binding] 319224011117 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 319224011118 dimerization interface [polypeptide binding]; other site 319224011119 DNA binding residues [nucleotide binding] 319224011120 DNA utilization protein GntX; Provisional; Region: PRK11595 319224011121 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 319224011122 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 319224011123 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 319224011124 Sulfatase; Region: Sulfatase; cl10460 319224011125 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 319224011126 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 319224011127 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 319224011128 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 319224011129 RNA binding site [nucleotide binding]; other site 319224011130 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 319224011131 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 319224011132 DNA binding site [nucleotide binding] 319224011133 active site 319224011134 Int/Topo IB signature motif; other site 319224011135 catalytic residues [active] 319224011136 Putative phage integrase; Region: Phage_Integr_2; pfam13009 319224011137 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 319224011138 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 319224011139 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 319224011140 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3415 319224011141 Helix-turn-helix domains; Region: HTH; cl00088 319224011142 Winged helix-turn helix; Region: HTH_33; pfam13592 319224011143 Major Facilitator Superfamily; Region: MFS_1; pfam07690 319224011144 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 319224011145 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224011146 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 319224011147 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 319224011148 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224011149 Predicted permease; Region: DUF318; pfam03773 319224011150 Low molecular weight phosphatase family; Region: LMWPc; cd00115 319224011151 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 319224011152 active site 319224011153 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 319224011154 dimerization interface [polypeptide binding]; other site 319224011155 putative DNA binding site [nucleotide binding]; other site 319224011156 putative Zn2+ binding site [ion binding]; other site 319224011157 Low molecular weight phosphatase family; Region: LMWPc; cd00115 319224011158 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 319224011159 active site 319224011160 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 319224011161 dimerization interface [polypeptide binding]; other site 319224011162 putative DNA binding site [nucleotide binding]; other site 319224011163 putative Zn2+ binding site [ion binding]; other site 319224011164 Predicted permease; Region: DUF318; pfam03773 319224011165 Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily; Region: eu-GS; cl00170 319224011166 glutathione (GSH) binding pocket [chemical binding]; other site 319224011167 active site residues [active] 319224011168 ATP binding pocket [chemical binding]; other site 319224011169 magnesium binding site [ion binding]; other site 319224011170 glycine rich loop; other site 319224011171 alanine rich loop; other site 319224011172 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 319224011173 4Fe-4S binding domain; Region: Fer4; cl02805 319224011174 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 319224011175 This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_Arsenate-R; cd02757 319224011176 putative [Fe4-S4] binding site [ion binding]; other site 319224011177 putative molybdopterin cofactor binding site [chemical binding]; other site 319224011178 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 319224011179 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 319224011180 putative molybdopterin cofactor binding site; other site 319224011181 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 319224011182 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 319224011183 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 319224011184 P loop; other site 319224011185 Nucleotide binding site [chemical binding]; other site 319224011186 DTAP/Switch II; other site 319224011187 Switch I; other site 319224011188 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 319224011189 Anion-transporting ATPase; Region: ArsA_ATPase; pfam02374 319224011190 P loop; other site 319224011191 Nucleotide binding site [chemical binding]; other site 319224011192 DTAP/Switch II; other site 319224011193 Switch I; other site 319224011194 arsenical pump membrane protein; Provisional; Region: PRK15445 319224011195 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 319224011196 transmembrane helices; other site 319224011197 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 319224011198 ArsC family; Region: ArsC; pfam03960 319224011199 catalytic residues [active] 319224011200 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 319224011201 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 319224011202 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 319224011203 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 319224011204 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 319224011205 dimerization interface [polypeptide binding]; other site 319224011206 putative DNA binding site [nucleotide binding]; other site 319224011207 putative Zn2+ binding site [ion binding]; other site 319224011208 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 319224011209 non-specific DNA binding site [nucleotide binding]; other site 319224011210 salt bridge; other site 319224011211 sequence-specific DNA binding site [nucleotide binding]; other site 319224011212 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 319224011213 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 319224011214 ATP binding site [chemical binding]; other site 319224011215 putative Mg++ binding site [ion binding]; other site 319224011216 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224011217 Walker A/P-loop; other site 319224011218 ATP binding site [chemical binding]; other site 319224011219 putative transposase OrfB; Reviewed; Region: PHA02517 319224011220 HTH-like domain; Region: HTH_21; pfam13276 319224011221 Integrase core domain; Region: rve; cl01316 319224011222 Integrase core domain; Region: rve_3; cl15866 319224011223 Helix-turn-helix domains; Region: HTH; cl00088 319224011224 DEAD-like helicases superfamily; Region: DEXDc; smart00487 319224011225 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 319224011226 ATP binding site [chemical binding]; other site 319224011227 putative Mg++ binding site [ion binding]; other site 319224011228 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 319224011229 nucleotide binding region [chemical binding]; other site 319224011230 ATP-binding site [chemical binding]; other site 319224011231 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 319224011232 osmolarity response regulator; Provisional; Region: ompR; PRK09468 319224011233 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 319224011234 active site 319224011235 phosphorylation site [posttranslational modification] 319224011236 intermolecular recognition site; other site 319224011237 dimerization interface [polypeptide binding]; other site 319224011238 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 319224011239 DNA binding site [nucleotide binding] 319224011240 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 319224011241 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 319224011242 dimerization interface [polypeptide binding]; other site 319224011243 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 319224011244 dimer interface [polypeptide binding]; other site 319224011245 phosphorylation site [posttranslational modification] 319224011246 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 319224011247 ATP binding site [chemical binding]; other site 319224011248 Mg2+ binding site [ion binding]; other site 319224011249 G-X-G motif; other site 319224011250 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 319224011251 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 319224011252 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 319224011253 dimer interface [polypeptide binding]; other site 319224011254 putative CheW interface [polypeptide binding]; other site 319224011255 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 319224011256 catalytic triad [active] 319224011257 dimer interface [polypeptide binding]; other site 319224011258 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 319224011259 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224011260 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 319224011261 active site 319224011262 phosphorylation site [posttranslational modification] 319224011263 intermolecular recognition site; other site 319224011264 dimerization interface [polypeptide binding]; other site 319224011265 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 319224011266 DNA binding site [nucleotide binding] 319224011267 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 319224011268 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 319224011269 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 319224011270 ATP binding site [chemical binding]; other site 319224011271 Mg2+ binding site [ion binding]; other site 319224011272 G-X-G motif; other site 319224011273 Protein of unknown function (DUF3300); Region: DUF3300; pfam11737 319224011274 ribonuclease E; Reviewed; Region: rne; PRK10811 319224011275 MASE1; Region: MASE1; pfam05231 319224011276 CHASE domain; Region: CHASE; cl01369 319224011277 PAS domain S-box; Region: sensory_box; TIGR00229 319224011278 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 319224011279 putative active site [active] 319224011280 heme pocket [chemical binding]; other site 319224011281 PAS domain S-box; Region: sensory_box; TIGR00229 319224011282 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 319224011283 putative active site [active] 319224011284 heme pocket [chemical binding]; other site 319224011285 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 319224011286 metal binding site [ion binding]; metal-binding site 319224011287 active site 319224011288 I-site; other site 319224011289 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 319224011290 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 319224011291 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 319224011292 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 319224011293 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 319224011294 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 319224011295 D-pathway; other site 319224011296 Putative ubiquinol binding site [chemical binding]; other site 319224011297 Low-spin heme (heme b) binding site [chemical binding]; other site 319224011298 Putative water exit pathway; other site 319224011299 Binuclear center (heme o3/CuB) [ion binding]; other site 319224011300 K-pathway; other site 319224011301 Putative proton exit pathway; other site 319224011302 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 319224011303 Subunit I/III interface [polypeptide binding]; other site 319224011304 Subunit III/IV interface [polypeptide binding]; other site 319224011305 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 319224011306 UbiA prenyltransferase family; Region: UbiA; cl00337 319224011307 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 319224011308 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 319224011309 N-terminal plug; other site 319224011310 ligand-binding site [chemical binding]; other site 319224011311 transporter, basic amino acid/polyamine antiporter (APA) family; Region: 2A0302; TIGR00905 319224011312 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 319224011313 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 319224011314 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 319224011315 non-specific DNA binding site [nucleotide binding]; other site 319224011316 salt bridge; other site 319224011317 sequence-specific DNA binding site [nucleotide binding]; other site 319224011318 Domain of unknown function (DUF955); Region: DUF955; cl01076 319224011319 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 319224011320 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 319224011321 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 319224011322 Paraquat-inducible protein A; Region: PqiA; pfam04403 319224011323 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 319224011324 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 319224011325 Zn2+ binding site [ion binding]; other site 319224011326 Mg2+ binding site [ion binding]; other site 319224011327 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 319224011328 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 319224011329 Walker A/P-loop; other site 319224011330 ATP binding site [chemical binding]; other site 319224011331 Q-loop/lid; other site 319224011332 ABC transporter signature motif; other site 319224011333 Walker B; other site 319224011334 D-loop; other site 319224011335 H-loop/switch region; other site 319224011336 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 319224011337 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224011338 Walker A/P-loop; other site 319224011339 ATP binding site [chemical binding]; other site 319224011340 Q-loop/lid; other site 319224011341 ABC transporter signature motif; other site 319224011342 Walker B; other site 319224011343 D-loop; other site 319224011344 H-loop/switch region; other site 319224011345 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 319224011346 chorismate binding enzyme; Region: Chorismate_bind; cl10555 319224011347 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 319224011348 substrate binding pocket [chemical binding]; other site 319224011349 membrane-bound complex binding site; other site 319224011350 hinge residues; other site 319224011351 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 319224011352 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 319224011353 Coenzyme A binding pocket [chemical binding]; other site 319224011354 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224011355 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 319224011356 dimer interface [polypeptide binding]; other site 319224011357 phosphorylation site [posttranslational modification] 319224011358 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 319224011359 ATP binding site [chemical binding]; other site 319224011360 Mg2+ binding site [ion binding]; other site 319224011361 G-X-G motif; other site 319224011362 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 319224011363 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 319224011364 active site 319224011365 phosphorylation site [posttranslational modification] 319224011366 intermolecular recognition site; other site 319224011367 dimerization interface [polypeptide binding]; other site 319224011368 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 319224011369 Walker A motif; other site 319224011370 ATP binding site [chemical binding]; other site 319224011371 Walker B motif; other site 319224011372 arginine finger; other site 319224011373 Helix-turn-helix domains; Region: HTH; cl00088 319224011374 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 319224011375 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 319224011376 dimerization interface [polypeptide binding]; other site 319224011377 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 319224011378 dimer interface [polypeptide binding]; other site 319224011379 conserved gate region; other site 319224011380 putative PBP binding loops; other site 319224011381 ABC-ATPase subunit interface; other site 319224011382 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 319224011383 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 319224011384 Walker A/P-loop; other site 319224011385 ATP binding site [chemical binding]; other site 319224011386 Q-loop/lid; other site 319224011387 ABC transporter signature motif; other site 319224011388 Walker B; other site 319224011389 D-loop; other site 319224011390 H-loop/switch region; other site 319224011391 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 319224011392 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 319224011393 GTP binding site; other site 319224011394 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional; Region: PRK14491 319224011395 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 319224011396 Walker A motif; other site 319224011397 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 319224011398 dimer interface [polypeptide binding]; other site 319224011399 putative functional site; other site 319224011400 putative MPT binding site; other site 319224011401 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 319224011402 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 319224011403 FeS/SAM binding site; other site 319224011404 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 319224011405 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 319224011406 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 319224011407 DNA binding site [nucleotide binding] 319224011408 catalytic residue [active] 319224011409 H2TH interface [polypeptide binding]; other site 319224011410 putative catalytic residues [active] 319224011411 turnover-facilitating residue; other site 319224011412 intercalation triad [nucleotide binding]; other site 319224011413 8OG recognition residue [nucleotide binding]; other site 319224011414 putative reading head residues; other site 319224011415 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 319224011416 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 319224011417 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 319224011418 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 319224011419 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 319224011420 active site 319224011421 (T/H)XGH motif; other site 319224011422 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 319224011423 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 319224011424 Sulfatase; Region: Sulfatase; cl10460 319224011425 Cupin domain; Region: Cupin_2; cl09118 319224011426 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 319224011427 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 319224011428 NADP binding site [chemical binding]; other site 319224011429 active site 319224011430 putative substrate binding site [chemical binding]; other site 319224011431 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 319224011432 putative metal binding site; other site 319224011433 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 319224011434 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 319224011435 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224011436 UDP-galactopyranose mutase; Region: GLF; pfam03275 319224011437 Protein of unknown function (DUF707); Region: DUF707; pfam05212 319224011438 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 319224011439 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 319224011440 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 319224011441 putative active site [active] 319224011442 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 319224011443 ATP binding site [chemical binding]; other site 319224011444 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 319224011445 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 319224011446 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 319224011447 Helix-turn-helix domains; Region: HTH; cl00088 319224011448 Bacterial transcriptional repressor; Region: TetR; pfam13972 319224011449 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 319224011450 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 319224011451 substrate-cofactor binding pocket; other site 319224011452 pyridoxal 5'-phosphate binding site [chemical binding]; other site 319224011453 catalytic residue [active] 319224011454 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 319224011455 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 319224011456 NAD(P) binding site [chemical binding]; other site 319224011457 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 319224011458 active site residue [active] 319224011459 Protein of unknown function (DUF3582); Region: DUF3582; pfam12122 319224011460 rhomboid family protease GlpG; Region: rhombo_GlpG; TIGR04239 319224011461 Rhomboid family; Region: Rhomboid; cl11446 319224011462 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 319224011463 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 319224011464 conserved cys residue [active] 319224011465 DNA polymerase I; Provisional; Region: PRK05755 319224011466 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 319224011467 active site 319224011468 metal binding site 1 [ion binding]; metal-binding site 319224011469 putative 5' ssDNA interaction site; other site 319224011470 metal binding site 3; metal-binding site 319224011471 metal binding site 2 [ion binding]; metal-binding site 319224011472 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 319224011473 putative DNA binding site [nucleotide binding]; other site 319224011474 putative metal binding site [ion binding]; other site 319224011475 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 319224011476 active site 319224011477 catalytic site [active] 319224011478 substrate binding site [chemical binding]; other site 319224011479 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 319224011480 active site 319224011481 DNA binding site [nucleotide binding] 319224011482 catalytic site [active] 319224011483 Predicted GTPase [General function prediction only]; Region: COG0218 319224011484 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 319224011485 G1 box; other site 319224011486 GTP/Mg2+ binding site [chemical binding]; other site 319224011487 Switch I region; other site 319224011488 G2 box; other site 319224011489 G3 box; other site 319224011490 Switch II region; other site 319224011491 G4 box; other site 319224011492 G5 box; other site 319224011493 Cytochrome c; Region: Cytochrom_C; cl11414 319224011494 Cytochrome c; Region: Cytochrom_C; cl11414 319224011495 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; cl16911 319224011496 Der GTPase activator (YihI); Region: YihI; cl01172 319224011497 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 319224011498 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 319224011499 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 319224011500 FeS/SAM binding site; other site 319224011501 HemN C-terminal domain; Region: HemN_C; pfam06969 319224011502 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 319224011503 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 319224011504 active site 319224011505 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 319224011506 lysophospholipase L2; Provisional; Region: PRK10749 319224011507 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 319224011508 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 319224011509 PAS fold; Region: PAS_3; pfam08447 319224011510 putative active site [active] 319224011511 heme pocket [chemical binding]; other site 319224011512 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 319224011513 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 319224011514 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 319224011515 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 319224011516 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 319224011517 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 319224011518 Enoyl-CoA hydratase/isomerase family; Region: ECH; pfam00378 319224011519 substrate binding site [chemical binding]; other site 319224011520 oxyanion hole (OAH) forming residues; other site 319224011521 trimer interface [polypeptide binding]; other site 319224011522 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 319224011523 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224011524 Family description; Region: UvrD_C_2; cl15862 319224011525 Helix-turn-helix domains; Region: HTH; cl00088 319224011526 putative transposase OrfB; Reviewed; Region: PHA02517 319224011527 HTH-like domain; Region: HTH_21; pfam13276 319224011528 Integrase core domain; Region: rve; cl01316 319224011529 Integrase core domain; Region: rve_3; cl15866 319224011530 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; cl16911 319224011531 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 319224011532 Helix-turn-helix domains; Region: HTH; cl00088 319224011533 putative DNA binding site [nucleotide binding]; other site 319224011534 putative Zn2+ binding site [ion binding]; other site 319224011535 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 319224011536 ATP-binding site [chemical binding]; other site 319224011537 AAA domain; Region: AAA_22; pfam13401 319224011538 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 319224011539 Walker A motif; other site 319224011540 ATP binding site [chemical binding]; other site 319224011541 Walker B motif; other site 319224011542 Tn7 transposition regulator TnsC; Region: Tn7_TnsC_Int; pfam11426 319224011543 Integrase core domain; Region: rve; cl01316 319224011544 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 319224011545 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; cl16911 319224011546 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; cl16911 319224011547 Helix-turn-helix domains; Region: HTH; cl00088 319224011548 Integrase core domain; Region: rve; cl01316 319224011549 Integrase core domain; Region: rve_3; cl15866 319224011550 Domain of unknown function DUF87; Region: DUF87; pfam01935 319224011551 HerA helicase [Replication, recombination, and repair]; Region: COG0433 319224011552 TniQ; Region: TniQ; pfam06527 319224011553 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 319224011554 AAA domain; Region: AAA_22; pfam13401 319224011555 Tn7 transposition regulator TnsC; Region: Tn7_TnsC_Int; pfam11426 319224011556 Integrase core domain; Region: rve; cl01316 319224011557 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 319224011558 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; cl07370 319224011559 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 319224011560 Abi-like protein; Region: Abi_2; cl01988 319224011561 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 319224011562 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 319224011563 glutaminase active site [active] 319224011564 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 319224011565 dimer interface [polypeptide binding]; other site 319224011566 active site 319224011567 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 319224011568 dimer interface [polypeptide binding]; other site 319224011569 active site 319224011570 DNA-bindng transcriptional repressor SrlR; Provisional; Region: srlR; PRK10434 319224011571 Helix-turn-helix domains; Region: HTH; cl00088 319224011572 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 319224011573 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 319224011574 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 319224011575 N-terminal plug; other site 319224011576 ligand-binding site [chemical binding]; other site 319224011577 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK09451 319224011578 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 319224011579 Substrate binding site; other site 319224011580 Mg++ binding site; other site 319224011581 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 319224011582 active site 319224011583 substrate binding site [chemical binding]; other site 319224011584 CoA binding site [chemical binding]; other site 319224011585 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 319224011586 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 319224011587 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 319224011588 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 319224011589 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 319224011590 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 319224011591 alpha subunit interaction interface [polypeptide binding]; other site 319224011592 Walker A motif; other site 319224011593 ATP binding site [chemical binding]; other site 319224011594 Walker B motif; other site 319224011595 inhibitor binding site; inhibition site 319224011596 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 319224011597 ATP synthase; Region: ATP-synt; cl00365 319224011598 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 319224011599 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 319224011600 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 319224011601 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 319224011602 beta subunit interaction interface [polypeptide binding]; other site 319224011603 Walker A motif; other site 319224011604 ATP binding site [chemical binding]; other site 319224011605 Walker B motif; other site 319224011606 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 319224011607 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 319224011608 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 319224011609 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 319224011610 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 319224011611 ATP synthase subunit C; Region: ATP-synt_C; cl00466 319224011612 ATP synthase A chain; Region: ATP-synt_A; cl00413 319224011613 ATP synthase I chain; Region: ATP_synt_I; cl09170 319224011614 ParB-like partition proteins; Region: parB_part; TIGR00180 319224011615 ParB-like nuclease domain; Region: ParBc; cl02129 319224011616 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 319224011617 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 319224011618 P-loop; other site 319224011619 Magnesium ion binding site [ion binding]; other site 319224011620 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 319224011621 Magnesium ion binding site [ion binding]; other site 319224011622 Methyltransferase domain; Region: Methyltransf_31; pfam13847 319224011623 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 319224011624 S-adenosylmethionine binding site [chemical binding]; other site 319224011625 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 319224011626 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 319224011627 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 319224011628 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 319224011629 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 319224011630 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 319224011631 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 319224011632 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 319224011633 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 319224011634 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 319224011635 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 319224011636 active site 319224011637 phosphorylation site [posttranslational modification] 319224011638 intermolecular recognition site; other site 319224011639 dimerization interface [polypeptide binding]; other site 319224011640 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 319224011641 DNA binding site [nucleotide binding] 319224011642 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 319224011643 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 319224011644 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 319224011645 dimer interface [polypeptide binding]; other site 319224011646 phosphorylation site [posttranslational modification] 319224011647 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 319224011648 ATP binding site [chemical binding]; other site 319224011649 Mg2+ binding site [ion binding]; other site 319224011650 G-X-G motif; other site 319224011651 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 319224011652 Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient...; Region: SR_Res_par; cd03767 319224011653 catalytic residues [active] 319224011654 catalytic nucleophile [active] 319224011655 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 319224011656 HsdM N-terminal domain; Region: HsdM_N; pfam12161 319224011657 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 319224011658 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; cl16911 319224011659 Domain of unknown function (DUF4062); Region: DUF4062; pfam13271 319224011660 Divergent AAA domain; Region: AAA_4; pfam04326 319224011661 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 319224011662 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 319224011663 HsdM N-terminal domain; Region: HsdM_N; pfam12161 319224011664 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; cl16911 319224011665 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 319224011666 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 319224011667 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 319224011668 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 319224011669 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 319224011670 ATP binding site [chemical binding]; other site 319224011671 putative Mg++ binding site [ion binding]; other site 319224011672 AAA domain; Region: AAA_13; pfam13166 319224011673 Virulence protein [General function prediction only]; Region: COG3943 319224011674 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 319224011675 Domain of unknown function (DUF927); Region: DUF927; cl12098 319224011676 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 319224011677 putative fimbrial outer membrane usher protein StfC; Provisional; Region: PRK15284 319224011678 HupE / UreJ protein; Region: HupE_UreJ; cl01011 319224011679 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 319224011680 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06549 319224011681 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 319224011682 E3 interaction surface; other site 319224011683 lipoyl attachment site [posttranslational modification]; other site 319224011684 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 319224011685 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 319224011686 BlaR1 peptidase M56; Region: Peptidase_M56; cl15829 319224011687 Helix-turn-helix domains; Region: HTH; cl00088 319224011688 Protein of unknown function (DUF3946); Region: DUF3946; pfam13102 319224011689 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the...; Region: INT_Tn4399; cd01185 319224011690 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 319224011691 Int/Topo IB signature motif; other site 319224011692 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 319224011693 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 319224011694 trmE is a tRNA modification GTPase; Region: trmE; cd04164 319224011695 G1 box; other site 319224011696 GTP/Mg2+ binding site [chemical binding]; other site 319224011697 Switch I region; other site 319224011698 G2 box; other site 319224011699 Switch II region; other site 319224011700 G3 box; other site 319224011701 G4 box; other site 319224011702 G5 box; other site 319224011703 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 319224011704 membrane protein insertase; Provisional; Region: PRK01318 319224011705 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 319224011706 Haemolytic domain; Region: Haemolytic; cl00506 319224011707 Ribonuclease P; Region: Ribonuclease_P; cl00457 319224011708 Ribosomal protein L34; Region: Ribosomal_L34; cl00370