-- dump date 20120504_151853 -- class Genbank::misc_feature -- table misc_feature_note -- id note 400668000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 400668000002 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000003 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 400668000004 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 400668000005 Walker A motif; other site 400668000006 ATP binding site [chemical binding]; other site 400668000007 Walker B motif; other site 400668000008 arginine finger; other site 400668000009 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 400668000010 DnaA box-binding interface [nucleotide binding]; other site 400668000011 DNA polymerase III subunit beta; Validated; Region: PRK05643 400668000012 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 400668000013 putative DNA binding surface [nucleotide binding]; other site 400668000014 dimer interface [polypeptide binding]; other site 400668000015 beta-clamp/clamp loader binding surface; other site 400668000016 beta-clamp/translesion DNA polymerase binding surface; other site 400668000017 recombination protein F; Reviewed; Region: recF; PRK00064 400668000018 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000019 Walker A/P-loop; other site 400668000020 ATP binding site [chemical binding]; other site 400668000021 Q-loop/lid; other site 400668000022 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000023 ABC transporter signature motif; other site 400668000024 Walker B; other site 400668000025 D-loop; other site 400668000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 400668000027 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 400668000028 Mg2+ binding site [ion binding]; other site 400668000029 G-X-G motif; other site 400668000030 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 400668000031 anchoring element; other site 400668000032 dimer interface [polypeptide binding]; other site 400668000033 ATP binding site [chemical binding]; other site 400668000034 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 400668000035 active site 400668000036 putative metal-binding site [ion binding]; other site 400668000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 400668000038 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 400668000039 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 400668000040 NADP binding site [chemical binding]; other site 400668000041 Helix-turn-helix domains; Region: HTH; cl00088 400668000042 siderophore ferric iron reductase, AHA_1954 family; Region: sidero_Fe_reduc; TIGR03950 400668000043 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 400668000044 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 400668000045 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 400668000046 N-terminal plug; other site 400668000047 ligand-binding site [chemical binding]; other site 400668000048 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668000049 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668000050 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 400668000051 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 400668000052 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668000053 putative substrate translocation pore; other site 400668000054 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 400668000055 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 400668000056 active site 400668000057 motif I; other site 400668000058 motif II; other site 400668000059 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 400668000060 putative deacylase active site [active] 400668000061 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 400668000062 Cation transport protein; Region: TrkH; cl10514 400668000063 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 400668000064 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000065 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 400668000066 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000067 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 400668000068 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 400668000069 putative RNA binding site [nucleotide binding]; other site 400668000070 16S rRNA methyltransferase B; Provisional; Region: PRK10901 400668000071 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668000072 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 400668000073 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 400668000074 putative active site [active] 400668000075 substrate binding site [chemical binding]; other site 400668000076 putative cosubstrate binding site; other site 400668000077 catalytic site [active] 400668000078 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 400668000079 substrate binding site [chemical binding]; other site 400668000080 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 400668000081 active site 400668000082 catalytic residues [active] 400668000083 metal binding site [ion binding]; metal-binding site 400668000084 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 400668000085 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 400668000086 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 400668000087 RNA binding surface [nucleotide binding]; other site 400668000088 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 400668000089 active site 400668000090 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 400668000091 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 400668000092 active site 400668000093 catalytic site [active] 400668000094 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668000095 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668000096 Walker A/P-loop; other site 400668000097 ATP binding site [chemical binding]; other site 400668000098 Q-loop/lid; other site 400668000099 ABC transporter signature motif; other site 400668000100 Walker B; other site 400668000101 D-loop; other site 400668000102 H-loop/switch region; other site 400668000103 TOBE domain; Region: TOBE_2; cl01440 400668000104 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668000105 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 400668000106 dimer interface [polypeptide binding]; other site 400668000107 conserved gate region; other site 400668000108 putative PBP binding loops; other site 400668000109 ABC-ATPase subunit interface; other site 400668000110 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668000111 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 400668000112 dimer interface [polypeptide binding]; other site 400668000113 conserved gate region; other site 400668000114 putative PBP binding loops; other site 400668000115 ABC-ATPase subunit interface; other site 400668000116 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 400668000117 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 400668000118 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668000119 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668000120 DNA binding site [nucleotide binding] 400668000121 domain linker motif; other site 400668000122 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 400668000123 ligand binding site [chemical binding]; other site 400668000124 dimerization interface [polypeptide binding]; other site 400668000125 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 400668000126 conserved cys residue [active] 400668000127 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668000128 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000129 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668000130 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668000131 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000132 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668000133 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668000134 Helix-turn-helix domains; Region: HTH; cl00088 400668000135 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06333 400668000136 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 400668000137 dimer interface [polypeptide binding]; other site 400668000138 active site 400668000139 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668000140 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668000141 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668000142 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668000143 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668000144 Helix-turn-helix domains; Region: HTH; cl00088 400668000145 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 400668000146 dimerization interface [polypeptide binding]; other site 400668000147 DNA-binding transcriptional repressor UxuR; Provisional; Region: PRK10225 400668000148 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668000149 DNA-binding site [nucleotide binding]; DNA binding site 400668000150 FCD domain; Region: FCD; cl11656 400668000151 bifunctional D-altronate/D-mannonate dehydratase; Provisional; Region: PRK15072 400668000152 The starvation sensing protein RpsA from E.coli and its homologs are lactonizing enzymes whose putative targets are homoserine lactone (HSL)-derivative. They are part of the mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of...; Region: rpsA; cd03322 400668000153 putative active site pocket [active] 400668000154 putative metal binding site [ion binding]; other site 400668000155 putative oxidoreductase; Provisional; Region: PRK10083 400668000156 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH7; cd08261 400668000157 putative NAD(P) binding site [chemical binding]; other site 400668000158 catalytic Zn binding site [ion binding]; other site 400668000159 structural Zn binding site [ion binding]; other site 400668000160 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668000161 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668000162 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668000163 DctM-like transporters; Region: DctM; pfam06808 400668000164 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668000165 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 400668000166 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668000167 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668000168 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668000169 DctM-like transporters; Region: DctM; pfam06808 400668000170 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668000171 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668000172 Helix-turn-helix domains; Region: HTH; cl00088 400668000173 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 400668000174 dimerization interface [polypeptide binding]; other site 400668000175 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 400668000176 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 400668000177 inhibitor-cofactor binding pocket; inhibition site 400668000178 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668000179 catalytic residue [active] 400668000180 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668000181 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668000182 tetramerization interface [polypeptide binding]; other site 400668000183 NAD(P) binding site [chemical binding]; other site 400668000184 catalytic residues [active] 400668000185 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 400668000186 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 400668000187 N-terminal plug; other site 400668000188 ligand-binding site [chemical binding]; other site 400668000189 Transcriptional regulators [Transcription]; Region: GntR; COG1802 400668000190 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668000191 DNA-binding site [nucleotide binding]; DNA binding site 400668000192 FCD domain; Region: FCD; cl11656 400668000193 hydroxyproline-2-epimerase; Provisional; Region: PRK13970 400668000194 hydroxyproline-2-epimerase; Provisional; Region: PRK13971 400668000195 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 400668000196 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 400668000197 inhibitor site; inhibition site 400668000198 active site 400668000199 dimer interface [polypeptide binding]; other site 400668000200 catalytic residue [active] 400668000201 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 400668000202 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 400668000203 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 400668000204 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000205 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668000206 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 400668000207 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668000208 Helix-turn-helix domains; Region: HTH; cl00088 400668000209 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 400668000210 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668000211 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 400668000212 putative acyl-acceptor binding pocket; other site 400668000213 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 400668000214 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 400668000215 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 400668000216 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 400668000217 shikimate binding site; other site 400668000218 NAD(P) binding site [chemical binding]; other site 400668000219 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668000220 Protein of unknown function, DUF482; Region: DUF482; pfam04339 400668000221 Predicted transcriptional regulator [Transcription]; Region: COG2378 400668000222 Helix-turn-helix domains; Region: HTH; cl00088 400668000223 WYL domain; Region: WYL; cl14852 400668000224 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 400668000225 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 400668000226 putative C-terminal domain interface [polypeptide binding]; other site 400668000227 putative GSH binding site (G-site) [chemical binding]; other site 400668000228 putative dimer interface [polypeptide binding]; other site 400668000229 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 400668000230 dimer interface [polypeptide binding]; other site 400668000231 N-terminal domain interface [polypeptide binding]; other site 400668000232 putative substrate binding pocket (H-site) [chemical binding]; other site 400668000233 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 400668000234 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 400668000235 heme-binding site [chemical binding]; other site 400668000236 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 400668000237 FAD binding pocket [chemical binding]; other site 400668000238 FAD binding motif [chemical binding]; other site 400668000239 phosphate binding motif [ion binding]; other site 400668000240 beta-alpha-beta structure motif; other site 400668000241 NAD binding pocket [chemical binding]; other site 400668000242 Heme binding pocket [chemical binding]; other site 400668000243 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 400668000244 GAF domain; Region: GAF; cl15785 400668000245 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 400668000246 Walker A motif; other site 400668000247 ATP binding site [chemical binding]; other site 400668000248 Walker B motif; other site 400668000249 arginine finger; other site 400668000250 Helix-turn-helix domains; Region: HTH; cl00088 400668000251 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 400668000252 apolar tunnel; other site 400668000253 heme binding site [chemical binding]; other site 400668000254 dimerization interface [polypeptide binding]; other site 400668000255 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 400668000256 MatE; Region: MatE; cl10513 400668000257 MatE; Region: MatE; cl10513 400668000258 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 400668000259 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 400668000260 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 400668000261 shikimate binding site; other site 400668000262 NAD(P) binding site [chemical binding]; other site 400668000263 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 400668000264 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668000265 DNA-binding site [nucleotide binding]; DNA binding site 400668000266 FCD domain; Region: FCD; cl11656 400668000267 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 400668000268 FAD binding domain; Region: FAD_binding_4; pfam01565 400668000269 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 400668000270 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 400668000271 active site 400668000272 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 400668000273 dimer interface [polypeptide binding]; other site 400668000274 active site 400668000275 Schiff base residues; other site 400668000276 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 400668000277 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 400668000278 Helix-turn-helix domains; Region: HTH; cl00088 400668000279 DNA binding residues [nucleotide binding] 400668000280 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 400668000281 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 400668000282 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668000283 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668000284 Helix-turn-helix domains; Region: HTH; cl00088 400668000285 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 400668000286 putative effector binding pocket; other site 400668000287 dimerization interface [polypeptide binding]; other site 400668000288 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 400668000289 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 400668000290 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 400668000291 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 400668000292 dimer interface [polypeptide binding]; other site 400668000293 motif 1; other site 400668000294 active site 400668000295 motif 2; other site 400668000296 motif 3; other site 400668000297 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 400668000298 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 400668000299 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 400668000300 putative substrate translocation pore; other site 400668000301 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668000302 Helix-turn-helix domains; Region: HTH; cl00088 400668000303 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 400668000304 dimerization interface [polypeptide binding]; other site 400668000305 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 400668000306 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 400668000307 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668000308 DNA-binding site [nucleotide binding]; DNA binding site 400668000309 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 400668000310 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668000311 homodimer interface [polypeptide binding]; other site 400668000312 catalytic residue [active] 400668000313 cytochrome o ubiquinol oxidase subunit II; Provisional; Region: PRK10525 400668000314 Protein of unknown function (DUF4079); Region: DUF4079; pfam13301 400668000315 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 400668000316 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 400668000317 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 400668000318 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 400668000319 D-pathway; other site 400668000320 Putative ubiquinol binding site [chemical binding]; other site 400668000321 Low-spin heme (heme b) binding site [chemical binding]; other site 400668000322 Putative water exit pathway; other site 400668000323 Binuclear center (heme o3/CuB) [ion binding]; other site 400668000324 K-pathway; other site 400668000325 Putative proton exit pathway; other site 400668000326 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 400668000327 Subunit I/III interface [polypeptide binding]; other site 400668000328 Subunit III/IV interface [polypeptide binding]; other site 400668000329 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 400668000330 UbiA prenyltransferase family; Region: UbiA; cl00337 400668000331 Tannase and feruloyl esterase; Region: Tannase; pfam07519 400668000332 short chain dehydrogenase; Provisional; Region: PRK06123 400668000333 classical (c) SDRs; Region: SDR_c; cd05233 400668000334 NAD(P) binding site [chemical binding]; other site 400668000335 active site 400668000336 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668000337 Helix-turn-helix domains; Region: HTH; cl00088 400668000338 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 400668000339 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 400668000340 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 400668000341 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 400668000342 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 400668000343 putative substrate translocation pore; other site 400668000344 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 400668000345 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 400668000346 putative active site pocket [active] 400668000347 dimerization interface [polypeptide binding]; other site 400668000348 putative catalytic residue [active] 400668000349 Methyltransferase small domain N-terminal; Region: MTS_N; pfam08468 400668000350 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 400668000351 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 400668000352 S-adenosylmethionine binding site [chemical binding]; other site 400668000353 LysE type translocator; Region: LysE; cl00565 400668000354 OpgC protein; Region: OpgC_C; cl00792 400668000355 Acyltransferase family; Region: Acyl_transf_3; pfam01757 400668000356 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 400668000357 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 400668000358 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 400668000359 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668000360 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668000361 penicillin-binding protein 1C; Provisional; Region: PRK11240 400668000362 Transglycosylase; Region: Transgly; cl07896 400668000363 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668000364 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 400668000365 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 400668000366 MG2 domain; Region: A2M_N; pfam01835 400668000367 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 400668000368 Alpha-2-macroglobulin family; Region: A2M; pfam00207 400668000369 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 400668000370 surface patch; other site 400668000371 thioester region; other site 400668000372 H+ Antiporter protein; Region: 2A0121; TIGR00900 400668000373 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 400668000374 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 400668000375 Walker A/P-loop; other site 400668000376 ATP binding site [chemical binding]; other site 400668000377 Q-loop/lid; other site 400668000378 ABC transporter signature motif; other site 400668000379 Walker B; other site 400668000380 D-loop; other site 400668000381 H-loop/switch region; other site 400668000382 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668000383 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 400668000384 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 400668000385 Walker A/P-loop; other site 400668000386 ATP binding site [chemical binding]; other site 400668000387 Q-loop/lid; other site 400668000388 ABC transporter signature motif; other site 400668000389 Walker B; other site 400668000390 D-loop; other site 400668000391 H-loop/switch region; other site 400668000392 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668000393 dipeptide transporter; Provisional; Region: PRK10913 400668000394 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 400668000395 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 400668000396 dimer interface [polypeptide binding]; other site 400668000397 conserved gate region; other site 400668000398 putative PBP binding loops; other site 400668000399 ABC-ATPase subunit interface; other site 400668000400 dipeptide transporter permease DppB; Provisional; Region: PRK10914 400668000401 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 400668000402 dimer interface [polypeptide binding]; other site 400668000403 conserved gate region; other site 400668000404 putative PBP binding loops; other site 400668000405 ABC-ATPase subunit interface; other site 400668000406 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 400668000407 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 400668000408 peptide binding site [polypeptide binding]; other site 400668000409 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 400668000410 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000411 SGNH_hydrolase subfamily, similar to arylesterase (7-aminocephalosporanic acid-deacetylating enzyme) of A. tumefaciens. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of...; Region: SGNH_arylesterase_like; cd01839 400668000412 active site 400668000413 catalytic triad [active] 400668000414 oxyanion hole [active] 400668000415 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 400668000416 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 400668000417 NAD(P) binding site [chemical binding]; other site 400668000418 catalytic residues [active] 400668000419 Cache domain; Region: Cache_1; pfam02743 400668000420 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 400668000421 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668000422 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668000423 dimer interface [polypeptide binding]; other site 400668000424 putative CheW interface [polypeptide binding]; other site 400668000425 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 400668000426 Helix-turn-helix domains; Region: HTH; cl00088 400668000427 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 400668000428 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 400668000429 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 400668000430 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 400668000431 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 400668000432 dimer interface [polypeptide binding]; other site 400668000433 conserved gate region; other site 400668000434 putative PBP binding loops; other site 400668000435 ABC-ATPase subunit interface; other site 400668000436 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 400668000437 dimer interface [polypeptide binding]; other site 400668000438 conserved gate region; other site 400668000439 putative PBP binding loops; other site 400668000440 ABC-ATPase subunit interface; other site 400668000441 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 400668000442 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000443 Walker A/P-loop; other site 400668000444 ATP binding site [chemical binding]; other site 400668000445 Q-loop/lid; other site 400668000446 ABC transporter signature motif; other site 400668000447 Walker B; other site 400668000448 D-loop; other site 400668000449 H-loop/switch region; other site 400668000450 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668000451 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 400668000452 catalytic core [active] 400668000453 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668000454 Aldose 1-epimerase, similar to Escherichia coli c4013; Region: Aldose_epim_Ec_c4013; cd09023 400668000455 active site 400668000456 catalytic residues [active] 400668000457 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 400668000458 putative active site pocket [active] 400668000459 dimerization interface [polypeptide binding]; other site 400668000460 putative catalytic residue [active] 400668000461 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 400668000462 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 400668000463 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 400668000464 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 400668000465 DNA binding site [nucleotide binding] 400668000466 active site 400668000467 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 400668000468 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 400668000469 Cache domain; Region: Cache_1; pfam02743 400668000470 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 400668000471 dimerization interface [polypeptide binding]; other site 400668000472 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668000473 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668000474 dimer interface [polypeptide binding]; other site 400668000475 putative CheW interface [polypeptide binding]; other site 400668000476 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668000477 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668000478 Pectate lyase; Region: Pec_lyase_C; cl01593 400668000479 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000480 metal binding site [ion binding]; metal-binding site 400668000481 active site 400668000482 I-site; other site 400668000483 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 400668000484 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 400668000485 active site 400668000486 phosphorylation site [posttranslational modification] 400668000487 intermolecular recognition site; other site 400668000488 dimerization interface [polypeptide binding]; other site 400668000489 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000490 metal binding site [ion binding]; metal-binding site 400668000491 active site 400668000492 I-site; other site 400668000493 PAS fold; Region: PAS_4; pfam08448 400668000494 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 400668000495 dimer interface [polypeptide binding]; other site 400668000496 phosphorylation site [posttranslational modification] 400668000497 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 400668000498 ATP binding site [chemical binding]; other site 400668000499 Mg2+ binding site [ion binding]; other site 400668000500 G-X-G motif; other site 400668000501 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 400668000502 Response regulator receiver domain; Region: Response_reg; pfam00072 400668000503 active site 400668000504 phosphorylation site [posttranslational modification] 400668000505 intermolecular recognition site; other site 400668000506 dimerization interface [polypeptide binding]; other site 400668000507 Response regulator receiver domain; Region: Response_reg; pfam00072 400668000508 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 400668000509 active site 400668000510 phosphorylation site [posttranslational modification] 400668000511 intermolecular recognition site; other site 400668000512 dimerization interface [polypeptide binding]; other site 400668000513 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 400668000514 putative binding surface; other site 400668000515 active site 400668000516 Protein of unknown function (DUF917); Region: DUF917; pfam06032 400668000517 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 400668000518 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668000519 putative substrate translocation pore; other site 400668000520 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668000521 Helix-turn-helix domains; Region: HTH; cl00088 400668000522 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 400668000523 dimerization interface [polypeptide binding]; other site 400668000524 PAS domain; Region: PAS_9; pfam13426 400668000525 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 400668000526 putative active site [active] 400668000527 heme pocket [chemical binding]; other site 400668000528 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 400668000529 PAS domain; Region: PAS_9; pfam13426 400668000530 putative active site [active] 400668000531 heme pocket [chemical binding]; other site 400668000532 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668000533 dimer interface [polypeptide binding]; other site 400668000534 putative CheW interface [polypeptide binding]; other site 400668000535 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 400668000536 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668000537 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668000538 D-lactate dehydrogenase [cytochrome]; Region: PLN02805 400668000539 FAD binding domain; Region: FAD_binding_4; pfam01565 400668000540 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 400668000541 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 400668000542 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668000543 Helix-turn-helix domains; Region: HTH; cl00088 400668000544 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 400668000545 dimerization interface [polypeptide binding]; other site 400668000546 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 400668000547 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 400668000548 substrate binding pocket [chemical binding]; other site 400668000549 membrane-bound complex binding site; other site 400668000550 hinge residues; other site 400668000551 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668000552 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 400668000553 dimer interface [polypeptide binding]; other site 400668000554 conserved gate region; other site 400668000555 ABC-ATPase subunit interface; other site 400668000556 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 400668000557 dimer interface [polypeptide binding]; other site 400668000558 conserved gate region; other site 400668000559 putative PBP binding loops; other site 400668000560 ABC-ATPase subunit interface; other site 400668000561 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668000562 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 400668000563 Walker A/P-loop; other site 400668000564 ATP binding site [chemical binding]; other site 400668000565 Q-loop/lid; other site 400668000566 ABC transporter signature motif; other site 400668000567 Walker B; other site 400668000568 D-loop; other site 400668000569 H-loop/switch region; other site 400668000570 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000571 FAD dependent oxidoreductase; Region: DAO; pfam01266 400668000572 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 400668000573 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668000574 Coenzyme A binding pocket [chemical binding]; other site 400668000575 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 400668000576 trimer interface [polypeptide binding]; other site 400668000577 active site 400668000578 substrate binding site [chemical binding]; other site 400668000579 CoA binding site [chemical binding]; other site 400668000580 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668000581 active site 400668000582 ATP binding site [chemical binding]; other site 400668000583 substrate binding site [chemical binding]; other site 400668000584 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 400668000585 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668000586 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668000587 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 400668000588 active site 400668000589 metal binding site [ion binding]; metal-binding site 400668000590 CHASE3 domain; Region: CHASE3; cl05000 400668000591 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 400668000592 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668000593 dimer interface [polypeptide binding]; other site 400668000594 putative CheW interface [polypeptide binding]; other site 400668000595 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 400668000596 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 400668000597 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; cl11399 400668000598 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668000599 Predicted permeases [General function prediction only]; Region: RarD; COG2962 400668000600 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 400668000601 EamA-like transporter family; Region: EamA; cl01037 400668000602 EamA-like transporter family; Region: EamA; cl01037 400668000603 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 400668000604 EamA-like transporter family; Region: EamA; cl01037 400668000605 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 400668000606 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 400668000607 conserved cys residue [active] 400668000608 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668000609 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668000610 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668000611 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 400668000612 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 400668000613 putative active site [active] 400668000614 metal binding site [ion binding]; metal-binding site 400668000615 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668000616 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668000617 tetramerization interface [polypeptide binding]; other site 400668000618 NAD(P) binding site [chemical binding]; other site 400668000619 catalytic residues [active] 400668000620 PAS fold; Region: PAS_4; pfam08448 400668000621 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 400668000622 putative active site [active] 400668000623 heme pocket [chemical binding]; other site 400668000624 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 400668000625 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 400668000626 Walker A motif; other site 400668000627 ATP binding site [chemical binding]; other site 400668000628 Walker B motif; other site 400668000629 arginine finger; other site 400668000630 Helix-turn-helix domains; Region: HTH; cl00088 400668000631 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 400668000632 putative substrate translocation pore; other site 400668000633 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 400668000634 mercuric reductase; Validated; Region: PRK06370 400668000635 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000636 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668000637 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 400668000638 Protein of unknown function, DUF547; Region: DUF547; pfam04784 400668000639 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668000640 Helix-turn-helix domains; Region: HTH; cl00088 400668000641 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 400668000642 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 400668000643 dimerization interface [polypeptide binding]; other site 400668000644 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668000645 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668000646 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668000647 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 400668000648 dimer interface [polypeptide binding]; other site 400668000649 conserved gate region; other site 400668000650 putative PBP binding loops; other site 400668000651 ABC-ATPase subunit interface; other site 400668000652 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 400668000653 dimer interface [polypeptide binding]; other site 400668000654 conserved gate region; other site 400668000655 putative PBP binding loops; other site 400668000656 ABC-ATPase subunit interface; other site 400668000657 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668000658 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 400668000659 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 400668000660 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000661 Walker A/P-loop; other site 400668000662 ATP binding site [chemical binding]; other site 400668000663 Q-loop/lid; other site 400668000664 ABC transporter signature motif; other site 400668000665 Walker B; other site 400668000666 D-loop; other site 400668000667 H-loop/switch region; other site 400668000668 TOBE domain; Region: TOBE_2; cl01440 400668000669 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668000670 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668000671 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668000672 DNA binding site [nucleotide binding] 400668000673 domain linker motif; other site 400668000674 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_2; cd06278 400668000675 putative dimerization interface [polypeptide binding]; other site 400668000676 putative ligand binding site [chemical binding]; other site 400668000677 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 400668000678 active site 400668000679 dimerization interface [polypeptide binding]; other site 400668000680 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 400668000681 PAS domain; Region: PAS_9; pfam13426 400668000682 GAF domain; Region: GAF_2; pfam13185 400668000683 GAF domain; Region: GAF; cl15785 400668000684 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000685 metal binding site [ion binding]; metal-binding site 400668000686 active site 400668000687 I-site; other site 400668000688 Protein of unknown function DUF45; Region: DUF45; cl00636 400668000689 Oligogalacturonate-specific porin protein (KdgM); Region: KdgM; cl11629 400668000690 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 400668000691 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 400668000692 HPP family; Region: HPP; pfam04982 400668000693 Helix-turn-helix domains; Region: HTH; cl00088 400668000694 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 400668000695 ATP binding site [chemical binding]; other site 400668000696 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000697 metal binding site [ion binding]; metal-binding site 400668000698 active site 400668000699 I-site; other site 400668000700 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 400668000701 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668000702 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668000703 dimer interface [polypeptide binding]; other site 400668000704 putative CheW interface [polypeptide binding]; other site 400668000705 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 400668000706 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 400668000707 ATP binding site [chemical binding]; other site 400668000708 Mg++ binding site [ion binding]; other site 400668000709 motif III; other site 400668000710 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 400668000711 nucleotide binding region [chemical binding]; other site 400668000712 ATP-binding site [chemical binding]; other site 400668000713 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 400668000714 DNA-binding transcriptional regulator TorR; Provisional; Region: PRK10766 400668000715 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 400668000716 active site 400668000717 phosphorylation site [posttranslational modification] 400668000718 intermolecular recognition site; other site 400668000719 dimerization interface [polypeptide binding]; other site 400668000720 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 400668000721 DNA binding site [nucleotide binding] 400668000722 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 400668000723 substrate binding pocket [chemical binding]; other site 400668000724 membrane-bound complex binding site; other site 400668000725 hinge residues; other site 400668000726 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 400668000727 dimer interface [polypeptide binding]; other site 400668000728 phosphorylation site [posttranslational modification] 400668000729 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 400668000730 ATP binding site [chemical binding]; other site 400668000731 Mg2+ binding site [ion binding]; other site 400668000732 G-X-G motif; other site 400668000733 Response regulator receiver domain; Region: Response_reg; pfam00072 400668000734 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 400668000735 active site 400668000736 phosphorylation site [posttranslational modification] 400668000737 intermolecular recognition site; other site 400668000738 dimerization interface [polypeptide binding]; other site 400668000739 FAD dependent oxidoreductase; Region: DAO; pfam01266 400668000740 ornithine cyclodeaminase; Validated; Region: PRK06141 400668000741 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000742 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668000743 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668000744 two component system sensor kinase SsrA; Provisional; Region: PRK15347 400668000745 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000746 metal binding site [ion binding]; metal-binding site 400668000747 active site 400668000748 I-site; other site 400668000749 DctM-like transporters; Region: DctM; pfam06808 400668000750 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668000751 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668000752 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668000753 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668000754 AAA domain; Region: AAA_33; pfam13671 400668000755 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000756 active site 400668000757 Transcriptional regulator [Transcription]; Region: IclR; COG1414 400668000758 Helix-turn-helix domains; Region: HTH; cl00088 400668000759 Bacterial transcriptional regulator; Region: IclR; pfam01614 400668000760 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 400668000761 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]; Region: Eda; COG0800 400668000762 active site 400668000763 intersubunit interface [polypeptide binding]; other site 400668000764 catalytic residue [active] 400668000765 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 400668000766 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 400668000767 Fibronectin type III-like domain; Region: Fn3-like; cl15273 400668000768 mycofactocin system transcriptional regulator; Region: mycofact_TetR; TIGR03968 400668000769 Helix-turn-helix domains; Region: HTH; cl00088 400668000770 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional; Region: PRK10507 400668000771 NlpC/P60 family; Region: NLPC_P60; cl11438 400668000772 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 400668000773 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 400668000774 FMN binding site [chemical binding]; other site 400668000775 active site 400668000776 substrate binding site [chemical binding]; other site 400668000777 catalytic residue [active] 400668000778 Malonate/sodium symporter MadM subunit; Region: MadM; cl04274 400668000779 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668000780 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668000781 dimer interface [polypeptide binding]; other site 400668000782 putative CheW interface [polypeptide binding]; other site 400668000783 methionine aminotransferase; Validated; Region: PRK09082 400668000784 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 400668000785 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668000786 homodimer interface [polypeptide binding]; other site 400668000787 catalytic residue [active] 400668000788 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 400668000789 Helix-turn-helix domains; Region: HTH; cl00088 400668000790 sensor protein QseC; Provisional; Region: PRK10337 400668000791 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 400668000792 ATP binding site [chemical binding]; other site 400668000793 Mg2+ binding site [ion binding]; other site 400668000794 G-X-G motif; other site 400668000795 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 400668000796 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 400668000797 active site 400668000798 phosphorylation site [posttranslational modification] 400668000799 intermolecular recognition site; other site 400668000800 dimerization interface [polypeptide binding]; other site 400668000801 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 400668000802 DNA binding site [nucleotide binding] 400668000803 FlgD Ig-like domain; Region: FlgD_ig; cl15790 400668000804 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 400668000805 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 400668000806 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668000807 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 400668000808 FAD binding pocket [chemical binding]; other site 400668000809 conserved FAD binding motif [chemical binding]; other site 400668000810 phosphate binding motif [ion binding]; other site 400668000811 beta-alpha-beta structure motif; other site 400668000812 NAD binding pocket [chemical binding]; other site 400668000813 GAF domain; Region: GAF; cl15785 400668000814 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 400668000815 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668000816 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668000817 Walker A/P-loop; other site 400668000818 ATP binding site [chemical binding]; other site 400668000819 Q-loop/lid; other site 400668000820 ABC transporter signature motif; other site 400668000821 Walker B; other site 400668000822 D-loop; other site 400668000823 H-loop/switch region; other site 400668000824 TOBE domain; Region: TOBE_2; cl01440 400668000825 Glycosyl hydrolase families 32 and 68, which for the clan GH-J; Region: GH_J; cd08979 400668000826 active site 400668000827 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668000828 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 400668000829 dimer interface [polypeptide binding]; other site 400668000830 conserved gate region; other site 400668000831 putative PBP binding loops; other site 400668000832 ABC-ATPase subunit interface; other site 400668000833 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668000834 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 400668000835 putative PBP binding loops; other site 400668000836 ABC-ATPase subunit interface; other site 400668000837 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668000838 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 400668000839 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668000840 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668000841 DNA binding site [nucleotide binding] 400668000842 domain linker motif; other site 400668000843 Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_sucrose_transcription_regulator; cd06288 400668000844 putative dimerization interface [polypeptide binding]; other site 400668000845 putative ligand binding site [chemical binding]; other site 400668000846 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH6; cd08260 400668000847 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 400668000848 putative NAD(P) binding site [chemical binding]; other site 400668000849 catalytic Zn binding site [ion binding]; other site 400668000850 structural Zn binding site [ion binding]; other site 400668000851 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668000852 Helix-turn-helix domains; Region: HTH; cl00088 400668000853 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000854 metal binding site [ion binding]; metal-binding site 400668000855 active site 400668000856 I-site; other site 400668000857 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 400668000858 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 400668000859 NAD binding site [chemical binding]; other site 400668000860 substrate binding site [chemical binding]; other site 400668000861 catalytic Zn binding site [ion binding]; other site 400668000862 tetramer interface [polypeptide binding]; other site 400668000863 structural Zn binding site [ion binding]; other site 400668000864 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000865 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 400668000866 BCCT family transporter; Region: BCCT; cl00569 400668000867 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 400668000868 hypothetical protein; Provisional; Region: PRK12361 400668000869 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 400668000870 active site 400668000871 catalytic residues [active] 400668000872 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 400668000873 Helix-turn-helix domains; Region: HTH; cl00088 400668000874 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 400668000875 dimerization interface [polypeptide binding]; other site 400668000876 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668000877 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 400668000878 putative substrate translocation pore; other site 400668000879 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 400668000880 binding surface 400668000881 TPR motif; other site 400668000882 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668000883 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 400668000884 active site 400668000885 nucleotide binding site [chemical binding]; other site 400668000886 HIGH motif; other site 400668000887 KMSKS motif; other site 400668000888 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 400668000889 B12 binding site [chemical binding]; other site 400668000890 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 400668000891 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 400668000892 Ligand Binding Site [chemical binding]; other site 400668000893 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 400668000894 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 400668000895 MOFRL family; Region: MOFRL; pfam05161 400668000896 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 400668000897 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 400668000898 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668000899 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 400668000900 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 400668000901 N-terminal plug; other site 400668000902 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 400668000903 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 400668000904 cobalamin binding residues [chemical binding]; other site 400668000905 putative BtuC binding residues; other site 400668000906 dimer interface [polypeptide binding]; other site 400668000907 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 400668000908 ABC-ATPase subunit interface; other site 400668000909 dimer interface [polypeptide binding]; other site 400668000910 putative PBP binding regions; other site 400668000911 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 400668000912 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 400668000913 Walker A/P-loop; other site 400668000914 ATP binding site [chemical binding]; other site 400668000915 Q-loop/lid; other site 400668000916 ABC transporter signature motif; other site 400668000917 Walker B; other site 400668000918 D-loop; other site 400668000919 H-loop/switch region; other site 400668000920 Transglycosylase; Region: Transgly; cl07896 400668000921 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 400668000922 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 400668000923 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 400668000924 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668000925 DNA-binding site [nucleotide binding]; DNA binding site 400668000926 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 400668000927 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668000928 homodimer interface [polypeptide binding]; other site 400668000929 catalytic residue [active] 400668000930 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668000931 EamA-like transporter family; Region: EamA; cl01037 400668000932 Abi-like protein; Region: Abi_2; cl01988 400668000933 Cupin domain; Region: Cupin_2; cl09118 400668000934 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668000935 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 400668000936 putative substrate translocation pore; other site 400668000937 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668000938 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000939 Walker A/P-loop; other site 400668000940 ATP binding site [chemical binding]; other site 400668000941 Q-loop/lid; other site 400668000942 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 400668000943 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668000944 Walker A/P-loop; other site 400668000945 ATP binding site [chemical binding]; other site 400668000946 Q-loop/lid; other site 400668000947 ABC transporter signature motif; other site 400668000948 Walker B; other site 400668000949 D-loop; other site 400668000950 H-loop/switch region; other site 400668000951 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668000952 Helix-turn-helix domains; Region: HTH; cl00088 400668000953 Transposase IS200 like; Region: Y1_Tnp; cl00848 400668000954 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 400668000955 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 400668000956 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668000957 DctM-like transporters; Region: DctM; pfam06808 400668000958 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668000959 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668000960 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668000961 Helix-turn-helix domains; Region: HTH; cl00088 400668000962 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 400668000963 putative dimerization interface [polypeptide binding]; other site 400668000964 LabA_like proteins; Region: LabA_like; cd06167 400668000965 putative metal binding site [ion binding]; other site 400668000966 Fic/DOC family; Region: Fic; cl00960 400668000967 Transposase; Region: DEDD_Tnp_IS110; pfam01548 400668000968 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 400668000969 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 400668000970 DNA polymerase I; Provisional; Region: PRK05755 400668000971 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 400668000972 active site 400668000973 metal binding site 1 [ion binding]; metal-binding site 400668000974 putative 5' ssDNA interaction site; other site 400668000975 metal binding site 3; metal-binding site 400668000976 metal binding site 2 [ion binding]; metal-binding site 400668000977 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 400668000978 putative DNA binding site [nucleotide binding]; other site 400668000979 putative metal binding site [ion binding]; other site 400668000980 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 400668000981 active site 400668000982 catalytic site [active] 400668000983 substrate binding site [chemical binding]; other site 400668000984 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 400668000985 active site 400668000986 DNA binding site [nucleotide binding] 400668000987 catalytic site [active] 400668000988 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 400668000989 active site 400668000990 metal binding site [ion binding]; metal-binding site 400668000991 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668000992 Helix-turn-helix domains; Region: HTH; cl00088 400668000993 WYL domain; Region: WYL; cl14852 400668000994 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668000995 metal binding site [ion binding]; metal-binding site 400668000996 active site 400668000997 I-site; other site 400668000998 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 400668000999 putative active site [active] 400668001000 putative substrate binding site [chemical binding]; other site 400668001001 ATP binding site [chemical binding]; other site 400668001002 Protein of unknown function (DUF1007); Region: DUF1007; cl01487 400668001003 LysE type translocator; Region: LysE; cl00565 400668001004 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668001005 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 400668001006 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 400668001007 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 400668001008 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 400668001009 Protein export membrane protein; Region: SecD_SecF; cl14618 400668001010 Protein export membrane protein; Region: SecD_SecF; cl14618 400668001011 MarC family integral membrane protein; Region: MarC; cl00919 400668001012 High-affinity nickel-transport protein; Region: NicO; cl00964 400668001013 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 400668001014 metal binding site 2 [ion binding]; metal-binding site 400668001015 putative DNA binding helix; other site 400668001016 metal binding site 1 [ion binding]; metal-binding site 400668001017 dimer interface [polypeptide binding]; other site 400668001018 structural Zn2+ binding site [ion binding]; other site 400668001019 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 400668001020 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 400668001021 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 400668001022 dimer interface [polypeptide binding]; other site 400668001023 ABC-ATPase subunit interface; other site 400668001024 putative PBP binding regions; other site 400668001025 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 400668001026 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 400668001027 Cadherin repeat-like domain; Region: CA_like; cl15786 400668001028 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 400668001029 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 400668001030 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 400668001031 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 400668001032 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 400668001033 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 400668001034 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 400668001035 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 400668001036 active site 400668001037 putative substrate binding region [chemical binding]; other site 400668001038 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 400668001039 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 400668001040 sensory histidine kinase CreC; Provisional; Region: PRK11100 400668001041 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 400668001042 ATP binding site [chemical binding]; other site 400668001043 Mg2+ binding site [ion binding]; other site 400668001044 G-X-G motif; other site 400668001045 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668001046 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 400668001047 active site 400668001048 phosphorylation site [posttranslational modification] 400668001049 intermolecular recognition site; other site 400668001050 dimerization interface [polypeptide binding]; other site 400668001051 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 400668001052 DNA binding site [nucleotide binding] 400668001053 Flp/Fap pilin component; Region: Flp_Fap; cl01585 400668001054 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 400668001055 SAF domain; Region: SAF; cl00555 400668001056 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 400668001057 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 400668001058 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 400668001059 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 400668001060 Type IV pili component [Cell motility and secretion]; Region: COG5461; cl02279 400668001061 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 400668001062 active site 400668001063 phosphorylation site [posttranslational modification] 400668001064 intermolecular recognition site; other site 400668001065 dimerization interface [polypeptide binding]; other site 400668001066 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 400668001067 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 400668001068 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 400668001069 ATP binding site [chemical binding]; other site 400668001070 Walker A motif; other site 400668001071 hexamer interface [polypeptide binding]; other site 400668001072 Walker B motif; other site 400668001073 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 400668001074 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 400668001075 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 400668001076 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 400668001077 binding surface 400668001078 TPR motif; other site 400668001079 TadE-like protein; Region: TadE; cl10688 400668001080 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 400668001081 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 400668001082 heme binding pocket [chemical binding]; other site 400668001083 heme ligand [chemical binding]; other site 400668001084 Putative zinc-finger; Region: zf-HC2; cl15806 400668001085 RNA polymerase sigma factor; Provisional; Region: PRK12544 400668001086 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668001087 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 400668001088 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 400668001089 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 400668001090 trimer interface [polypeptide binding]; other site 400668001091 putative metal binding site [ion binding]; other site 400668001092 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 400668001093 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 400668001094 active site 400668001095 Zn binding site [ion binding]; other site 400668001096 Probable metal-binding protein (DUF2387); Region: DUF2387; cl01410 400668001097 HipA-like N-terminal domain; Region: HipA_N; pfam07805 400668001098 Protein of unknown function (DUF3037); Region: DUF3037; pfam11236 400668001099 Alpha amylase catalytic domain found in Amylosucrase; Region: AmyAc_Amylosucrase; cd11324 400668001100 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 400668001101 active site 400668001102 catalytic site [active] 400668001103 Protein of unknown function (DUF3750); Region: DUF3750; pfam12570 400668001104 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 400668001105 dimer interface [polypeptide binding]; other site 400668001106 FMN binding site [chemical binding]; other site 400668001107 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 400668001108 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 400668001109 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 400668001110 H+ Antiporter protein; Region: 2A0121; TIGR00900 400668001111 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 400668001112 putative substrate translocation pore; other site 400668001113 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 400668001114 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 400668001115 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains; Region: ACT_GcvR_2; cd04869 400668001116 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001117 Helix-turn-helix domains; Region: HTH; cl00088 400668001118 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 400668001119 putative effector binding pocket; other site 400668001120 dimerization interface [polypeptide binding]; other site 400668001121 EamA-like transporter family; Region: EamA; cl01037 400668001122 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668001123 EamA-like transporter family; Region: EamA; cl01037 400668001124 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 400668001125 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 400668001126 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 400668001127 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 400668001128 DNA photolyase; Region: DNA_photolyase; pfam00875 400668001129 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 400668001130 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001131 Helix-turn-helix domains; Region: HTH; cl00088 400668001132 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 400668001133 dimerization interface [polypeptide binding]; other site 400668001134 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001135 MAPEG family; Region: MAPEG; cl09190 400668001136 hypothetical protein; Provisional; Region: PRK10220 400668001137 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 400668001138 PhnA protein; Region: PhnA; pfam03831 400668001139 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 400668001140 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 400668001141 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668001142 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668001143 dimer interface [polypeptide binding]; other site 400668001144 putative CheW interface [polypeptide binding]; other site 400668001145 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 400668001146 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 400668001147 FAD binding pocket [chemical binding]; other site 400668001148 FAD binding motif [chemical binding]; other site 400668001149 phosphate binding motif [ion binding]; other site 400668001150 NAD binding pocket [chemical binding]; other site 400668001151 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 400668001152 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 400668001153 N-terminal plug; other site 400668001154 ligand-binding site [chemical binding]; other site 400668001155 siderophore transporter, RhtX/FptX family; Region: sider_RhtX_FptX; TIGR02718 400668001156 muropeptide transporter; Validated; Region: ampG; PRK11010 400668001157 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668001158 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668001159 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668001160 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 400668001161 Helix-turn-helix domains; Region: HTH; cl00088 400668001162 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 400668001163 short chain dehydrogenase; Provisional; Region: PRK06523 400668001164 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001165 NAD(P) binding site [chemical binding]; other site 400668001166 active site 400668001167 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668001168 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 400668001169 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 400668001170 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 400668001171 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 400668001172 catalytic residue [active] 400668001173 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 400668001174 catalytic residues [active] 400668001175 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668001176 peroxiredoxin; Region: AhpC; TIGR03137 400668001177 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 400668001178 dimer interface [polypeptide binding]; other site 400668001179 decamer (pentamer of dimers) interface [polypeptide binding]; other site 400668001180 catalytic triad [active] 400668001181 peroxidatic and resolving cysteines [active] 400668001182 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 400668001183 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 400668001184 active site 400668001185 phosphorylation site [posttranslational modification] 400668001186 intermolecular recognition site; other site 400668001187 dimerization interface [polypeptide binding]; other site 400668001188 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 400668001189 Zn2+ binding site [ion binding]; other site 400668001190 Mg2+ binding site [ion binding]; other site 400668001191 PAS domain S-box; Region: sensory_box; TIGR00229 400668001192 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 400668001193 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 400668001194 dimer interface [polypeptide binding]; other site 400668001195 phosphorylation site [posttranslational modification] 400668001196 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 400668001197 ATP binding site [chemical binding]; other site 400668001198 Mg2+ binding site [ion binding]; other site 400668001199 G-X-G motif; other site 400668001200 Response regulator receiver domain; Region: Response_reg; pfam00072 400668001201 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 400668001202 active site 400668001203 phosphorylation site [posttranslational modification] 400668001204 intermolecular recognition site; other site 400668001205 dimerization interface [polypeptide binding]; other site 400668001206 Response regulator receiver domain; Region: Response_reg; pfam00072 400668001207 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 400668001208 active site 400668001209 phosphorylation site [posttranslational modification] 400668001210 intermolecular recognition site; other site 400668001211 dimerization interface [polypeptide binding]; other site 400668001212 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 400668001213 putative binding surface; other site 400668001214 active site 400668001215 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 400668001216 putative ligand binding site [chemical binding]; other site 400668001217 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 400668001218 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 400668001219 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 400668001220 LamB/YcsF family; Region: LamB_YcsF; cl00664 400668001221 Amidase; Region: Amidase; cl11426 400668001222 Protein of unknown function (DUF502); Region: DUF502; cl01107 400668001223 HI0933-like protein; Region: HI0933_like; pfam03486 400668001224 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668001225 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001226 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 400668001227 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 400668001228 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668001229 ligand binding site [chemical binding]; other site 400668001230 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 400668001231 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001232 Rrf2 family protein; Region: rrf2_super; TIGR00738 400668001233 Helix-turn-helix domains; Region: HTH; cl00088 400668001234 Helix-turn-helix domains; Region: HTH; cl00088 400668001235 WYL domain; Region: WYL; cl14852 400668001236 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668001237 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_11; cd07261 400668001238 putative dimer interface [polypeptide binding]; other site 400668001239 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 400668001240 putative active site [active] 400668001241 metal binding site [ion binding]; metal-binding site 400668001242 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 400668001243 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 400668001244 putative C-terminal domain interface [polypeptide binding]; other site 400668001245 putative GSH binding site (G-site) [chemical binding]; other site 400668001246 putative dimer interface [polypeptide binding]; other site 400668001247 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 400668001248 putative N-terminal domain interface [polypeptide binding]; other site 400668001249 putative dimer interface [polypeptide binding]; other site 400668001250 putative substrate binding pocket (H-site) [chemical binding]; other site 400668001251 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 400668001252 Predicted small integral membrane protein (DUF2160); Region: DUF2160; cl02294 400668001253 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 400668001254 dimer interface [polypeptide binding]; other site 400668001255 conserved gate region; other site 400668001256 putative PBP binding loops; other site 400668001257 ABC-ATPase subunit interface; other site 400668001258 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 400668001259 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 400668001260 putative PBP binding loops; other site 400668001261 dimer interface [polypeptide binding]; other site 400668001262 ABC-ATPase subunit interface; other site 400668001263 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 400668001264 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 400668001265 Walker A/P-loop; other site 400668001266 ATP binding site [chemical binding]; other site 400668001267 Q-loop/lid; other site 400668001268 ABC transporter signature motif; other site 400668001269 Walker B; other site 400668001270 D-loop; other site 400668001271 H-loop/switch region; other site 400668001272 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 400668001273 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 400668001274 Walker A/P-loop; other site 400668001275 ATP binding site [chemical binding]; other site 400668001276 Q-loop/lid; other site 400668001277 ABC transporter signature motif; other site 400668001278 Walker B; other site 400668001279 D-loop; other site 400668001280 H-loop/switch region; other site 400668001281 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 400668001282 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 400668001283 Walker A motif; other site 400668001284 ATP binding site [chemical binding]; other site 400668001285 Walker B motif; other site 400668001286 arginine finger; other site 400668001287 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 400668001288 homotrimer interaction site [polypeptide binding]; other site 400668001289 putative active site [active] 400668001290 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001291 Helix-turn-helix domains; Region: HTH; cl00088 400668001292 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_3; cd08461 400668001293 putative substrate binding pocket [chemical binding]; other site 400668001294 putative dimerization interface [polypeptide binding]; other site 400668001295 Domain of unknown function (DUF1852); Region: DUF1852; pfam08908 400668001296 methionine synthase; Provisional; Region: PRK01207 400668001297 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 400668001298 substrate binding site [chemical binding]; other site 400668001299 THF binding site; other site 400668001300 zinc-binding site [ion binding]; other site 400668001301 Cupin domain; Region: Cupin_2; cl09118 400668001302 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668001303 Platelet-activating factor acetylhydrolase, isoform II; Region: PAF-AH_p_II; pfam03403 400668001304 LabA_like proteins; Region: LabA_like/DUF88; cl10034 400668001305 putative metal binding site [ion binding]; other site 400668001306 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 400668001307 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 400668001308 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cd03873 400668001309 metal binding site [ion binding]; metal-binding site 400668001310 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668001311 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 400668001312 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 400668001313 N-terminal plug; other site 400668001314 ligand-binding site [chemical binding]; other site 400668001315 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 400668001316 S-adenosylmethionine binding site [chemical binding]; other site 400668001317 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 400668001318 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668001319 putative substrate translocation pore; other site 400668001320 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 400668001321 PAS domain; Region: PAS_9; pfam13426 400668001322 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 400668001323 PAS domain; Region: PAS_9; pfam13426 400668001324 putative active site [active] 400668001325 heme pocket [chemical binding]; other site 400668001326 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668001327 dimer interface [polypeptide binding]; other site 400668001328 putative CheW interface [polypeptide binding]; other site 400668001329 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 400668001330 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 400668001331 FeS/SAM binding site; other site 400668001332 Cupin domain; Region: Cupin_2; cl09118 400668001333 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668001334 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668001335 2-isopropylmalate synthase; Validated; Region: PRK03739 400668001336 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 400668001337 active site 400668001338 catalytic residues [active] 400668001339 metal binding site [ion binding]; metal-binding site 400668001340 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 400668001341 diguanylate cyclase; Provisional; Region: PRK09894 400668001342 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 400668001343 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668001344 metal binding site [ion binding]; metal-binding site 400668001345 active site 400668001346 I-site; other site 400668001347 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 400668001348 dimer interface [polypeptide binding]; other site 400668001349 putative PBP binding regions; other site 400668001350 ABC-ATPase subunit interface; other site 400668001351 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 400668001352 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 400668001353 putative ligand binding residues [chemical binding]; other site 400668001354 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 400668001355 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 400668001356 Walker A/P-loop; other site 400668001357 ATP binding site [chemical binding]; other site 400668001358 Q-loop/lid; other site 400668001359 ABC transporter signature motif; other site 400668001360 Walker B; other site 400668001361 D-loop; other site 400668001362 H-loop/switch region; other site 400668001363 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 400668001364 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 400668001365 Walker A motif; other site 400668001366 ATP binding site [chemical binding]; other site 400668001367 Walker B motif; other site 400668001368 arginine finger; other site 400668001369 phage shock protein A; Region: phageshock_pspA; TIGR02977 400668001370 Phage shock protein B; Region: PspB; cl05946 400668001371 phage shock protein C; Region: phageshock_pspC; TIGR02978 400668001372 PspC domain; Region: PspC; cl00864 400668001373 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 400668001374 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 400668001375 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668001376 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668001377 dimer interface [polypeptide binding]; other site 400668001378 putative CheW interface [polypeptide binding]; other site 400668001379 OsmC-like protein; Region: OsmC; cl00767 400668001380 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 400668001381 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 400668001382 putative C-terminal domain interface [polypeptide binding]; other site 400668001383 putative GSH binding site (G-site) [chemical binding]; other site 400668001384 putative dimer interface [polypeptide binding]; other site 400668001385 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 400668001386 N-terminal domain interface [polypeptide binding]; other site 400668001387 dimer interface [polypeptide binding]; other site 400668001388 substrate binding pocket (H-site) [chemical binding]; other site 400668001389 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001390 Helix-turn-helix domains; Region: HTH; cl00088 400668001391 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 400668001392 dimerization interface [polypeptide binding]; other site 400668001393 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 400668001394 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668001395 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 400668001396 Coenzyme A binding pocket [chemical binding]; other site 400668001397 EamA-like transporter family; Region: EamA; cl01037 400668001398 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668001399 EamA-like transporter family; Region: EamA; cl01037 400668001400 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668001401 Helix-turn-helix domains; Region: HTH; cl00088 400668001402 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668001403 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 400668001404 dimerization interface [polypeptide binding]; other site 400668001405 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 400668001406 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 400668001407 ATP binding site [chemical binding]; other site 400668001408 Mg2+ binding site [ion binding]; other site 400668001409 G-X-G motif; other site 400668001410 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668001411 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 400668001412 active site 400668001413 phosphorylation site [posttranslational modification] 400668001414 intermolecular recognition site; other site 400668001415 dimerization interface [polypeptide binding]; other site 400668001416 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 400668001417 DNA binding site [nucleotide binding] 400668001418 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 400668001419 Peptidase propeptide and YPEB domain; Region: PepSY; cl15815 400668001420 Transcriptional regulators [Transcription]; Region: MarR; COG1846 400668001421 Helix-turn-helix domains; Region: HTH; cl00088 400668001422 OsmC-like protein; Region: OsmC; cl00767 400668001423 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_b; cd00914 400668001424 aromatic arch; other site 400668001425 DCoH dimer interaction site [polypeptide binding]; other site 400668001426 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 400668001427 DCoH tetramer interaction site [polypeptide binding]; other site 400668001428 substrate binding site [chemical binding]; other site 400668001429 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 400668001430 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 400668001431 Platelet-activating factor acetylhydrolase, isoform II; Region: PAF-AH_p_II; pfam03403 400668001432 Helix-turn-helix domain; Region: HTH_18; pfam12833 400668001433 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668001434 Protein of unknown function (DUF805); Region: DUF805; cl01224 400668001435 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001436 Helix-turn-helix domains; Region: HTH; cl00088 400668001437 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 400668001438 HPP family; Region: HPP; pfam04982 400668001439 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 400668001440 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668001441 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668001442 topology modulation protein; Reviewed; Region: PRK08118 400668001443 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668001444 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668001445 putative acetyltransferase; Provisional; Region: PRK03624 400668001446 Coenzyme A binding pocket [chemical binding]; other site 400668001447 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 400668001448 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668001449 Coenzyme A binding pocket [chemical binding]; other site 400668001450 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 400668001451 intersubunit interface [polypeptide binding]; other site 400668001452 active site 400668001453 Zn2+ binding site [ion binding]; other site 400668001454 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 400668001455 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668001456 substrate binding pocket [chemical binding]; other site 400668001457 membrane-bound complex binding site; other site 400668001458 hinge residues; other site 400668001459 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 400668001460 dimer interface [polypeptide binding]; other site 400668001461 conserved gate region; other site 400668001462 putative PBP binding loops; other site 400668001463 ABC-ATPase subunit interface; other site 400668001464 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668001465 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 400668001466 Walker A/P-loop; other site 400668001467 ATP binding site [chemical binding]; other site 400668001468 Q-loop/lid; other site 400668001469 ABC transporter signature motif; other site 400668001470 Walker B; other site 400668001471 D-loop; other site 400668001472 H-loop/switch region; other site 400668001473 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001474 Helix-turn-helix domains; Region: HTH; cl00088 400668001475 The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_PAO1_like; cd08412 400668001476 putative substrate binding pocket [chemical binding]; other site 400668001477 dimerization interface [polypeptide binding]; other site 400668001478 flavin-dependent oxidoreductase, MSMEG_0569 family; Region: MSMEG_0569_nitr; TIGR04046 400668001479 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001480 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 400668001481 homotrimer interaction site [polypeptide binding]; other site 400668001482 putative active site [active] 400668001483 Family of unknown function (DUF1028); Region: DUF1028; pfam06267 400668001484 acetylornithine deacetylase (ArgE); Region: AcOrn-deacetyl; TIGR01892 400668001485 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 400668001486 metal binding site [ion binding]; metal-binding site 400668001487 putative dimer interface [polypeptide binding]; other site 400668001488 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668001489 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 400668001490 Walker A/P-loop; other site 400668001491 ATP binding site [chemical binding]; other site 400668001492 Q-loop/lid; other site 400668001493 ABC transporter signature motif; other site 400668001494 Walker B; other site 400668001495 D-loop; other site 400668001496 H-loop/switch region; other site 400668001497 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668001498 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 400668001499 dimer interface [polypeptide binding]; other site 400668001500 conserved gate region; other site 400668001501 putative PBP binding loops; other site 400668001502 ABC-ATPase subunit interface; other site 400668001503 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 400668001504 dimer interface [polypeptide binding]; other site 400668001505 conserved gate region; other site 400668001506 putative PBP binding loops; other site 400668001507 ABC-ATPase subunit interface; other site 400668001508 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668001509 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 400668001510 substrate binding pocket [chemical binding]; other site 400668001511 membrane-bound complex binding site; other site 400668001512 hinge residues; other site 400668001513 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 400668001514 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 400668001515 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 400668001516 putative active site [active] 400668001517 Amidase; Region: Amidase; cl11426 400668001518 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 400668001519 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 400668001520 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668001521 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 400668001522 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 400668001523 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668001524 catalytic residue [active] 400668001525 allantoate amidohydrolase; Reviewed; Region: PRK09290 400668001526 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 400668001527 active site 400668001528 metal binding site [ion binding]; metal-binding site 400668001529 dimer interface [polypeptide binding]; other site 400668001530 Cupin domain; Region: Cupin_2; cl09118 400668001531 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668001532 dimer interface [polypeptide binding]; other site 400668001533 putative CheW interface [polypeptide binding]; other site 400668001534 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 400668001535 FAD dependent oxidoreductase; Region: DAO; pfam01266 400668001536 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001537 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_6; cd06154 400668001538 homotrimer interaction site [polypeptide binding]; other site 400668001539 putative active site [active] 400668001540 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001541 Ornithine cyclodeaminase/mu-crystallin family; Region: OCD_Mu_crystall; pfam02423 400668001542 Helix-turn-helix domain; Region: HTH_18; pfam12833 400668001543 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668001544 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 400668001545 siderophore binding site; other site 400668001546 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 400668001547 ABC-ATPase subunit interface; other site 400668001548 dimer interface [polypeptide binding]; other site 400668001549 putative PBP binding regions; other site 400668001550 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 400668001551 ABC-ATPase subunit interface; other site 400668001552 dimer interface [polypeptide binding]; other site 400668001553 putative PBP binding regions; other site 400668001554 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 400668001555 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 400668001556 Walker A/P-loop; other site 400668001557 ATP binding site [chemical binding]; other site 400668001558 Q-loop/lid; other site 400668001559 ABC transporter signature motif; other site 400668001560 Walker B; other site 400668001561 D-loop; other site 400668001562 H-loop/switch region; other site 400668001563 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 400668001564 FhuF 2Fe-2S C-terminal domain; Region: FhuF_C; pfam11575 400668001565 putative outer membrane receptor; Provisional; Region: PRK13513 400668001566 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 400668001567 N-terminal plug; other site 400668001568 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 400668001569 ligand-binding site [chemical binding]; other site 400668001570 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 400668001571 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 400668001572 active site 400668001573 catalytic site [active] 400668001574 tetramer interface [polypeptide binding]; other site 400668001575 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 400668001576 Transcriptional regulators [Transcription]; Region: GntR; COG1802 400668001577 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668001578 DNA-binding site [nucleotide binding]; DNA binding site 400668001579 FCD domain; Region: FCD; cl11656 400668001580 Sodium:solute symporter family; Region: SSF; cl00456 400668001581 Transcriptional regulator [Transcription]; Region: IclR; COG1414 400668001582 Helix-turn-helix domains; Region: HTH; cl00088 400668001583 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668001584 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 400668001585 ethanolamine permease; Region: 2A0305; TIGR00908 400668001586 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 400668001587 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 400668001588 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 400668001589 transcriptional regulator EutR; Provisional; Region: PRK10130 400668001590 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668001591 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668001592 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 400668001593 active site 400668001594 phosphorylation site [posttranslational modification] 400668001595 intermolecular recognition site; other site 400668001596 dimerization interface [polypeptide binding]; other site 400668001597 Helix-turn-helix domains; Region: HTH; cl00088 400668001598 DNA binding site [nucleotide binding] 400668001599 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 400668001600 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 400668001601 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 400668001602 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 400668001603 haemagglutination activity domain; Region: Haemagg_act; cl05436 400668001604 flagellin; Validated; Region: PRK08026 400668001605 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 400668001606 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 400668001607 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 400668001608 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001609 Helix-turn-helix domains; Region: HTH; cl00088 400668001610 The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold; Region: PBP2_ToxR; cd08465 400668001611 putative substrate binding pocket [chemical binding]; other site 400668001612 putative dimerization interface [polypeptide binding]; other site 400668001613 Protein of unknown function, DUF606; Region: DUF606; cl01273 400668001614 Domain of unknown function (DUF4394); Region: DUF4394; pfam14339 400668001615 Polysaccharide lyase; Region: Polysacc_lyase; pfam14099 400668001616 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 400668001617 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668001618 EamA-like transporter family; Region: EamA; cl01037 400668001619 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668001620 Polysaccharide lyase; Region: Polysacc_lyase; pfam14099 400668001621 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 400668001622 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668001623 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001624 Helix-turn-helix domains; Region: HTH; cl00088 400668001625 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 400668001626 dimerization interface [polypeptide binding]; other site 400668001627 SAF domain; Region: SAF; cl00555 400668001628 Altronate dehydratase [Carbohydrate transport and metabolism]; Region: UxaA; COG2721 400668001629 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 400668001630 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668001631 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668001632 tetramerization interface [polypeptide binding]; other site 400668001633 NAD(P) binding site [chemical binding]; other site 400668001634 catalytic residues [active] 400668001635 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 400668001636 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 400668001637 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668001638 NMT1-like family; Region: NMT1_2; cl15260 400668001639 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668001640 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668001641 N-acetyltransferase; Region: Acetyltransf_2; cl00949 400668001642 EamA-like transporter family; Region: EamA; cl01037 400668001643 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 400668001644 ligand binding site [chemical binding]; other site 400668001645 flexible hinge region; other site 400668001646 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001647 NAD(P) binding site [chemical binding]; other site 400668001648 3-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK12428 400668001649 active site 400668001650 Activator of aromatic catabolism; Region: XylR_N; pfam06505 400668001651 Heme NO binding; Region: HNOB; cl15268 400668001652 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 400668001653 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 400668001654 Walker A motif; other site 400668001655 ATP binding site [chemical binding]; other site 400668001656 Walker B motif; other site 400668001657 arginine finger; other site 400668001658 Helix-turn-helix domains; Region: HTH; cl00088 400668001659 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668001660 NAD-dependent benzaldehyde dehydrogenase II-like; Region: ALDH_BenzADH; cd07152 400668001661 NAD(P) binding site [chemical binding]; other site 400668001662 catalytic residues [active] 400668001663 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668001664 Helix-turn-helix domains; Region: HTH; cl00088 400668001665 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 400668001666 dimerization interface [polypeptide binding]; other site 400668001667 The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit; Region: PCA_45_Doxase_A; cd07924 400668001668 tetramer interface [polypeptide binding]; other site 400668001669 dimer interface [polypeptide binding]; other site 400668001670 active site 400668001671 Subunit B of Class III Extradiol ring-cleavage dioxygenases; Region: Extradiol_Dioxygenase_3B_like; cl00599 400668001672 active site 400668001673 metal binding site [ion binding]; metal-binding site 400668001674 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668001675 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 400668001676 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668001677 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668001678 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668001679 DctM-like transporters; Region: DctM; pfam06808 400668001680 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668001681 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 400668001682 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 400668001683 catalytic residues [active] 400668001684 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 400668001685 classical (c) SDRs; Region: SDR_c; cd05233 400668001686 NAD(P) binding site [chemical binding]; other site 400668001687 active site 400668001688 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668001689 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668001690 tetramerization interface [polypeptide binding]; other site 400668001691 NAD(P) binding site [chemical binding]; other site 400668001692 catalytic residues [active] 400668001693 Dehydratase family; Region: ILVD_EDD; cl00340 400668001694 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 400668001695 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 400668001696 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668001697 DctM-like transporters; Region: DctM; pfam06808 400668001698 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668001699 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668001700 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668001701 Helix-turn-helix domains; Region: HTH; cl00088 400668001702 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 400668001703 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 400668001704 active site 400668001705 catalytic tetrad [active] 400668001706 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 400668001707 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668001708 DNA-binding site [nucleotide binding]; DNA binding site 400668001709 UTRA domain; Region: UTRA; cl01230 400668001710 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668001711 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668001712 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 400668001713 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 400668001714 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 400668001715 Helix-turn-helix domains; Region: HTH; cl00088 400668001716 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 400668001717 dimerization interface [polypeptide binding]; other site 400668001718 substrate binding pocket [chemical binding]; other site 400668001719 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668001720 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001721 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668001722 Membrane transport protein; Region: Mem_trans; cl09117 400668001723 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 400668001724 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668001725 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 400668001726 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 400668001727 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668001728 active site 400668001729 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 400668001730 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 400668001731 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001732 dihydroorotase; Validated; Region: pyrC; PRK09357 400668001733 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 400668001734 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 400668001735 active site 400668001736 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668001737 metal binding site [ion binding]; metal-binding site 400668001738 active site 400668001739 I-site; other site 400668001740 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 400668001741 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668001742 catalytic residue [active] 400668001743 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 400668001744 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001745 YGGT family; Region: YGGT; cl00508 400668001746 YGGT family; Region: YGGT; cl00508 400668001747 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 400668001748 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 400668001749 active site 400668001750 (T/H)XGH motif; other site 400668001751 ferredoxin; Validated; Region: PRK07118 400668001752 potassium/proton antiporter; Reviewed; Region: PRK05326 400668001753 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 400668001754 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 400668001755 Transporter associated domain; Region: CorC_HlyC; cl08393 400668001756 Ion channel; Region: Ion_trans_2; cl11596 400668001757 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668001758 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 400668001759 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 400668001760 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 400668001761 DNA binding site [nucleotide binding] 400668001762 Int/Topo IB signature motif; other site 400668001763 active site 400668001764 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 400668001765 DNA binding residues [nucleotide binding] 400668001766 dimerization interface [polypeptide binding]; other site 400668001767 KilA-N domain; Region: KilA-N; pfam04383 400668001768 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 400668001769 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 400668001770 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 400668001771 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 400668001772 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 400668001773 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 400668001774 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VgrG; COG3501 400668001775 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 400668001776 Baseplate J-like protein; Region: Baseplate_J; cl01294 400668001777 Protein of unknown function (DUF2590); Region: DUF2590; pfam10761 400668001778 Phage-related minor tail protein; Region: PhageMin_Tail; pfam10145 400668001779 Protein of unknown function (DUF2765); Region: DUF2765; pfam10963 400668001780 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 400668001781 Protein of unknown function (DUF2597); Region: DUF2597; pfam10772 400668001782 Protein of unknown function (DUF2586); Region: DUF2586; pfam10758 400668001783 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 400668001784 Phage head completion protein (GPL); Region: Phage_GPL; pfam05926 400668001785 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 400668001786 Phage major capsid protein, P2 family; Region: Phage_cap_P2; cl04947 400668001787 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; cl15838 400668001788 terminase ATPase subunit; Provisional; Region: P; PHA02535 400668001789 Helix-turn-helix domains; Region: HTH; cl00088 400668001790 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 400668001791 Phage-related protein [Function unknown]; Region: COG4695; cl01923 400668001792 phage portal protein, PBSX family; Region: portal_PBSX; TIGR01540 400668001793 DNA ligase; Provisional; Region: PRK09125 400668001794 Nucleoid-associated protein [General function prediction only]; Region: COG3081 400668001795 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 400668001796 Ion transport protein; Region: Ion_trans; pfam00520 400668001797 Ion channel; Region: Ion_trans_2; cl11596 400668001798 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 400668001799 active site 400668001800 MASE1; Region: MASE1; pfam05231 400668001801 CHASE domain; Region: CHASE; cl01369 400668001802 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 400668001803 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 400668001804 dimer interface [polypeptide binding]; other site 400668001805 phosphorylation site [posttranslational modification] 400668001806 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 400668001807 ATP binding site [chemical binding]; other site 400668001808 Mg2+ binding site [ion binding]; other site 400668001809 G-X-G motif; other site 400668001810 Response regulator receiver domain; Region: Response_reg; pfam00072 400668001811 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 400668001812 active site 400668001813 phosphorylation site [posttranslational modification] 400668001814 intermolecular recognition site; other site 400668001815 dimerization interface [polypeptide binding]; other site 400668001816 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 400668001817 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668001818 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 400668001819 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 400668001820 dimer interface [polypeptide binding]; other site 400668001821 conserved gate region; other site 400668001822 putative PBP binding loops; other site 400668001823 ABC-ATPase subunit interface; other site 400668001824 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668001825 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 400668001826 dimer interface [polypeptide binding]; other site 400668001827 conserved gate region; other site 400668001828 putative PBP binding loops; other site 400668001829 ABC-ATPase subunit interface; other site 400668001830 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668001831 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668001832 Walker A/P-loop; other site 400668001833 ATP binding site [chemical binding]; other site 400668001834 Q-loop/lid; other site 400668001835 ABC transporter signature motif; other site 400668001836 Walker B; other site 400668001837 D-loop; other site 400668001838 H-loop/switch region; other site 400668001839 TOBE domain; Region: TOBE_2; cl01440 400668001840 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 400668001841 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 400668001842 putative active site [active] 400668001843 catalytic site [active] 400668001844 putative metal binding site [ion binding]; other site 400668001845 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 400668001846 Helix-turn-helix domains; Region: HTH; cl00088 400668001847 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 400668001848 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 400668001849 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 400668001850 active site 400668001851 motif I; other site 400668001852 motif II; other site 400668001853 Protein of unknown function (DUF808); Region: DUF808; cl01002 400668001854 Transcriptional regulator [Transcription]; Region: IclR; COG1414 400668001855 Helix-turn-helix domains; Region: HTH; cl00088 400668001856 Bacterial transcriptional regulator; Region: IclR; pfam01614 400668001857 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 400668001858 phosphate binding site [ion binding]; other site 400668001859 putative substrate binding pocket [chemical binding]; other site 400668001860 dimer interface [polypeptide binding]; other site 400668001861 Response regulator receiver domain; Region: Response_reg; pfam00072 400668001862 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 400668001863 active site 400668001864 phosphorylation site [posttranslational modification] 400668001865 intermolecular recognition site; other site 400668001866 dimerization interface [polypeptide binding]; other site 400668001867 Chemotaxis protein CheC, inhibitor of MCP methylation [Cell motility and secretion / Signal transduction mechanisms]; Region: CheC; COG1776 400668001868 Chemotaxis phosphatase CheX; Region: CheX; cl15816 400668001869 PAS fold; Region: PAS; pfam00989 400668001870 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668001871 metal binding site [ion binding]; metal-binding site 400668001872 active site 400668001873 I-site; other site 400668001874 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 400668001875 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 400668001876 active site 400668001877 phosphate binding residues; other site 400668001878 catalytic residues [active] 400668001879 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 400668001880 putative active site [active] 400668001881 putative DNA binding site [nucleotide binding]; other site 400668001882 putative phosphate binding site [ion binding]; other site 400668001883 putative catalytic site [active] 400668001884 metal binding site A [ion binding]; metal-binding site 400668001885 putative AP binding site [nucleotide binding]; other site 400668001886 putative metal binding site B [ion binding]; other site 400668001887 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 400668001888 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668001889 active site 400668001890 division inhibitor protein; Provisional; Region: slmA; PRK09480 400668001891 Helix-turn-helix domains; Region: HTH; cl00088 400668001892 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 400668001893 feedback inhibition sensing region; other site 400668001894 homohexameric interface [polypeptide binding]; other site 400668001895 nucleotide binding site [chemical binding]; other site 400668001896 N-acetyl-L-glutamate binding site [chemical binding]; other site 400668001897 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 400668001898 trimer interface [polypeptide binding]; other site 400668001899 active site 400668001900 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 400668001901 Flavoprotein; Region: Flavoprotein; cl08021 400668001902 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 400668001903 hypothetical protein; Reviewed; Region: PRK00024 400668001904 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 400668001905 MPN+ (JAMM) motif; other site 400668001906 Zinc-binding site [ion binding]; other site 400668001907 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 400668001908 putative transposase OrfB; Reviewed; Region: PHA02517 400668001909 HTH-like domain; Region: HTH_21; pfam13276 400668001910 Integrase core domain; Region: rve; cl01316 400668001911 Integrase core domain; Region: rve_3; cl15866 400668001912 Helix-turn-helix domains; Region: HTH; cl00088 400668001913 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 400668001914 HipA N-terminal domain; Region: Couple_hipA; cl11853 400668001915 HipA-like N-terminal domain; Region: HipA_N; pfam07805 400668001916 HipA-like C-terminal domain; Region: HipA_C; pfam07804 400668001917 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 400668001918 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 400668001919 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 400668001920 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 400668001921 DNA binding site [nucleotide binding] 400668001922 catalytic residue [active] 400668001923 H2TH interface [polypeptide binding]; other site 400668001924 putative catalytic residues [active] 400668001925 turnover-facilitating residue; other site 400668001926 intercalation triad [nucleotide binding]; other site 400668001927 8OG recognition residue [nucleotide binding]; other site 400668001928 putative reading head residues; other site 400668001929 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 400668001930 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 400668001931 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 400668001932 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 400668001933 ligand binding site [chemical binding]; other site 400668001934 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 400668001935 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 400668001936 Walker A/P-loop; other site 400668001937 ATP binding site [chemical binding]; other site 400668001938 Q-loop/lid; other site 400668001939 ABC transporter signature motif; other site 400668001940 Walker B; other site 400668001941 D-loop; other site 400668001942 H-loop/switch region; other site 400668001943 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 400668001944 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 400668001945 TM-ABC transporter signature motif; other site 400668001946 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 400668001947 TM-ABC transporter signature motif; other site 400668001948 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 400668001949 active site 400668001950 catalytic motif [active] 400668001951 Zn binding site [ion binding]; other site 400668001952 Putative ammonia monooxygenase [General function prediction only]; Region: AbrB; COG3180 400668001953 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 400668001954 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 400668001955 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 400668001956 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 400668001957 CoA-ligase; Region: Ligase_CoA; cl02894 400668001958 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 400668001959 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668001960 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 400668001961 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668001962 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 400668001963 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 400668001964 2-deoxyglucose-6-phosphatase; Provisional; Region: PRK10826 400668001965 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 400668001966 motif II; other site 400668001967 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668001968 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668001969 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668001970 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668001971 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668001972 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668001973 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668001974 DctM-like transporters; Region: DctM; pfam06808 400668001975 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668001976 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 400668001977 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 400668001978 conserved cys residue [active] 400668001979 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668001980 sulfate/thiosulfate transporter subunit; Provisional; Region: PRK10851 400668001981 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 400668001982 Walker A/P-loop; other site 400668001983 ATP binding site [chemical binding]; other site 400668001984 Q-loop/lid; other site 400668001985 ABC transporter signature motif; other site 400668001986 Walker B; other site 400668001987 D-loop; other site 400668001988 H-loop/switch region; other site 400668001989 TOBE-like domain; Region: TOBE_3; pfam12857 400668001990 sulfate transport protein; Provisional; Region: cysT; CHL00187 400668001991 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 400668001992 dimer interface [polypeptide binding]; other site 400668001993 conserved gate region; other site 400668001994 putative PBP binding loops; other site 400668001995 ABC-ATPase subunit interface; other site 400668001996 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 400668001997 dimer interface [polypeptide binding]; other site 400668001998 conserved gate region; other site 400668001999 putative PBP binding loops; other site 400668002000 ABC-ATPase subunit interface; other site 400668002001 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 400668002002 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 400668002003 FeoA domain; Region: FeoA; cl00838 400668002004 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 400668002005 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 400668002006 G1 box; other site 400668002007 GTP/Mg2+ binding site [chemical binding]; other site 400668002008 Switch I region; other site 400668002009 G2 box; other site 400668002010 G3 box; other site 400668002011 Switch II region; other site 400668002012 G4 box; other site 400668002013 Nucleoside recognition; Region: Gate; cl00486 400668002014 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 400668002015 Nucleoside recognition; Region: Gate; cl00486 400668002016 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668002017 metal binding site [ion binding]; metal-binding site 400668002018 active site 400668002019 I-site; other site 400668002020 Cupin domain; Region: Cupin_2; cl09118 400668002021 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 400668002022 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 400668002023 binding surface 400668002024 TPR motif; other site 400668002025 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668002026 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 400668002027 binding surface 400668002028 TPR motif; other site 400668002029 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 400668002030 non-specific DNA binding site [nucleotide binding]; other site 400668002031 salt bridge; other site 400668002032 sequence-specific DNA binding site [nucleotide binding]; other site 400668002033 Helix-turn-helix domains; Region: HTH; cl00088 400668002034 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 400668002035 anthranilate synthase component I, archaeal clade; Region: TrpE-arch; TIGR01820 400668002036 chorismate binding enzyme; Region: Chorismate_bind; cl10555 400668002037 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 400668002038 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 400668002039 glutamine binding [chemical binding]; other site 400668002040 catalytic triad [active] 400668002041 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 400668002042 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 400668002043 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 400668002044 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 400668002045 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 400668002046 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB2; cd01048 400668002047 diiron binding motif [ion binding]; other site 400668002048 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 400668002049 putative active site [active] 400668002050 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 400668002051 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668002052 Coenzyme A binding pocket [chemical binding]; other site 400668002053 PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate...; Region: PAF_acetylesterase_like; cd01820 400668002054 active site 400668002055 catalytic triad [active] 400668002056 oxyanion hole [active] 400668002057 specificity pocket; other site 400668002058 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668002059 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668002060 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002061 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 400668002062 Cache domain; Region: Cache_2; cl07034 400668002063 Histidine kinase; Region: HisKA_3; pfam07730 400668002064 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 400668002065 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668002066 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 400668002067 active site 400668002068 phosphorylation site [posttranslational modification] 400668002069 intermolecular recognition site; other site 400668002070 dimerization interface [polypeptide binding]; other site 400668002071 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 400668002072 DNA binding site [nucleotide binding] 400668002073 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 400668002074 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 400668002075 dimer interface [polypeptide binding]; other site 400668002076 phosphorylation site [posttranslational modification] 400668002077 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 400668002078 ATP binding site [chemical binding]; other site 400668002079 Mg2+ binding site [ion binding]; other site 400668002080 G-X-G motif; other site 400668002081 putative metal dependent hydrolase; Provisional; Region: PRK11598 400668002082 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 400668002083 Sulfatase; Region: Sulfatase; cl10460 400668002084 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 400668002085 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 400668002086 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 400668002087 active site 400668002088 phosphorylation site [posttranslational modification] 400668002089 intermolecular recognition site; other site 400668002090 dimerization interface [polypeptide binding]; other site 400668002091 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 400668002092 DNA binding residues [nucleotide binding] 400668002093 dimerization interface [polypeptide binding]; other site 400668002094 diaminopimelate epimerase; Provisional; Region: PRK13577 400668002095 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 400668002096 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 400668002097 TM1410 hypothetical-related protein; Region: DUF297; cl00997 400668002098 Stress responsive A/B Barrel Domain; Region: Dabb; cl15807 400668002099 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 400668002100 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 400668002101 potential catalytic triad [active] 400668002102 conserved cys residue [active] 400668002103 transcriptional regulator; Provisional; Region: PRK10632 400668002104 Helix-turn-helix domains; Region: HTH; cl00088 400668002105 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 400668002106 putative effector binding pocket; other site 400668002107 dimerization interface [polypeptide binding]; other site 400668002108 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 400668002109 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668002110 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668002111 dimer interface [polypeptide binding]; other site 400668002112 putative CheW interface [polypeptide binding]; other site 400668002113 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668002114 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668002115 dimer interface [polypeptide binding]; other site 400668002116 putative CheW interface [polypeptide binding]; other site 400668002117 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 400668002118 Isochorismatase family; Region: Isochorismatase; pfam00857 400668002119 catalytic triad [active] 400668002120 conserved cis-peptide bond; other site 400668002121 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 400668002122 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 400668002123 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668002124 homodimer interface [polypeptide binding]; other site 400668002125 catalytic residue [active] 400668002126 iron-dicitrate transporter ATP-binding subunit; Provisional; Region: fecE; PRK11231 400668002127 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 400668002128 Walker A/P-loop; other site 400668002129 ATP binding site [chemical binding]; other site 400668002130 Q-loop/lid; other site 400668002131 ABC transporter signature motif; other site 400668002132 Walker B; other site 400668002133 D-loop; other site 400668002134 H-loop/switch region; other site 400668002135 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 400668002136 ABC-ATPase subunit interface; other site 400668002137 dimer interface [polypeptide binding]; other site 400668002138 putative PBP binding regions; other site 400668002139 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 400668002140 ABC-ATPase subunit interface; other site 400668002141 dimer interface [polypeptide binding]; other site 400668002142 putative PBP binding regions; other site 400668002143 ABC-type Fe3+-citrate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FecB; COG4594 400668002144 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 400668002145 siderophore binding site; other site 400668002146 gluconate operon transcriptional regulator; Provisional; Region: PRK14987 400668002147 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668002148 DNA binding site [nucleotide binding] 400668002149 domain linker motif; other site 400668002150 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 400668002151 putative ligand binding site [chemical binding]; other site 400668002152 putative dimerization interface [polypeptide binding]; other site 400668002153 Shikimate kinase; Region: SKI; pfam01202 400668002154 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 400668002155 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002156 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668002157 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668002158 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 400668002159 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 400668002160 ligand binding site [chemical binding]; other site 400668002161 flexible hinge region; other site 400668002162 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 400668002163 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 400668002164 metal binding triad; other site 400668002165 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 400668002166 active site 400668002167 substrate binding site [chemical binding]; other site 400668002168 catalytic site [active] 400668002169 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 400668002170 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; cl00246 400668002171 FAD binding site [chemical binding]; other site 400668002172 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 400668002173 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 400668002174 putative active site [active] 400668002175 putative metal binding site [ion binding]; other site 400668002176 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 400668002177 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 400668002178 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668002179 metal binding site [ion binding]; metal-binding site 400668002180 active site 400668002181 I-site; other site 400668002182 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 400668002183 Cupin domain; Region: Cupin_2; cl09118 400668002184 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668002185 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 400668002186 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002187 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family; Region: SWIM_PBPRA1643; TIGR04102 400668002188 SEC-C motif; Region: SEC-C; pfam02810 400668002189 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668002190 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668002191 DctM-like transporters; Region: DctM; pfam06808 400668002192 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002193 LPP20 lipoprotein; Region: LPP20; cl15824 400668002194 TolB amino-terminal domain; Region: TolB_N; cl00639 400668002195 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 400668002196 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 400668002197 SecA binding site; other site 400668002198 Preprotein binding site; other site 400668002199 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 400668002200 GSH binding site [chemical binding]; other site 400668002201 catalytic residues [active] 400668002202 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 400668002203 active site residue [active] 400668002204 Domain of unknown function (DUF1338); Region: DUF1338; cl02226 400668002205 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668002206 Helix-turn-helix domains; Region: HTH; cl00088 400668002207 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 400668002208 dimerization interface [polypeptide binding]; other site 400668002209 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 400668002210 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668002211 tetrameric interface [polypeptide binding]; other site 400668002212 NAD binding site [chemical binding]; other site 400668002213 catalytic residues [active] 400668002214 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002215 FAD dependent oxidoreductase; Region: DAO; pfam01266 400668002216 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668002217 Helix-turn-helix domains; Region: HTH; cl00088 400668002218 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 400668002219 dimerization interface [polypeptide binding]; other site 400668002220 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 400668002221 Sulfatase; Region: Sulfatase; cl10460 400668002222 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 400668002223 Haemolysin XhlA; Region: XhlA; pfam10779 400668002224 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 400668002225 C-terminal peptidase (prc); Region: prc; TIGR00225 400668002226 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 400668002227 protein binding site [polypeptide binding]; other site 400668002228 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 400668002229 Catalytic dyad [active] 400668002230 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 400668002231 NodB motif; other site 400668002232 putative active site [active] 400668002233 putative catalytic site [active] 400668002234 Zn binding site [ion binding]; other site 400668002235 leucine ABC transporter subunit substrate-binding protein LivK; Provisional; Region: PRK15404 400668002236 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 400668002237 dimerization interface [polypeptide binding]; other site 400668002238 ligand binding site [chemical binding]; other site 400668002239 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 400668002240 TM-ABC transporter signature motif; other site 400668002241 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 400668002242 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 400668002243 TM-ABC transporter signature motif; other site 400668002244 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 400668002245 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 400668002246 Walker A/P-loop; other site 400668002247 ATP binding site [chemical binding]; other site 400668002248 Q-loop/lid; other site 400668002249 ABC transporter signature motif; other site 400668002250 Walker B; other site 400668002251 D-loop; other site 400668002252 H-loop/switch region; other site 400668002253 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 400668002254 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 400668002255 Walker A/P-loop; other site 400668002256 ATP binding site [chemical binding]; other site 400668002257 Q-loop/lid; other site 400668002258 ABC transporter signature motif; other site 400668002259 Walker B; other site 400668002260 D-loop; other site 400668002261 H-loop/switch region; other site 400668002262 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 400668002263 Protein of unknown function (DUF3461); Region: DUF3461; cl10125 400668002264 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 400668002265 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 400668002266 active site 400668002267 phosphorylation site [posttranslational modification] 400668002268 intermolecular recognition site; other site 400668002269 dimerization interface [polypeptide binding]; other site 400668002270 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 400668002271 Walker A motif; other site 400668002272 ATP binding site [chemical binding]; other site 400668002273 Walker B motif; other site 400668002274 arginine finger; other site 400668002275 Helix-turn-helix domains; Region: HTH; cl00088 400668002276 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 400668002277 nitrogen regulation protein NR(II); Provisional; Region: glnL; PRK11073 400668002278 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 400668002279 dimer interface [polypeptide binding]; other site 400668002280 phosphorylation site [posttranslational modification] 400668002281 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 400668002282 ATP binding site [chemical binding]; other site 400668002283 Mg2+ binding site [ion binding]; other site 400668002284 G-X-G motif; other site 400668002285 glutamine synthetase; Provisional; Region: glnA; PRK09469 400668002286 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 400668002287 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 400668002288 tRNA s(4)U8 sulfurtransferase; Provisional; Region: PRK01269 400668002289 THUMP domain; Region: THUMP; cl12076 400668002290 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 400668002291 Ligand Binding Site [chemical binding]; other site 400668002292 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 400668002293 active site residue [active] 400668002294 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 400668002295 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 400668002296 G1 box; other site 400668002297 putative GEF interaction site [polypeptide binding]; other site 400668002298 GTP/Mg2+ binding site [chemical binding]; other site 400668002299 Switch I region; other site 400668002300 G2 box; other site 400668002301 G3 box; other site 400668002302 Switch II region; other site 400668002303 G4 box; other site 400668002304 G5 box; other site 400668002305 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 400668002306 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 400668002307 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 400668002308 putative active site [active] 400668002309 dimerization interface [polypeptide binding]; other site 400668002310 putative tRNAtyr binding site [nucleotide binding]; other site 400668002311 Pectinesterase; Region: Pectinesterase; cl01911 400668002312 Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are...; Region: Rhamnogalacturan_acetylesterase_like; cd01821 400668002313 active site 400668002314 catalytic triad [active] 400668002315 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 400668002316 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 400668002317 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 400668002318 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 400668002319 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 400668002320 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668002321 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 400668002322 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 400668002323 S-adenosylmethionine binding site [chemical binding]; other site 400668002324 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668002325 metal binding site [ion binding]; metal-binding site 400668002326 active site 400668002327 I-site; other site 400668002328 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 400668002329 catalytic residues [active] 400668002330 hinge region; other site 400668002331 alpha helical domain; other site 400668002332 Predicted GTPase [General function prediction only]; Region: COG0218 400668002333 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 400668002334 G1 box; other site 400668002335 GTP/Mg2+ binding site [chemical binding]; other site 400668002336 Switch I region; other site 400668002337 G2 box; other site 400668002338 G3 box; other site 400668002339 Switch II region; other site 400668002340 G4 box; other site 400668002341 G5 box; other site 400668002342 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl15791 400668002343 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 400668002344 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 400668002345 substrate binding site [chemical binding]; other site 400668002346 glutamase interaction surface [polypeptide binding]; other site 400668002347 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 400668002348 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 400668002349 putative active site [active] 400668002350 oxyanion strand; other site 400668002351 catalytic triad [active] 400668002352 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 400668002353 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 400668002354 putative active site pocket [active] 400668002355 4-fold oligomerization interface [polypeptide binding]; other site 400668002356 metal binding residues [ion binding]; metal-binding site 400668002357 3-fold/trimer interface [polypeptide binding]; other site 400668002358 AsmA family; Region: AsmA; pfam05170 400668002359 AsmA-like C-terminal region; Region: AsmA_2; cl15864 400668002360 adenine DNA glycosylase; Provisional; Region: PRK10880 400668002361 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 400668002362 minor groove reading motif; other site 400668002363 helix-hairpin-helix signature motif; other site 400668002364 substrate binding pocket [chemical binding]; other site 400668002365 active site 400668002366 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 400668002367 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 400668002368 DNA binding and oxoG recognition site [nucleotide binding] 400668002369 Chromate transporter; Region: Chromate_transp; pfam02417 400668002370 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 400668002371 Chromate transporter; Region: Chromate_transp; pfam02417 400668002372 putative transposase OrfB; Reviewed; Region: PHA02517 400668002373 HTH-like domain; Region: HTH_21; pfam13276 400668002374 Integrase core domain; Region: rve; cl01316 400668002375 Integrase core domain; Region: rve_3; cl15866 400668002376 Helix-turn-helix domains; Region: HTH; cl00088 400668002377 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 400668002378 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 400668002379 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 400668002380 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 400668002381 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 400668002382 structural tetrad; other site 400668002383 Protein of unknown function (DUF423); Region: DUF423; cl01008 400668002384 Methyltransferase domain; Region: Methyltransf_31; pfam13847 400668002385 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 400668002386 S-adenosylmethionine binding site [chemical binding]; other site 400668002387 H-NS histone family; Region: Histone_HNS; pfam00816 400668002388 Domain in histone-like proteins of HNS family; Region: HNS; cl09251 400668002389 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 400668002390 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 400668002391 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 400668002392 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 400668002393 RNA binding site [nucleotide binding]; other site 400668002394 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668002395 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668002396 Helix-turn-helix domains; Region: HTH; cl00088 400668002397 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 400668002398 dimerization interface [polypeptide binding]; other site 400668002399 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 400668002400 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 400668002401 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 400668002402 Substrate binding site; other site 400668002403 Mg++ binding site; other site 400668002404 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 400668002405 active site 400668002406 substrate binding site [chemical binding]; other site 400668002407 CoA binding site [chemical binding]; other site 400668002408 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 400668002409 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 400668002410 glutaminase active site [active] 400668002411 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 400668002412 dimer interface [polypeptide binding]; other site 400668002413 active site 400668002414 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 400668002415 dimer interface [polypeptide binding]; other site 400668002416 active site 400668002417 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 400668002418 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668002419 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 400668002420 dimer interface [polypeptide binding]; other site 400668002421 conserved gate region; other site 400668002422 putative PBP binding loops; other site 400668002423 ABC-ATPase subunit interface; other site 400668002424 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668002425 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 400668002426 dimer interface [polypeptide binding]; other site 400668002427 conserved gate region; other site 400668002428 putative PBP binding loops; other site 400668002429 ABC-ATPase subunit interface; other site 400668002430 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668002431 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668002432 Walker A/P-loop; other site 400668002433 ATP binding site [chemical binding]; other site 400668002434 Q-loop/lid; other site 400668002435 ABC transporter signature motif; other site 400668002436 Walker B; other site 400668002437 D-loop; other site 400668002438 H-loop/switch region; other site 400668002439 TOBE domain; Region: TOBE_2; cl01440 400668002440 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668002441 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 400668002442 2-deoxy-D-gluconate 3-dehydrogenase; Validated; Region: PRK08993 400668002443 gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs; Region: Ga5DH-like_SDR_c; cd05347 400668002444 NADP binding site [chemical binding]; other site 400668002445 homodimer interface [polypeptide binding]; other site 400668002446 active site 400668002447 DNA-binding transcriptional regulator KdgR; Provisional; Region: PRK15090 400668002448 Helix-turn-helix domains; Region: HTH; cl00088 400668002449 Bacterial transcriptional regulator; Region: IclR; pfam01614 400668002450 Cupin domain; Region: Cupin_2; cl09118 400668002451 hypothetical protein; Provisional; Region: PRK09273 400668002452 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 400668002453 Ribose-5-phosphate isomerase; Region: DUF3666; pfam12408 400668002454 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 400668002455 DNA binding residues [nucleotide binding] 400668002456 dimerization interface [polypeptide binding]; other site 400668002457 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 400668002458 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 400668002459 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668002460 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668002461 Walker A/P-loop; other site 400668002462 ATP binding site [chemical binding]; other site 400668002463 Q-loop/lid; other site 400668002464 ABC transporter signature motif; other site 400668002465 Walker B; other site 400668002466 D-loop; other site 400668002467 H-loop/switch region; other site 400668002468 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 400668002469 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 400668002470 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 400668002471 Transposase IS200 like; Region: Y1_Tnp; cl00848 400668002472 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 400668002473 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 400668002474 Protein of unknown function (DUF2886); Region: DUF2886; pfam11102 400668002475 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 400668002476 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 400668002477 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 400668002478 SLBB domain; Region: SLBB; pfam10531 400668002479 SLBB domain; Region: SLBB; pfam10531 400668002480 SLBB domain; Region: SLBB; pfam10531 400668002481 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 400668002482 Chain length determinant protein; Region: Wzz; cl15801 400668002483 Transposase IS200 like; Region: Y1_Tnp; cl00848 400668002484 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 400668002485 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668002486 Beta-Casp domain; Region: Beta-Casp; cl12567 400668002487 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 400668002488 Helix-turn-helix domains; Region: HTH; cl00088 400668002489 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 400668002490 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 400668002491 putative NAD(P) binding site [chemical binding]; other site 400668002492 active site 400668002493 putative substrate binding site [chemical binding]; other site 400668002494 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 400668002495 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002496 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 400668002497 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002498 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 400668002499 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 400668002500 active site 400668002501 homodimer interface [polypeptide binding]; other site 400668002502 UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional; Region: wecC; PRK11064 400668002503 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 400668002504 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002505 MatE; Region: MatE; cl10513 400668002506 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 400668002507 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 400668002508 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 400668002509 putative active site [active] 400668002510 putative metal binding site [ion binding]; other site 400668002511 AMP-binding enzyme; Region: AMP-binding; cl15778 400668002512 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 400668002513 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members; Region: 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_; cd08255 400668002514 putative NAD(P) binding site [chemical binding]; other site 400668002515 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002516 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668002517 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668002518 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 400668002519 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 400668002520 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 400668002521 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 400668002522 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 400668002523 putative NAD(P) binding site [chemical binding]; other site 400668002524 active site 400668002525 putative substrate binding site [chemical binding]; other site 400668002526 Bacterial sugar transferase; Region: Bac_transf; cl00939 400668002527 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 400668002528 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 400668002529 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 400668002530 NAD(P) binding site [chemical binding]; other site 400668002531 homodimer interface [polypeptide binding]; other site 400668002532 substrate binding site [chemical binding]; other site 400668002533 active site 400668002534 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 400668002535 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668002536 UDP-glucose 4-epimerase; Region: PLN02240 400668002537 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 400668002538 NAD binding site [chemical binding]; other site 400668002539 homodimer interface [polypeptide binding]; other site 400668002540 active site 400668002541 substrate binding site [chemical binding]; other site 400668002542 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 400668002543 active site 400668002544 NTP binding site [chemical binding]; other site 400668002545 metal binding triad [ion binding]; metal-binding site 400668002546 antibiotic binding site [chemical binding]; other site 400668002547 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 400668002548 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 400668002549 Substrate binding site; other site 400668002550 Cupin domain; Region: Cupin_2; cl09118 400668002551 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 400668002552 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002553 NAD(P) binding site [chemical binding]; other site 400668002554 active site 400668002555 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 400668002556 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002557 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668002558 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002559 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668002560 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 400668002561 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 400668002562 putative trimer interface [polypeptide binding]; other site 400668002563 putative active site [active] 400668002564 putative substrate binding site [chemical binding]; other site 400668002565 putative CoA binding site [chemical binding]; other site 400668002566 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 400668002567 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 400668002568 inhibitor-cofactor binding pocket; inhibition site 400668002569 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668002570 catalytic residue [active] 400668002571 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 400668002572 4-alpha-L-fucosyltransferase glycosyl transferase group 56; Region: Glyco_transf_56; cl07929 400668002573 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 400668002574 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 400668002575 putative trimer interface [polypeptide binding]; other site 400668002576 putative CoA binding site [chemical binding]; other site 400668002577 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 400668002578 active site 400668002579 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668002580 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668002581 WbqC-like protein family; Region: WbqC; pfam08889 400668002582 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 400668002583 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 400668002584 inhibitor-cofactor binding pocket; inhibition site 400668002585 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668002586 catalytic residue [active] 400668002587 OpgC protein; Region: OpgC_C; cl00792 400668002588 Acyltransferase family; Region: Acyl_transf_3; pfam01757 400668002589 MatE; Region: MatE; cl10513 400668002590 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 400668002591 active site 400668002592 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 400668002593 homodimer interface [polypeptide binding]; other site 400668002594 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 400668002595 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 400668002596 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 400668002597 NAD binding site [chemical binding]; other site 400668002598 substrate binding site [chemical binding]; other site 400668002599 homodimer interface [polypeptide binding]; other site 400668002600 active site 400668002601 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 400668002602 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 400668002603 substrate binding site; other site 400668002604 tetramer interface; other site 400668002605 Cupin domain; Region: Cupin_2; cl09118 400668002606 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 400668002607 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 400668002608 NADP binding site [chemical binding]; other site 400668002609 active site 400668002610 putative substrate binding site [chemical binding]; other site 400668002611 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 400668002612 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 400668002613 active site 400668002614 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 400668002615 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002616 Bacterial sugar transferase; Region: Bac_transf; cl00939 400668002617 O-Antigen ligase; Region: Wzy_C; cl04850 400668002618 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 400668002619 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 400668002620 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668002621 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 400668002622 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 400668002623 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 400668002624 putative ADP-binding pocket [chemical binding]; other site 400668002625 Membrane protein of unknown function (DUF340); Region: DUF340; cl01028 400668002626 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 400668002627 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 400668002628 multidrug efflux protein; Reviewed; Region: PRK01766 400668002629 MatE; Region: MatE; cl10513 400668002630 MatE; Region: MatE; cl10513 400668002631 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 400668002632 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 400668002633 Walker A/P-loop; other site 400668002634 ATP binding site [chemical binding]; other site 400668002635 Q-loop/lid; other site 400668002636 ABC transporter signature motif; other site 400668002637 Walker B; other site 400668002638 D-loop; other site 400668002639 H-loop/switch region; other site 400668002640 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 400668002641 ABC-ATPase subunit interface; other site 400668002642 dimer interface [polypeptide binding]; other site 400668002643 putative PBP binding regions; other site 400668002644 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 400668002645 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 400668002646 putative hemin binding site; other site 400668002647 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 400668002648 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 400668002649 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 400668002650 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 400668002651 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 400668002652 N-terminal plug; other site 400668002653 ligand-binding site [chemical binding]; other site 400668002654 Cupin domain; Region: Cupin_2; cl09118 400668002655 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668002656 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668002657 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002658 DctM-like transporters; Region: DctM; pfam06808 400668002659 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668002660 Dehydratase family; Region: ILVD_EDD; cl00340 400668002661 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 400668002662 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668002663 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 400668002664 Helix-turn-helix domains; Region: HTH; cl00088 400668002665 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 400668002666 putative dimerization interface [polypeptide binding]; other site 400668002667 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 400668002668 dimer interface [polypeptide binding]; other site 400668002669 NADP binding site [chemical binding]; other site 400668002670 catalytic residues [active] 400668002671 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668002672 human DHRS6-like, classical (c) SDRs; Region: DHRS6_like_SDR_c; cd05368 400668002673 NAD binding site [chemical binding]; other site 400668002674 homotetramer interface [polypeptide binding]; other site 400668002675 homodimer interface [polypeptide binding]; other site 400668002676 active site 400668002677 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 400668002678 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668002679 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668002680 high affinity sulphate transporter 1; Region: sulP; TIGR00815 400668002681 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668002682 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 400668002683 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 400668002684 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 400668002685 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 400668002686 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668002687 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 400668002688 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 400668002689 Walker B motif; other site 400668002690 arginine finger; other site 400668002691 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 400668002692 substrate binding site [chemical binding]; other site 400668002693 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668002694 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668002695 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 400668002696 ABC-2 type transporter; Region: ABC2_membrane; cl11417 400668002697 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 400668002698 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 400668002699 Walker A/P-loop; other site 400668002700 ATP binding site [chemical binding]; other site 400668002701 Q-loop/lid; other site 400668002702 ABC transporter signature motif; other site 400668002703 Walker B; other site 400668002704 D-loop; other site 400668002705 H-loop/switch region; other site 400668002706 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 400668002707 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 400668002708 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 400668002709 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668002710 Helix-turn-helix domains; Region: HTH; cl00088 400668002711 Cache domain; Region: Cache_2; cl07034 400668002712 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 400668002713 dimerization interface [polypeptide binding]; other site 400668002714 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668002715 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668002716 dimer interface [polypeptide binding]; other site 400668002717 putative CheW interface [polypeptide binding]; other site 400668002718 short chain dehydrogenase; Validated; Region: PRK06182 400668002719 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 400668002720 NADP binding site [chemical binding]; other site 400668002721 active site 400668002722 steroid binding site; other site 400668002723 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 400668002724 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 400668002725 Transcriptional activator HlyU; Region: HlyU; cl02273 400668002726 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668002727 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668002728 DNA binding site [nucleotide binding] 400668002729 domain linker motif; other site 400668002730 Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Region: PBP1_GalS_like; cd06270 400668002731 dimerization interface (closed form) [polypeptide binding]; other site 400668002732 ligand binding site [chemical binding]; other site 400668002733 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668002734 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 400668002735 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 400668002736 dimer interface [polypeptide binding]; other site 400668002737 conserved gate region; other site 400668002738 putative PBP binding loops; other site 400668002739 ABC-ATPase subunit interface; other site 400668002740 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668002741 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 400668002742 dimer interface [polypeptide binding]; other site 400668002743 conserved gate region; other site 400668002744 putative PBP binding loops; other site 400668002745 ABC-ATPase subunit interface; other site 400668002746 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668002747 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668002748 Walker A/P-loop; other site 400668002749 ATP binding site [chemical binding]; other site 400668002750 Q-loop/lid; other site 400668002751 ABC transporter signature motif; other site 400668002752 Walker B; other site 400668002753 D-loop; other site 400668002754 H-loop/switch region; other site 400668002755 TOBE domain; Region: TOBE_2; cl01440 400668002756 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 400668002757 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668002758 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002759 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668002760 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 400668002761 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 400668002762 Metal-binding active site; metal-binding site 400668002763 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 400668002764 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668002765 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002766 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668002767 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 400668002768 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668002769 metal binding site [ion binding]; metal-binding site 400668002770 active site 400668002771 I-site; other site 400668002772 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668002773 metal binding site [ion binding]; metal-binding site 400668002774 active site 400668002775 I-site; other site 400668002776 LabA_like proteins; Region: LabA; cd10911 400668002777 putative metal binding site [ion binding]; other site 400668002778 Predicted membrane protein [Function unknown]; Region: COG3671 400668002779 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 400668002780 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 400668002781 active site 400668002782 putative substrate binding pocket [chemical binding]; other site 400668002783 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 400668002784 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668002785 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 400668002786 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 400668002787 Radical SAM superfamily; Region: Radical_SAM; pfam04055 400668002788 FeS/SAM binding site; other site 400668002789 elongation factor P; Validated; Region: PRK00529 400668002790 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 400668002791 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 400668002792 RNA binding site [nucleotide binding]; other site 400668002793 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 400668002794 RNA binding site [nucleotide binding]; other site 400668002795 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668002796 Helix-turn-helix domains; Region: HTH; cl00088 400668002797 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 400668002798 putative effector binding pocket; other site 400668002799 putative dimerization interface [polypeptide binding]; other site 400668002800 Agrobacterium tumefaciens protein Atu4866; Region: Atu4866; pfam11512 400668002801 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668002802 Coenzyme A binding pocket [chemical binding]; other site 400668002803 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668002804 Helix-turn-helix domains; Region: HTH; cl00088 400668002805 DoxX; Region: DoxX; cl00976 400668002806 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 400668002807 classical (c) SDRs; Region: SDR_c; cd05233 400668002808 NAD(P) binding site [chemical binding]; other site 400668002809 active site 400668002810 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 400668002811 Prostaglandin dehydrogenases; Region: PGDH; cd05288 400668002812 NAD(P) binding site [chemical binding]; other site 400668002813 substrate binding site [chemical binding]; other site 400668002814 dimer interface [polypeptide binding]; other site 400668002815 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 400668002816 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668002817 DNA-binding site [nucleotide binding]; DNA binding site 400668002818 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 400668002819 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668002820 homodimer interface [polypeptide binding]; other site 400668002821 catalytic residue [active] 400668002822 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 400668002823 LysE type translocator; Region: LysE; cl00565 400668002824 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 400668002825 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 400668002826 motif 1; other site 400668002827 dimer interface [polypeptide binding]; other site 400668002828 active site 400668002829 motif 2; other site 400668002830 motif 3; other site 400668002831 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 400668002832 PAS fold; Region: PAS; pfam00989 400668002833 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 400668002834 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 400668002835 dimer interface [polypeptide binding]; other site 400668002836 phosphorylation site [posttranslational modification] 400668002837 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 400668002838 ATP binding site [chemical binding]; other site 400668002839 G-X-G motif; other site 400668002840 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668002841 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 400668002842 active site 400668002843 phosphorylation site [posttranslational modification] 400668002844 intermolecular recognition site; other site 400668002845 dimerization interface [polypeptide binding]; other site 400668002846 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 400668002847 Walker A motif; other site 400668002848 ATP binding site [chemical binding]; other site 400668002849 Walker B motif; other site 400668002850 arginine finger; other site 400668002851 Helix-turn-helix domains; Region: HTH; cl00088 400668002852 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 400668002853 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 400668002854 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002855 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002856 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668002857 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668002858 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668002859 Domain of unknown function (DUF1726); Region: DUF1726; pfam08351 400668002860 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668002861 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668002862 Possible tRNA binding domain; Region: tRNA_bind_2; pfam13725 400668002863 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 400668002864 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668002865 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668002866 dimer interface [polypeptide binding]; other site 400668002867 putative CheW interface [polypeptide binding]; other site 400668002868 Cache domain; Region: Cache_2; cl07034 400668002869 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 400668002870 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668002871 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668002872 dimer interface [polypeptide binding]; other site 400668002873 putative CheW interface [polypeptide binding]; other site 400668002874 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 400668002875 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 400668002876 dimer interface [polypeptide binding]; other site 400668002877 Citrate synthase; Region: Citrate_synt; pfam00285 400668002878 active site 400668002879 citrylCoA binding site [chemical binding]; other site 400668002880 oxalacetate/citrate binding site [chemical binding]; other site 400668002881 coenzyme A binding site [chemical binding]; other site 400668002882 catalytic triad [active] 400668002883 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 400668002884 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 400668002885 tetramer interface [polypeptide binding]; other site 400668002886 active site 400668002887 Mg2+/Mn2+ binding site [ion binding]; other site 400668002888 Transcriptional regulators [Transcription]; Region: GntR; COG1802 400668002889 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668002890 DNA-binding site [nucleotide binding]; DNA binding site 400668002891 FCD domain; Region: FCD; cl11656 400668002892 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668002893 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 400668002894 putative DNA binding site [nucleotide binding]; other site 400668002895 putative Zn2+ binding site [ion binding]; other site 400668002896 Helix-turn-helix domains; Region: HTH; cl00088 400668002897 Protein of unknown function (DUF1826); Region: DUF1826; pfam08856 400668002898 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668002899 NAD(P) binding site [chemical binding]; other site 400668002900 active site 400668002901 Protein of unknown function, DUF393; Region: DUF393; cl01136 400668002902 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 400668002903 glycyl-tRNA synthetase; Provisional; Region: PRK04173 400668002904 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3'...; Region: GlyRS-like_core; cd00774 400668002905 dimer interface [polypeptide binding]; other site 400668002906 motif 1; other site 400668002907 active site 400668002908 motif 2; other site 400668002909 motif 3; other site 400668002910 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 400668002911 anticodon binding site; other site 400668002912 putative outer membrane receptor; Provisional; Region: PRK13513 400668002913 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 400668002914 N-terminal plug; other site 400668002915 ligand-binding site [chemical binding]; other site 400668002916 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668002917 Helix-turn-helix domains; Region: HTH; cl00088 400668002918 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 400668002919 dimerization interface [polypeptide binding]; other site 400668002920 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668002921 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668002922 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 400668002923 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 400668002924 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668002925 Helix-turn-helix domains; Region: HTH; cl00088 400668002926 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 400668002927 putative effector binding pocket; other site 400668002928 dimerization interface [polypeptide binding]; other site 400668002929 Helix-turn-helix domains; Region: HTH; cl00088 400668002930 WYL domain; Region: WYL; cl14852 400668002931 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 400668002932 Predicted permease [General function prediction only]; Region: COG2056 400668002933 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 400668002934 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668002935 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 400668002936 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668002937 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668002938 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668002939 Helix-turn-helix domains; Region: HTH; cl00088 400668002940 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 400668002941 dimerization interface [polypeptide binding]; other site 400668002942 Protein of unknown function (DUF2806); Region: DUF2806; cl12560 400668002943 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 400668002944 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 400668002945 putative ligand binding site [chemical binding]; other site 400668002946 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 400668002947 TM-ABC transporter signature motif; other site 400668002948 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 400668002949 TM-ABC transporter signature motif; other site 400668002950 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 400668002951 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 400668002952 Walker A/P-loop; other site 400668002953 ATP binding site [chemical binding]; other site 400668002954 Q-loop/lid; other site 400668002955 ABC transporter signature motif; other site 400668002956 Walker B; other site 400668002957 D-loop; other site 400668002958 H-loop/switch region; other site 400668002959 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 400668002960 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 400668002961 Walker A/P-loop; other site 400668002962 ATP binding site [chemical binding]; other site 400668002963 Q-loop/lid; other site 400668002964 ABC transporter signature motif; other site 400668002965 Walker B; other site 400668002966 D-loop; other site 400668002967 H-loop/switch region; other site 400668002968 UreD urease accessory protein; Region: UreD; cl00530 400668002969 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 400668002970 alpha-gamma subunit interface [polypeptide binding]; other site 400668002971 beta-gamma subunit interface [polypeptide binding]; other site 400668002972 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 400668002973 gamma-beta subunit interface [polypeptide binding]; other site 400668002974 alpha-beta subunit interface [polypeptide binding]; other site 400668002975 urease subunit alpha; Reviewed; Region: ureC; PRK13207 400668002976 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 400668002977 subunit interactions [polypeptide binding]; other site 400668002978 active site 400668002979 flap region; other site 400668002980 urease accessory protein UreE; Provisional; Region: PRK14113 400668002981 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 400668002982 dimer interface [polypeptide binding]; other site 400668002983 catalytic residues [active] 400668002984 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 400668002985 UreF; Region: UreF; pfam01730 400668002986 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668002987 HupE / UreJ protein; Region: HupE_UreJ; cl01011 400668002988 Sodium:solute symporter family; Region: SSF; cl00456 400668002989 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 400668002990 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 400668002991 dimer interface [polypeptide binding]; other site 400668002992 phosphorylation site [posttranslational modification] 400668002993 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 400668002994 ATP binding site [chemical binding]; other site 400668002995 Mg2+ binding site [ion binding]; other site 400668002996 G-X-G motif; other site 400668002997 Response regulator receiver domain; Region: Response_reg; pfam00072 400668002998 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 400668002999 active site 400668003000 phosphorylation site [posttranslational modification] 400668003001 intermolecular recognition site; other site 400668003002 dimerization interface [polypeptide binding]; other site 400668003003 Response regulator receiver domain; Region: Response_reg; pfam00072 400668003004 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 400668003005 active site 400668003006 phosphorylation site [posttranslational modification] 400668003007 intermolecular recognition site; other site 400668003008 dimerization interface [polypeptide binding]; other site 400668003009 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 400668003010 DNA binding residues [nucleotide binding] 400668003011 dimerization interface [polypeptide binding]; other site 400668003012 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 400668003013 Helix-turn-helix domains; Region: HTH; cl00088 400668003014 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 400668003015 substrate binding site [chemical binding]; other site 400668003016 dimerization interface [polypeptide binding]; other site 400668003017 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 400668003018 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 400668003019 Walker A/P-loop; other site 400668003020 ATP binding site [chemical binding]; other site 400668003021 Q-loop/lid; other site 400668003022 ABC transporter signature motif; other site 400668003023 Walker B; other site 400668003024 D-loop; other site 400668003025 H-loop/switch region; other site 400668003026 TOBE-like domain; Region: TOBE_3; pfam12857 400668003027 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 400668003028 dimer interface [polypeptide binding]; other site 400668003029 conserved gate region; other site 400668003030 putative PBP binding loops; other site 400668003031 ABC-ATPase subunit interface; other site 400668003032 sulfate transport protein; Provisional; Region: cysT; CHL00187 400668003033 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 400668003034 dimer interface [polypeptide binding]; other site 400668003035 conserved gate region; other site 400668003036 putative PBP binding loops; other site 400668003037 ABC-ATPase subunit interface; other site 400668003038 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 400668003039 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 400668003040 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668003041 Cache domain; Region: Cache_1; pfam02743 400668003042 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 400668003043 dimerization interface [polypeptide binding]; other site 400668003044 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668003045 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668003046 dimer interface [polypeptide binding]; other site 400668003047 putative CheW interface [polypeptide binding]; other site 400668003048 Dicarboxylate carrier protein MatC N-terminus; Region: MatC_N; pfam07158 400668003049 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668003050 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 400668003051 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 400668003052 active site 400668003053 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 400668003054 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668003055 DNA-binding site [nucleotide binding]; DNA binding site 400668003056 UTRA domain; Region: UTRA; cl01230 400668003057 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 400668003058 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_2; cd03138 400668003059 conserved cys residue [active] 400668003060 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003061 Isochorismatase family; Region: Isochorismatase; pfam00857 400668003062 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 400668003063 catalytic triad [active] 400668003064 conserved cis-peptide bond; other site 400668003065 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 400668003066 Helix-turn-helix domains; Region: HTH; cl00088 400668003067 TOBE domain; Region: TOBE_2; cl01440 400668003068 TOBE domain; Region: TOBE_2; cl01440 400668003069 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 400668003070 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668003071 Walker A/P-loop; other site 400668003072 ATP binding site [chemical binding]; other site 400668003073 Q-loop/lid; other site 400668003074 ABC transporter signature motif; other site 400668003075 Walker B; other site 400668003076 D-loop; other site 400668003077 H-loop/switch region; other site 400668003078 TOBE domain; Region: TOBE_2; cl01440 400668003079 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 400668003080 putative PBP binding loops; other site 400668003081 dimer interface [polypeptide binding]; other site 400668003082 ABC-ATPase subunit interface; other site 400668003083 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 400668003084 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 400668003085 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 400668003086 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668003087 substrate binding pocket [chemical binding]; other site 400668003088 membrane-bound complex binding site; other site 400668003089 hinge residues; other site 400668003090 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 400668003091 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 400668003092 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 400668003093 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 400668003094 Nitrate and nitrite sensing; Region: NIT; pfam08376 400668003095 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 400668003096 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668003097 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668003098 dimer interface [polypeptide binding]; other site 400668003099 putative CheW interface [polypeptide binding]; other site 400668003100 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 400668003101 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 400668003102 ATP binding site [chemical binding]; other site 400668003103 Mg++ binding site [ion binding]; other site 400668003104 motif III; other site 400668003105 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 400668003106 nucleotide binding region [chemical binding]; other site 400668003107 ATP-binding site [chemical binding]; other site 400668003108 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 400668003109 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 400668003110 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 400668003111 Uncharacterized conserved protein [Function unknown]; Region: COG2308 400668003112 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 400668003113 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; cl00980 400668003114 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 400668003115 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 400668003116 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 400668003117 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 400668003118 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 400668003119 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; cl00980 400668003120 Uncharacterized conserved protein [Function unknown]; Region: COG2308 400668003121 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl00503 400668003122 salicylate hydroxylase; Provisional; Region: PRK06475 400668003123 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003124 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family; Region: PQQ_membr_DH; TIGR03074 400668003125 Membrane-bound PQQ-dependent glucose dehydrogenase; Region: PQQ_mGDH; cd10280 400668003126 Trp docking motif [polypeptide binding]; other site 400668003127 putative active site [active] 400668003128 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 400668003129 EamA-like transporter family; Region: EamA; cl01037 400668003130 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668003131 EamA-like transporter family; Region: EamA; cl01037 400668003132 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 400668003133 Helix-turn-helix domains; Region: HTH; cl00088 400668003134 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 400668003135 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 400668003136 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 400668003137 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 400668003138 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 400668003139 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 400668003140 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668003141 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 400668003142 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 400668003143 dimer interface [polypeptide binding]; other site 400668003144 conserved gate region; other site 400668003145 ABC-ATPase subunit interface; other site 400668003146 phosphonate ABC transporter, ATP-binding protein; Region: ABC_phnC; TIGR02315 400668003147 ABC-type phosphate/phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all...; Region: ABC_PhnC_transporter; cd03256 400668003148 Walker A/P-loop; other site 400668003149 ATP binding site [chemical binding]; other site 400668003150 Q-loop/lid; other site 400668003151 ABC transporter signature motif; other site 400668003152 Walker B; other site 400668003153 D-loop; other site 400668003154 H-loop/switch region; other site 400668003155 NMT1-like family; Region: NMT1_2; cl15260 400668003156 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 400668003157 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668003158 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 400668003159 active site 400668003160 phosphorylation site [posttranslational modification] 400668003161 intermolecular recognition site; other site 400668003162 dimerization interface [polypeptide binding]; other site 400668003163 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 400668003164 Walker A motif; other site 400668003165 ATP binding site [chemical binding]; other site 400668003166 Walker B motif; other site 400668003167 arginine finger; other site 400668003168 Helix-turn-helix domains; Region: HTH; cl00088 400668003169 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]; Region: COG4192 400668003170 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 400668003171 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 400668003172 dimer interface [polypeptide binding]; other site 400668003173 phosphorylation site [posttranslational modification] 400668003174 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 400668003175 ATP binding site [chemical binding]; other site 400668003176 Mg2+ binding site [ion binding]; other site 400668003177 G-X-G motif; other site 400668003178 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 400668003179 putative FMN binding site [chemical binding]; other site 400668003180 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 400668003181 ferrichrome receptor precursor protein; Provisional; Region: PRK14050 400668003182 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 400668003183 N-terminal plug; other site 400668003184 ligand-binding site [chemical binding]; other site 400668003185 multidrug transporter membrane component/ATP-binding component; Provisional; Region: PRK10522 400668003186 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668003187 Walker A/P-loop; other site 400668003188 ATP binding site [chemical binding]; other site 400668003189 Q-loop/lid; other site 400668003190 ABC transporter signature motif; other site 400668003191 Walker B; other site 400668003192 D-loop; other site 400668003193 H-loop/switch region; other site 400668003194 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 400668003195 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 400668003196 ABC-ATPase subunit interface; other site 400668003197 dimer interface [polypeptide binding]; other site 400668003198 putative PBP binding regions; other site 400668003199 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 400668003200 ABC-ATPase subunit interface; other site 400668003201 dimer interface [polypeptide binding]; other site 400668003202 putative PBP binding regions; other site 400668003203 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 400668003204 siderophore binding site; other site 400668003205 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 400668003206 iron-hydroxamate transporter ATP-binding subunit; Provisional; Region: PRK10575 400668003207 Walker A/P-loop; other site 400668003208 ATP binding site [chemical binding]; other site 400668003209 Q-loop/lid; other site 400668003210 ABC transporter signature motif; other site 400668003211 Walker B; other site 400668003212 D-loop; other site 400668003213 H-loop/switch region; other site 400668003214 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 400668003215 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 400668003216 G1 box; other site 400668003217 putative GEF interaction site [polypeptide binding]; other site 400668003218 GTP/Mg2+ binding site [chemical binding]; other site 400668003219 Switch I region; other site 400668003220 G2 box; other site 400668003221 G3 box; other site 400668003222 Switch II region; other site 400668003223 G4 box; other site 400668003224 G5 box; other site 400668003225 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 400668003226 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 400668003227 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 400668003228 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 400668003229 dimer interface [polypeptide binding]; other site 400668003230 phosphorylation site [posttranslational modification] 400668003231 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 400668003232 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 400668003233 ATP binding site [chemical binding]; other site 400668003234 Mg2+ binding site [ion binding]; other site 400668003235 G-X-G motif; other site 400668003236 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668003237 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 400668003238 active site 400668003239 phosphorylation site [posttranslational modification] 400668003240 intermolecular recognition site; other site 400668003241 dimerization interface [polypeptide binding]; other site 400668003242 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 400668003243 DNA binding site [nucleotide binding] 400668003244 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 400668003245 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 400668003246 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 400668003247 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 400668003248 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 400668003249 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 400668003250 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 400668003251 S-adenosylmethionine binding site [chemical binding]; other site 400668003252 FtsH Extracellular; Region: FtsH_ext; pfam06480 400668003253 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 400668003254 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 400668003255 Walker A motif; other site 400668003256 ATP binding site [chemical binding]; other site 400668003257 Walker B motif; other site 400668003258 arginine finger; other site 400668003259 Peptidase family M41; Region: Peptidase_M41; pfam01434 400668003260 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 400668003261 dihydropteroate synthase; Region: DHPS; TIGR01496 400668003262 substrate binding pocket [chemical binding]; other site 400668003263 dimer interface [polypeptide binding]; other site 400668003264 inhibitor binding site; inhibition site 400668003265 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 400668003266 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 400668003267 active site 400668003268 substrate binding site [chemical binding]; other site 400668003269 metal binding site [ion binding]; metal-binding site 400668003270 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 400668003271 substrate binding site [chemical binding]; other site 400668003272 dimer interface [polypeptide binding]; other site 400668003273 catalytic triad [active] 400668003274 Preprotein translocase SecG subunit; Region: SecG; cl09123 400668003275 ribosome maturation protein RimP; Reviewed; Region: PRK00092 400668003276 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 400668003277 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 400668003278 Sm1 motif; other site 400668003279 D3 - B interaction site; other site 400668003280 D1 - D2 interaction site; other site 400668003281 Hfq - Hfq interaction site; other site 400668003282 RNA binding pocket [nucleotide binding]; other site 400668003283 Sm2 motif; other site 400668003284 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 400668003285 NusA N-terminal domain; Region: NusA_N; pfam08529 400668003286 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 400668003287 RNA binding site [nucleotide binding]; other site 400668003288 homodimer interface [polypeptide binding]; other site 400668003289 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 400668003290 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 400668003291 G-X-X-G motif; other site 400668003292 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 400668003293 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 400668003294 translation initiation factor IF-2; Validated; Region: infB; PRK05306 400668003295 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 400668003296 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 400668003297 G1 box; other site 400668003298 putative GEF interaction site [polypeptide binding]; other site 400668003299 GTP/Mg2+ binding site [chemical binding]; other site 400668003300 Switch I region; other site 400668003301 G2 box; other site 400668003302 G3 box; other site 400668003303 Switch II region; other site 400668003304 G4 box; other site 400668003305 G5 box; other site 400668003306 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 400668003307 Translation-initiation factor 2; Region: IF-2; pfam11987 400668003308 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 400668003309 Ribosome-binding factor A; Region: RBFA; cl00542 400668003310 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 400668003311 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 400668003312 RNA binding site [nucleotide binding]; other site 400668003313 active site 400668003314 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 400668003315 16S/18S rRNA binding site [nucleotide binding]; other site 400668003316 S13e-L30e interaction site [polypeptide binding]; other site 400668003317 25S rRNA binding site [nucleotide binding]; other site 400668003318 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 400668003319 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 400668003320 RNase E interface [polypeptide binding]; other site 400668003321 trimer interface [polypeptide binding]; other site 400668003322 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 400668003323 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 400668003324 RNase E interface [polypeptide binding]; other site 400668003325 trimer interface [polypeptide binding]; other site 400668003326 active site 400668003327 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 400668003328 putative nucleic acid binding region [nucleotide binding]; other site 400668003329 G-X-X-G motif; other site 400668003330 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 400668003331 RNA binding site [nucleotide binding]; other site 400668003332 domain interface; other site 400668003333 LPP20 lipoprotein; Region: LPP20; cl15824 400668003334 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 400668003335 Protein of unknown function (DUF3080); Region: DUF3080; pfam11279 400668003336 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668003337 metal binding site [ion binding]; metal-binding site 400668003338 active site 400668003339 I-site; other site 400668003340 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 400668003341 glucokinase, proteobacterial type; Region: glk; TIGR00749 400668003342 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 400668003343 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 400668003344 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 400668003345 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 400668003346 active site 400668003347 intersubunit interface [polypeptide binding]; other site 400668003348 catalytic residue [active] 400668003349 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 400668003350 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 400668003351 putative active site [active] 400668003352 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668003353 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 400668003354 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 400668003355 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 400668003356 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 400668003357 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668003358 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 400668003359 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 400668003360 DNA binding residues [nucleotide binding] 400668003361 DNA primase, catalytic core; Region: dnaG; TIGR01391 400668003362 CHC2 zinc finger; Region: zf-CHC2; cl15369 400668003363 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 400668003364 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 400668003365 active site 400668003366 metal binding site [ion binding]; metal-binding site 400668003367 interdomain interaction site; other site 400668003368 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 400668003369 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 400668003370 GatB domain; Region: GatB_Yqey; cl11497 400668003371 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 400668003372 UGMP family protein; Validated; Region: PRK09604 400668003373 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 400668003374 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 400668003375 homooctamer interface [polypeptide binding]; other site 400668003376 active site 400668003377 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 400668003378 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 400668003379 active site 400668003380 NTP binding site [chemical binding]; other site 400668003381 metal binding triad [ion binding]; metal-binding site 400668003382 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 400668003383 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 400668003384 active site residue [active] 400668003385 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 400668003386 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 400668003387 active site 400668003388 metal binding site [ion binding]; metal-binding site 400668003389 Protein of unknown function (DUF525); Region: DUF525; cl01119 400668003390 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003391 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 400668003392 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 400668003393 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 400668003394 SurA N-terminal domain; Region: SurA_N_3; cl07813 400668003395 PPIC-type PPIASE domain; Region: Rotamase; cl08278 400668003396 PPIC-type PPIASE domain; Region: Rotamase; cl08278 400668003397 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 400668003398 Organic solvent tolerance protein; Region: OstA_C; pfam04453 400668003399 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 400668003400 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 400668003401 putative metal binding site [ion binding]; other site 400668003402 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 400668003403 HSP70 interaction site [polypeptide binding]; other site 400668003404 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 400668003405 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 400668003406 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 400668003407 substrate binding site [chemical binding]; other site 400668003408 hexamer interface [polypeptide binding]; other site 400668003409 metal binding site [ion binding]; metal-binding site 400668003410 phosphoglycolate phosphatase; Provisional; Region: PRK13222 400668003411 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 400668003412 motif II; other site 400668003413 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 400668003414 Mechanosensitive ion channel; Region: MS_channel; pfam00924 400668003415 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 400668003416 MgtE intracellular N domain; Region: MgtE_N; cl15244 400668003417 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 400668003418 Divalent cation transporter; Region: MgtE; cl00786 400668003419 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 400668003420 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 400668003421 glutamine binding [chemical binding]; other site 400668003422 catalytic triad [active] 400668003423 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 400668003424 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 400668003425 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 400668003426 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 400668003427 active site 400668003428 ribulose/triose binding site [chemical binding]; other site 400668003429 phosphate binding site [ion binding]; other site 400668003430 substrate (anthranilate) binding pocket [chemical binding]; other site 400668003431 product (indole) binding pocket [chemical binding]; other site 400668003432 OsmC-like protein; Region: OsmC; cl00767 400668003433 FlgN protein; Region: FlgN; cl09176 400668003434 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 400668003435 SAF domain; Region: SAF; cl00555 400668003436 SAF-like; Region: SAF_2; pfam13144 400668003437 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 400668003438 Response regulator receiver domain; Region: Response_reg; pfam00072 400668003439 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 400668003440 active site 400668003441 phosphorylation site [posttranslational modification] 400668003442 intermolecular recognition site; other site 400668003443 dimerization interface [polypeptide binding]; other site 400668003444 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 400668003445 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 400668003446 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003447 putative peptidase; Provisional; Region: PRK11649 400668003448 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 400668003449 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 400668003450 active site 400668003451 HIGH motif; other site 400668003452 dimer interface [polypeptide binding]; other site 400668003453 KMSKS motif; other site 400668003454 Proteolipid membrane potential modulator; Region: Pmp3; cl00431 400668003455 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668003456 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668003457 Helix-turn-helix domains; Region: HTH; cl00088 400668003458 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 400668003459 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668003460 AIR carboxylase; Region: AIRC; cl00310 400668003461 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 400668003462 active site 400668003463 dimer interfaces [polypeptide binding]; other site 400668003464 catalytic residues [active] 400668003465 pyruvate kinase; Provisional; Region: PRK05826 400668003466 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 400668003467 domain interfaces; other site 400668003468 active site 400668003469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003470 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 400668003471 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 400668003472 Dehydratase family; Region: ILVD_EDD; cl00340 400668003473 6-phosphogluconate dehydratase; Region: edd; TIGR01196 400668003474 Sodium:solute symporter family; Region: SSF; cl00456 400668003475 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 400668003476 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 400668003477 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 400668003478 putative active site [active] 400668003479 Phosphotransferase enzyme family; Region: APH; pfam01636 400668003480 Choline Kinase (ChoK). The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: ChoK; cd05151 400668003481 active site 400668003482 substrate binding site [chemical binding]; other site 400668003483 ATP binding site [chemical binding]; other site 400668003484 dimer interface [polypeptide binding]; other site 400668003485 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 400668003486 ligand binding site [chemical binding]; other site 400668003487 active site 400668003488 UGI interface [polypeptide binding]; other site 400668003489 catalytic site [active] 400668003490 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 400668003491 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 400668003492 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 400668003493 Response regulator receiver domain; Region: Response_reg; pfam00072 400668003494 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 400668003495 active site 400668003496 phosphorylation site [posttranslational modification] 400668003497 intermolecular recognition site; other site 400668003498 dimerization interface [polypeptide binding]; other site 400668003499 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 400668003500 Zn2+ binding site [ion binding]; other site 400668003501 Mg2+ binding site [ion binding]; other site 400668003502 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 400668003503 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 400668003504 PAS domain S-box; Region: sensory_box; TIGR00229 400668003505 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 400668003506 putative active site [active] 400668003507 heme pocket [chemical binding]; other site 400668003508 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 400668003509 PAS fold; Region: PAS_3; pfam08447 400668003510 putative active site [active] 400668003511 heme pocket [chemical binding]; other site 400668003512 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 400668003513 dimer interface [polypeptide binding]; other site 400668003514 phosphorylation site [posttranslational modification] 400668003515 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 400668003516 ATP binding site [chemical binding]; other site 400668003517 Mg2+ binding site [ion binding]; other site 400668003518 G-X-G motif; other site 400668003519 Response regulator receiver domain; Region: Response_reg; pfam00072 400668003520 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 400668003521 active site 400668003522 phosphorylation site [posttranslational modification] 400668003523 intermolecular recognition site; other site 400668003524 dimerization interface [polypeptide binding]; other site 400668003525 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 400668003526 D-xylulose kinases, Escherichia coli xylulokinase-like subgroup; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 400668003527 N- and C-terminal domain interface [polypeptide binding]; other site 400668003528 D-xylulose kinase; Region: XylB; TIGR01312 400668003529 active site 400668003530 catalytic site [active] 400668003531 metal binding site [ion binding]; metal-binding site 400668003532 xylulose binding site [chemical binding]; other site 400668003533 putative ATP binding site [chemical binding]; other site 400668003534 homodimer interface [polypeptide binding]; other site 400668003535 Cupin domain; Region: Cupin_2; cl09118 400668003536 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003537 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668003538 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003539 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 400668003540 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 400668003541 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 400668003542 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668003543 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668003544 Walker A/P-loop; other site 400668003545 ATP binding site [chemical binding]; other site 400668003546 Q-loop/lid; other site 400668003547 ABC transporter signature motif; other site 400668003548 Walker B; other site 400668003549 D-loop; other site 400668003550 H-loop/switch region; other site 400668003551 TOBE domain; Region: TOBE_2; cl01440 400668003552 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668003553 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 400668003554 dimer interface [polypeptide binding]; other site 400668003555 conserved gate region; other site 400668003556 putative PBP binding loops; other site 400668003557 ABC-ATPase subunit interface; other site 400668003558 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 400668003559 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668003560 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 400668003561 dimer interface [polypeptide binding]; other site 400668003562 conserved gate region; other site 400668003563 putative PBP binding loops; other site 400668003564 ABC-ATPase subunit interface; other site 400668003565 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668003566 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 400668003567 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 400668003568 L-aspartate oxidase; Provisional; Region: PRK09077 400668003569 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003570 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 400668003571 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 400668003572 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668003573 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 400668003574 DNA binding residues [nucleotide binding] 400668003575 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 400668003576 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 400668003577 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; cl01178 400668003578 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 400668003579 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 400668003580 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 400668003581 protein binding site [polypeptide binding]; other site 400668003582 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 400668003583 protein binding site [polypeptide binding]; other site 400668003584 N-acetylglutamate synthase; Validated; Region: PRK05279 400668003585 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 400668003586 putative feedback inhibition sensing region; other site 400668003587 putative nucleotide binding site [chemical binding]; other site 400668003588 putative substrate binding site [chemical binding]; other site 400668003589 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668003590 Coenzyme A binding pocket [chemical binding]; other site 400668003591 acetylornithine deacetylase; Provisional; Region: PRK05111 400668003592 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 400668003593 metal binding site [ion binding]; metal-binding site 400668003594 putative dimer interface [polypeptide binding]; other site 400668003595 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 400668003596 putative active site [active] 400668003597 putative metal binding residues [ion binding]; other site 400668003598 signature motif; other site 400668003599 putative triphosphate binding site [ion binding]; other site 400668003600 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 400668003601 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 400668003602 metal binding triad; other site 400668003603 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 400668003604 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 400668003605 metal binding triad; other site 400668003606 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 400668003607 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668003608 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 400668003609 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 400668003610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 400668003611 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 400668003612 inhibitor-cofactor binding pocket; inhibition site 400668003613 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668003614 catalytic residue [active] 400668003615 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 400668003616 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003617 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 400668003618 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 400668003619 conserved cys residue [active] 400668003620 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003621 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003622 ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]; Region: HisP; COG4598 400668003623 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 400668003624 Walker A/P-loop; other site 400668003625 ATP binding site [chemical binding]; other site 400668003626 Q-loop/lid; other site 400668003627 ABC transporter signature motif; other site 400668003628 Walker B; other site 400668003629 D-loop; other site 400668003630 H-loop/switch region; other site 400668003631 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 400668003632 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 400668003633 substrate binding pocket [chemical binding]; other site 400668003634 membrane-bound complex binding site; other site 400668003635 hinge residues; other site 400668003636 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668003637 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 400668003638 dimer interface [polypeptide binding]; other site 400668003639 conserved gate region; other site 400668003640 putative PBP binding loops; other site 400668003641 ABC-ATPase subunit interface; other site 400668003642 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 400668003643 dimer interface [polypeptide binding]; other site 400668003644 conserved gate region; other site 400668003645 putative PBP binding loops; other site 400668003646 ABC-ATPase subunit interface; other site 400668003647 Nitrogen regulatory protein P-II; Region: P-II; cl00412 400668003648 Nitrogen regulatory protein P-II; Region: P-II; smart00938 400668003649 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 400668003650 substrate binding site [chemical binding]; other site 400668003651 active site 400668003652 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 400668003653 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 400668003654 nudix motif; other site 400668003655 Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily; Region: M14_ASTE; cd03855 400668003656 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 400668003657 putative active site [active] 400668003658 Zn binding site [ion binding]; other site 400668003659 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 400668003660 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 400668003661 metal binding site [ion binding]; metal-binding site 400668003662 KpsF/GutQ family protein; Region: kpsF; TIGR00393 400668003663 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 400668003664 putative active site [active] 400668003665 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 400668003666 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 400668003667 NeuB family; Region: NeuB; cl00496 400668003668 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 400668003669 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 400668003670 active site 400668003671 motif I; other site 400668003672 motif II; other site 400668003673 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 400668003674 Ligand binding site; other site 400668003675 oligomer interface; other site 400668003676 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 400668003677 Cell division protein ZapA; Region: ZapA; cl01146 400668003678 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 400668003679 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 400668003680 dimer interface [polypeptide binding]; other site 400668003681 putative anticodon binding site; other site 400668003682 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 400668003683 motif 1; other site 400668003684 active site 400668003685 motif 2; other site 400668003686 motif 3; other site 400668003687 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 400668003688 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 400668003689 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668003690 homodimer interface [polypeptide binding]; other site 400668003691 catalytic residue [active] 400668003692 Uncharacterized conserved protein [Function unknown]; Region: COG3760 400668003693 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 400668003694 putative deacylase active site [active] 400668003695 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage...; Region: Peptidase_C39_like; cl00296 400668003696 putative active site [active] 400668003697 RNA polymerase sigma factor; Provisional; Region: PRK12514 400668003698 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668003699 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 400668003700 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5343 400668003701 Anti-sigma-K factor rskA; Region: RskA; pfam10099 400668003702 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 400668003703 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668003704 Coenzyme A binding pocket [chemical binding]; other site 400668003705 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668003706 Uncharacterized BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 400668003707 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 400668003708 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 400668003709 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668003710 Helix-turn-helix domains; Region: HTH; cl00088 400668003711 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 400668003712 dimerization interface [polypeptide binding]; other site 400668003713 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668003714 Peptidase M14 Aspartoacylase (ASPA) subfamily; Region: M14_ASPA; cd06909 400668003715 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 400668003716 active site 400668003717 Zn binding site [ion binding]; other site 400668003718 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 400668003719 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 400668003720 TPP-binding site; other site 400668003721 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 400668003722 PYR/PP interface [polypeptide binding]; other site 400668003723 dimer interface [polypeptide binding]; other site 400668003724 TPP binding site [chemical binding]; other site 400668003725 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 400668003726 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 400668003727 substrate binding pocket [chemical binding]; other site 400668003728 chain length determination region; other site 400668003729 substrate-Mg2+ binding site; other site 400668003730 catalytic residues [active] 400668003731 aspartate-rich region 1; other site 400668003732 active site lid residues [active] 400668003733 aspartate-rich region 2; other site 400668003734 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 400668003735 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 400668003736 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 400668003737 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 400668003738 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 400668003739 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668003740 ligand binding site [chemical binding]; other site 400668003741 dihydrodipicolinate reductase; Provisional; Region: PRK00048 400668003742 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003743 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 400668003744 Transcriptional regulators [Transcription]; Region: MarR; COG1846 400668003745 Helix-turn-helix domains; Region: HTH; cl00088 400668003746 Helix-turn-helix domains; Region: HTH; cl00088 400668003747 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 400668003748 DNA photolyase; Region: DNA_photolyase; pfam00875 400668003749 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 400668003750 Protein of unknown function (DUF523); Region: DUF523; cl00733 400668003751 Protein of unknown function (DUF1722); Region: DUF1722; cl01284 400668003752 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 400668003753 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668003754 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 400668003755 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 400668003756 DNA binding residues [nucleotide binding] 400668003757 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 400668003758 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 400668003759 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668003760 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 400668003761 Coenzyme A binding pocket [chemical binding]; other site 400668003762 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 400668003763 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 400668003764 inhibitor-cofactor binding pocket; inhibition site 400668003765 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668003766 catalytic residue [active] 400668003767 Cupin domain; Region: Cupin_2; cl09118 400668003768 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668003769 aspartate kinase; Validated; Region: PRK09181 400668003770 AAK_AK-Ectoine: Amino Acid Kinase Superfamily (AAK), AK-Ectoine; this CD includes the N-terminal catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium...; Region: AAK_AK-Ectoine; cd04248 400668003771 putative catalytic residues [active] 400668003772 putative nucleotide binding site [chemical binding]; other site 400668003773 putative aspartate binding site [chemical binding]; other site 400668003774 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway; Region: ACT_AK-Ectoine_1; cd04910 400668003775 allosteric regulatory residue; other site 400668003776 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway; Region: ACT_AK-Ectoine_2; cd04915 400668003777 CHASE domain; Region: CHASE; cl01369 400668003778 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668003779 metal binding site [ion binding]; metal-binding site 400668003780 active site 400668003781 I-site; other site 400668003782 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 400668003783 HupE / UreJ protein; Region: HupE_UreJ; cl01011 400668003784 Protein of unknown function (DUF2834); Region: DUF2834; pfam11196 400668003785 LysE type translocator; Region: LysE; cl00565 400668003786 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 400668003787 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 400668003788 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668003789 active site 400668003790 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 400668003791 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 400668003792 dimer interface [polypeptide binding]; other site 400668003793 ADP-ribose binding site [chemical binding]; other site 400668003794 active site 400668003795 nudix motif; other site 400668003796 metal binding site [ion binding]; metal-binding site 400668003797 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668003798 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668003799 DNA binding site [nucleotide binding] 400668003800 domain linker motif; other site 400668003801 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 400668003802 dimerization interface [polypeptide binding]; other site 400668003803 ligand binding site [chemical binding]; other site 400668003804 Platelet-activating factor acetylhydrolase, isoform II; Region: PAF-AH_p_II; pfam03403 400668003805 Predicted dienelactone hydrolase [General function prediction only]; Region: COG4188 400668003806 Cupin domain; Region: Cupin_2; cl09118 400668003807 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003808 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668003809 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668003810 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 400668003811 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668003812 putative substrate translocation pore; other site 400668003813 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 400668003814 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 400668003815 non-specific DNA binding site [nucleotide binding]; other site 400668003816 salt bridge; other site 400668003817 sequence-specific DNA binding site [nucleotide binding]; other site 400668003818 Domain of unknown function (DUF955); Region: DUF955; cl01076 400668003819 Protein of unknown function (DUF3612); Region: DUF3612; pfam12268 400668003820 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 400668003821 active site 400668003822 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 400668003823 tetramer interface [polypeptide binding]; other site 400668003824 active site 400668003825 Mg2+/Mn2+ binding site [ion binding]; other site 400668003826 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 400668003827 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 400668003828 dimer interface [polypeptide binding]; other site 400668003829 phosphorylation site [posttranslational modification] 400668003830 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 400668003831 ATP binding site [chemical binding]; other site 400668003832 Mg2+ binding site [ion binding]; other site 400668003833 G-X-G motif; other site 400668003834 Response regulator receiver domain; Region: Response_reg; pfam00072 400668003835 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 400668003836 active site 400668003837 phosphorylation site [posttranslational modification] 400668003838 intermolecular recognition site; other site 400668003839 dimerization interface [polypeptide binding]; other site 400668003840 Protein of unknown function (DUF796); Region: DUF796; cl01226 400668003841 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 400668003842 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 400668003843 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 400668003844 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 400668003845 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 400668003846 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 400668003847 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 400668003848 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668003849 putative peptidoglycan binding site; other site 400668003850 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 400668003851 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 400668003852 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 400668003853 Protein of unknown function (DUF796); Region: DUF796; cl01226 400668003854 Protein of unknown function (DUF770); Region: DUF770; cl01402 400668003855 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517; cl05484 400668003856 Protein of unknown function (DUF877); Region: DUF877; pfam05943 400668003857 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 400668003858 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 400668003859 Bacterial protein of unknown function (DUF879); Region: DUF879; cl15462 400668003860 Protein of unknown function (DUF1305); Region: DUF1305; cl01404 400668003861 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 400668003862 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]; Region: COG3456 400668003863 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 400668003864 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522; cl01406 400668003865 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 400668003866 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 400668003867 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 400668003868 Clp amino terminal domain; Region: Clp_N; pfam02861 400668003869 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 400668003870 Walker A motif; other site 400668003871 ATP binding site [chemical binding]; other site 400668003872 Walker B motif; other site 400668003873 arginine finger; other site 400668003874 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 400668003875 Walker A motif; other site 400668003876 ATP binding site [chemical binding]; other site 400668003877 Walker B motif; other site 400668003878 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 400668003879 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668003880 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 400668003881 Walker A motif; other site 400668003882 ATP binding site [chemical binding]; other site 400668003883 Walker B motif; other site 400668003884 arginine finger; other site 400668003885 Protein of unknown function (DUF3121); Region: DUF3121; cl11879 400668003886 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 400668003887 type VI secretion-associated protein, VC_A0119 family; Region: VI_chp_7; TIGR03362 400668003888 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 400668003889 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 400668003890 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 400668003891 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 400668003892 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3515 400668003893 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 400668003894 Protein of unknown function (DUF796); Region: DUF796; cl01226 400668003895 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 400668003896 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 400668003897 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 400668003898 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 400668003899 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668003900 putative peptidoglycan binding site; other site 400668003901 Esterase-like activity of phytase; Region: Phytase-like; pfam13449 400668003902 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668003903 Helix-turn-helix domains; Region: HTH; cl00088 400668003904 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 400668003905 putative dimerization interface [polypeptide binding]; other site 400668003906 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668003907 Citrate transporter; Region: CitMHS; pfam03600 400668003908 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 400668003909 MgtC family; Region: MgtC; pfam02308 400668003910 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668003911 Coenzyme A binding pocket [chemical binding]; other site 400668003912 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668003913 metal binding site [ion binding]; metal-binding site 400668003914 active site 400668003915 I-site; other site 400668003916 Uncharacterized protein conserved in bacteria (DUF2057); Region: DUF2057; cl11437 400668003917 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 400668003918 Integrase core domain; Region: rve; cl01316 400668003919 Integrase core domain; Region: rve_3; cl15866 400668003920 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668003921 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 400668003922 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668003923 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 400668003924 iron-sulfur cluster [ion binding]; other site 400668003925 [2Fe-2S] cluster binding site [ion binding]; other site 400668003926 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 400668003927 Transglycosylase; Region: Transgly; cl07896 400668003928 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668003929 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 400668003930 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668003931 substrate binding pocket [chemical binding]; other site 400668003932 membrane-bound complex binding site; other site 400668003933 hinge residues; other site 400668003934 glycogen synthase; Provisional; Region: glgA; PRK00654 400668003935 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 400668003936 ADP-binding pocket [chemical binding]; other site 400668003937 homodimer interface [polypeptide binding]; other site 400668003938 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 400668003939 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 400668003940 ligand binding site; other site 400668003941 oligomer interface; other site 400668003942 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 400668003943 dimer interface [polypeptide binding]; other site 400668003944 N-terminal domain interface [polypeptide binding]; other site 400668003945 sulfate 1 binding site; other site 400668003946 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 400668003947 Lumazine binding domain; Region: Lum_binding; pfam00677 400668003948 Lumazine binding domain; Region: Lum_binding; pfam00677 400668003949 GTP-binding protein LepA; Provisional; Region: PRK05433 400668003950 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 400668003951 G1 box; other site 400668003952 putative GEF interaction site [polypeptide binding]; other site 400668003953 GTP/Mg2+ binding site [chemical binding]; other site 400668003954 Switch I region; other site 400668003955 G2 box; other site 400668003956 G3 box; other site 400668003957 Switch II region; other site 400668003958 G4 box; other site 400668003959 G5 box; other site 400668003960 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 400668003961 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 400668003962 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 400668003963 signal peptidase I; Provisional; Region: PRK10861 400668003964 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 400668003965 Catalytic site [active] 400668003966 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 400668003967 ribonuclease III; Reviewed; Region: rnc; PRK00102 400668003968 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 400668003969 dimerization interface [polypeptide binding]; other site 400668003970 active site 400668003971 metal binding site [ion binding]; metal-binding site 400668003972 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 400668003973 dsRNA binding site [nucleotide binding]; other site 400668003974 GTPase Era; Reviewed; Region: era; PRK00089 400668003975 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 400668003976 G1 box; other site 400668003977 GTP/Mg2+ binding site [chemical binding]; other site 400668003978 Switch I region; other site 400668003979 G2 box; other site 400668003980 Switch II region; other site 400668003981 G3 box; other site 400668003982 G4 box; other site 400668003983 G5 box; other site 400668003984 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 400668003985 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 400668003986 Recombination protein O N terminal; Region: RecO_N; cl15812 400668003987 Recombination protein O C terminal; Region: RecO_C; pfam02565 400668003988 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 400668003989 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 400668003990 Uncharacterized signal transduction histidine kinase domain (DUF2222); Region: DUF2222; pfam09984 400668003991 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 400668003992 dimer interface [polypeptide binding]; other site 400668003993 phosphorylation site [posttranslational modification] 400668003994 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 400668003995 ATP binding site [chemical binding]; other site 400668003996 Mg2+ binding site [ion binding]; other site 400668003997 G-X-G motif; other site 400668003998 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 400668003999 active site 400668004000 phosphorylation site [posttranslational modification] 400668004001 intermolecular recognition site; other site 400668004002 dimerization interface [polypeptide binding]; other site 400668004003 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 400668004004 cysteine synthase B; Region: cysM; TIGR01138 400668004005 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 400668004006 dimer interface [polypeptide binding]; other site 400668004007 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668004008 catalytic residue [active] 400668004009 TRAM domain; Region: TRAM; cl01282 400668004010 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 400668004011 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 400668004012 S-adenosylmethionine binding site [chemical binding]; other site 400668004013 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 400668004014 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668004015 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 400668004016 synthetase active site [active] 400668004017 NTP binding site [chemical binding]; other site 400668004018 metal binding site [ion binding]; metal-binding site 400668004019 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 400668004020 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 400668004021 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 400668004022 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 400668004023 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 400668004024 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl14656 400668004025 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 400668004026 adenylate kinase; Reviewed; Region: adk; PRK00279 400668004027 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 400668004028 AMP-binding site [chemical binding]; other site 400668004029 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 400668004030 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 400668004031 Bacitracin resistance protein BacA; Region: BacA; cl00858 400668004032 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004033 SlyX; Region: SlyX; cl01090 400668004034 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 400668004035 DNA-binding site [nucleotide binding]; DNA binding site 400668004036 RNA-binding motif; other site 400668004037 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 400668004038 dimer interface [polypeptide binding]; other site 400668004039 catalytic triad [active] 400668004040 peroxidatic and resolving cysteines [active] 400668004041 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 400668004042 tetramerization interface [polypeptide binding]; other site 400668004043 active site 400668004044 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 400668004045 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 400668004046 metal binding site [ion binding]; metal-binding site 400668004047 dimer interface [polypeptide binding]; other site 400668004048 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 400668004049 ArsC family; Region: ArsC; pfam03960 400668004050 putative catalytic residues [active] 400668004051 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Region: DapD_gpp; TIGR03536 400668004052 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 400668004053 putative trimer interface [polypeptide binding]; other site 400668004054 putative CoA binding site [chemical binding]; other site 400668004055 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 400668004056 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 400668004057 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668004058 homodimer interface [polypeptide binding]; other site 400668004059 catalytic residue [active] 400668004060 PII uridylyl-transferase; Provisional; Region: glnD; PRK00275 400668004061 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 400668004062 metal binding triad; other site 400668004063 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 400668004064 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668004065 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 400668004066 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 400668004067 methionine aminopeptidase; Provisional; Region: PRK08671 400668004068 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 400668004069 active site 400668004070 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 400668004071 rRNA interaction site [nucleotide binding]; other site 400668004072 S8 interaction site; other site 400668004073 putative laminin-1 binding site; other site 400668004074 elongation factor Ts; Provisional; Region: tsf; PRK09377 400668004075 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 400668004076 Elongation factor TS; Region: EF_TS; pfam00889 400668004077 Elongation factor TS; Region: EF_TS; pfam00889 400668004078 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 400668004079 putative nucleotide binding site [chemical binding]; other site 400668004080 uridine monophosphate binding site [chemical binding]; other site 400668004081 homohexameric interface [polypeptide binding]; other site 400668004082 ribosome recycling factor; Reviewed; Region: frr; PRK00083 400668004083 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 400668004084 hinge region; other site 400668004085 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 400668004086 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 400668004087 catalytic residue [active] 400668004088 putative FPP diphosphate binding site; other site 400668004089 putative FPP binding hydrophobic cleft; other site 400668004090 dimer interface [polypeptide binding]; other site 400668004091 putative IPP diphosphate binding site; other site 400668004092 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 400668004093 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 400668004094 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 400668004095 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 400668004096 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 400668004097 zinc metallopeptidase RseP; Provisional; Region: PRK10779 400668004098 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 400668004099 active site 400668004100 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 400668004101 protein binding site [polypeptide binding]; other site 400668004102 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 400668004103 protein binding site [polypeptide binding]; other site 400668004104 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 400668004105 putative substrate binding region [chemical binding]; other site 400668004106 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 400668004107 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 400668004108 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 400668004109 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 400668004110 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 400668004111 Surface antigen; Region: Bac_surface_Ag; cl03097 400668004112 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 400668004113 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 400668004114 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 400668004115 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 400668004116 trimer interface [polypeptide binding]; other site 400668004117 active site 400668004118 UDP-GlcNAc binding site [chemical binding]; other site 400668004119 lipid binding site [chemical binding]; lipid-binding site 400668004120 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 400668004121 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 400668004122 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 400668004123 active site 400668004124 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 400668004125 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 400668004126 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 400668004127 RNA/DNA hybrid binding site [nucleotide binding]; other site 400668004128 active site 400668004129 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 400668004130 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 400668004131 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 400668004132 generic binding surface II; other site 400668004133 generic binding surface I; other site 400668004134 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 400668004135 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 400668004136 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 400668004137 Ligand Binding Site [chemical binding]; other site 400668004138 TilS substrate binding domain; Region: TilS; pfam09179 400668004139 B3/4 domain; Region: B3_4; cl11458 400668004140 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 400668004141 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 400668004142 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 400668004143 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 400668004144 Fusaric acid resistance protein family; Region: FUSC; pfam04632 400668004145 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 400668004146 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668004147 active site 400668004148 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668004149 DNA-binding transcriptional regulator GlcC; Provisional; Region: PRK09990 400668004150 DNA-binding site [nucleotide binding]; DNA binding site 400668004151 FCD domain; Region: FCD; cl11656 400668004152 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 400668004153 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 400668004154 iron-sulfur cluster [ion binding]; other site 400668004155 [2Fe-2S] cluster binding site [ion binding]; other site 400668004156 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 400668004157 alpha subunit interface [polypeptide binding]; other site 400668004158 active site 400668004159 substrate binding site [chemical binding]; other site 400668004160 Fe binding site [ion binding]; other site 400668004161 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 400668004162 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 400668004163 FMN-binding pocket [chemical binding]; other site 400668004164 flavin binding motif; other site 400668004165 phosphate binding motif [ion binding]; other site 400668004166 beta-alpha-beta structure motif; other site 400668004167 NAD binding pocket [chemical binding]; other site 400668004168 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 400668004169 catalytic loop [active] 400668004170 iron binding site [ion binding]; other site 400668004171 CTP synthetase; Validated; Region: pyrG; PRK05380 400668004172 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 400668004173 Catalytic site [active] 400668004174 active site 400668004175 UTP binding site [chemical binding]; other site 400668004176 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 400668004177 active site 400668004178 putative oxyanion hole; other site 400668004179 catalytic triad [active] 400668004180 enolase; Provisional; Region: eno; PRK00077 400668004181 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 400668004182 dimer interface [polypeptide binding]; other site 400668004183 metal binding site [ion binding]; metal-binding site 400668004184 substrate binding pocket [chemical binding]; other site 400668004185 Septum formation initiator; Region: DivIC; cl11433 400668004186 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 400668004187 substrate binding site; other site 400668004188 dimer interface; other site 400668004189 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 400668004190 homotrimer interaction site [polypeptide binding]; other site 400668004191 zinc binding site [ion binding]; other site 400668004192 CDP-binding sites; other site 400668004193 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 400668004194 PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_EcTruD; cd02575 400668004195 Permutation of conserved domain; other site 400668004196 active site 400668004197 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 400668004198 Survival protein SurE; Region: SurE; cl00448 400668004199 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004200 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 400668004201 Domain of unknown function (DUF368); Region: DUF368; cl00893 400668004202 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 400668004203 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668004204 putative peptidoglycan binding site; other site 400668004205 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 400668004206 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 400668004207 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668004208 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 400668004209 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 400668004210 DNA binding residues [nucleotide binding] 400668004211 cyclase homology domain; Region: CHD; cd07302 400668004212 nucleotidyl binding site; other site 400668004213 metal binding site [ion binding]; metal-binding site 400668004214 dimer interface [polypeptide binding]; other site 400668004215 phosphoserine phosphatase SerB; Region: serB; TIGR00338 400668004216 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668004217 DNA-binding transcriptional regulator YidZ; Provisional; Region: PRK10216 400668004218 Helix-turn-helix domains; Region: HTH; cl00088 400668004219 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 400668004220 substrate binding pocket [chemical binding]; other site 400668004221 dimerization interface [polypeptide binding]; other site 400668004222 Protein of unknown function DUF86; Region: DUF86; cl01031 400668004223 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 400668004224 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 400668004225 dimer interface [polypeptide binding]; other site 400668004226 putative functional site; other site 400668004227 putative MPT binding site; other site 400668004228 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 400668004229 MPT binding site; other site 400668004230 trimer interface [polypeptide binding]; other site 400668004231 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 400668004232 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 400668004233 FeS/SAM binding site; other site 400668004234 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 400668004235 acyl-CoA thioesterase II; Provisional; Region: PRK10526 400668004236 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 400668004237 active site 400668004238 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 400668004239 catalytic triad [active] 400668004240 dimer interface [polypeptide binding]; other site 400668004241 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 400668004242 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 400668004243 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 400668004244 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 400668004245 PYR/PP interface [polypeptide binding]; other site 400668004246 dimer interface [polypeptide binding]; other site 400668004247 TPP binding site [chemical binding]; other site 400668004248 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 400668004249 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 400668004250 TPP-binding site [chemical binding]; other site 400668004251 dimer interface [polypeptide binding]; other site 400668004252 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 400668004253 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 400668004254 putative valine binding site [chemical binding]; other site 400668004255 dimer interface [polypeptide binding]; other site 400668004256 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 400668004257 Helix-turn-helix domains; Region: HTH; cl00088 400668004258 EamA-like transporter family; Region: EamA; cl01037 400668004259 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668004260 EamA-like transporter family; Region: EamA; cl01037 400668004261 LysE type translocator; Region: LysE; cl00565 400668004262 S-Ribosylhomocysteinase (LuxS); Region: LuxS; cl00802 400668004263 putative transporter; Provisional; Region: PRK11021 400668004264 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668004265 Helix-turn-helix domains; Region: HTH; cl00088 400668004266 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 400668004267 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 400668004268 Cl- selectivity filter; other site 400668004269 Cl- binding residues [ion binding]; other site 400668004270 pore gating glutamate residue; other site 400668004271 dimer interface [polypeptide binding]; other site 400668004272 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 400668004273 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 400668004274 inhibitor-cofactor binding pocket; inhibition site 400668004275 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668004276 catalytic residue [active] 400668004277 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 400668004278 TMAO/DMSO reductase; Reviewed; Region: PRK05363 400668004279 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 400668004280 Moco binding site; other site 400668004281 metal coordination site [ion binding]; other site 400668004282 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 400668004283 Protein of unknown function (DUF3015); Region: DUF3015; pfam11220 400668004284 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 400668004285 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668004286 Helix-turn-helix domains; Region: HTH; cl00088 400668004287 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 400668004288 dimerization interface [polypeptide binding]; other site 400668004289 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668004290 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668004291 Helix-turn-helix domains; Region: HTH; cl00088 400668004292 WHG domain; Region: WHG; pfam13305 400668004293 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 400668004294 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 400668004295 active site 400668004296 FMN binding site [chemical binding]; other site 400668004297 2,4-decadienoyl-CoA binding site; other site 400668004298 catalytic residue [active] 400668004299 4Fe-4S cluster binding site [ion binding]; other site 400668004300 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004301 Flagellin N-methylase; Region: FliB; cl00497 400668004302 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 400668004303 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 400668004304 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 400668004305 putative active site [active] 400668004306 catalytic site [active] 400668004307 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 400668004308 putative active site [active] 400668004309 catalytic site [active] 400668004310 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 400668004311 putative catalytic site [active] 400668004312 putative metal binding site [ion binding]; other site 400668004313 putative phosphate binding site [ion binding]; other site 400668004314 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 400668004315 Helix-turn-helix domains; Region: HTH; cl00088 400668004316 Rrf2 family protein; Region: rrf2_super; TIGR00738 400668004317 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 400668004318 putative ABC transporter; Region: ycf24; CHL00085 400668004319 FeS assembly ATPase SufC; Region: sufC; TIGR01978 400668004320 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 400668004321 Walker A/P-loop; other site 400668004322 ATP binding site [chemical binding]; other site 400668004323 Q-loop/lid; other site 400668004324 ABC transporter signature motif; other site 400668004325 Walker B; other site 400668004326 D-loop; other site 400668004327 H-loop/switch region; other site 400668004328 Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]; Region: SufB; COG0719 400668004329 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 400668004330 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 400668004331 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 400668004332 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668004333 catalytic residue [active] 400668004334 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 400668004335 Domain of unknown function DUF59; Region: DUF59; cl00941 400668004336 Fe-S metabolism associated domain; Region: SufE; cl00951 400668004337 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 400668004338 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 400668004339 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668004340 catalytic residue [active] 400668004341 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 400668004342 active site 400668004343 multimer interface [polypeptide binding]; other site 400668004344 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 400668004345 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 400668004346 FeS/SAM binding site; other site 400668004347 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 400668004348 binding surface 400668004349 TPR motif; other site 400668004350 cytoskeletal protein RodZ; Provisional; Region: PRK10856 400668004351 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 400668004352 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 400668004353 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 400668004354 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 400668004355 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 400668004356 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 400668004357 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 400668004358 dimer interface [polypeptide binding]; other site 400668004359 motif 1; other site 400668004360 active site 400668004361 motif 2; other site 400668004362 motif 3; other site 400668004363 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 400668004364 anticodon binding site; other site 400668004365 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 400668004366 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 400668004367 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 400668004368 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 400668004369 Trp docking motif [polypeptide binding]; other site 400668004370 active site 400668004371 GTP-binding protein Der; Reviewed; Region: PRK00093 400668004372 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 400668004373 G1 box; other site 400668004374 GTP/Mg2+ binding site [chemical binding]; other site 400668004375 Switch I region; other site 400668004376 G2 box; other site 400668004377 Switch II region; other site 400668004378 G3 box; other site 400668004379 G4 box; other site 400668004380 G5 box; other site 400668004381 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 400668004382 G1 box; other site 400668004383 GTP/Mg2+ binding site [chemical binding]; other site 400668004384 Switch I region; other site 400668004385 G2 box; other site 400668004386 G3 box; other site 400668004387 Switch II region; other site 400668004388 G4 box; other site 400668004389 G5 box; other site 400668004390 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 400668004391 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668004392 Predicted deacylase [General function prediction only]; Region: COG3608 400668004393 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 400668004394 putative active site [active] 400668004395 Zn binding site [ion binding]; other site 400668004396 hypothetical protein; Provisional; Region: PRK01254 400668004397 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 400668004398 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 400668004399 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668004400 Protein of unknown function (DUF2496); Region: DUF2496; cl11670 400668004401 Protein of unknown function (DUF1304); Region: DUF1304; cl01533 400668004402 Mycothiol maleylpyruvate isomerase N-terminal domain; Region: MDMPI_N; cl00986 400668004403 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 400668004404 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668004405 active site 400668004406 ATP binding site [chemical binding]; other site 400668004407 substrate binding site [chemical binding]; other site 400668004408 activation loop (A-loop); other site 400668004409 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 400668004410 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 400668004411 Integrase core domain; Region: rve; cl01316 400668004412 Integrase core domain; Region: rve_3; cl15866 400668004413 lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) biosynthetic pathway; Region: Lumazine_synthase-like; cl00317 400668004414 active site 400668004415 homopentamer interface [polypeptide binding]; other site 400668004416 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 400668004417 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 400668004418 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 400668004419 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 400668004420 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 400668004421 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 400668004422 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668004423 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 400668004424 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 400668004425 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 400668004426 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 400668004427 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]; Region: COG2138 400668004428 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 400668004429 putative active site [active] 400668004430 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_C; cd03414 400668004431 putative active site [active] 400668004432 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 400668004433 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 400668004434 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 400668004435 dimer interface [polypeptide binding]; other site 400668004436 active site 400668004437 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668004438 catalytic residues [active] 400668004439 substrate binding site [chemical binding]; other site 400668004440 Phospholipid methyltransferase; Region: PEMT; cl00763 400668004441 Cache domain; Region: Cache_1; pfam02743 400668004442 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 400668004443 dimerization interface [polypeptide binding]; other site 400668004444 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668004445 dimer interface [polypeptide binding]; other site 400668004446 putative CheW interface [polypeptide binding]; other site 400668004447 putative chaperone; Provisional; Region: PRK11678 400668004448 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 400668004449 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 400668004450 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668004451 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668004452 dimer interface [polypeptide binding]; other site 400668004453 putative CheW interface [polypeptide binding]; other site 400668004454 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 400668004455 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 400668004456 Fusaric acid resistance protein-like; Region: FUSC_2; cl15844 400668004457 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 400668004458 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668004459 Helix-turn-helix domains; Region: HTH; cl00088 400668004460 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 400668004461 dimerization interface [polypeptide binding]; other site 400668004462 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 400668004463 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 400668004464 putative substrate translocation pore; other site 400668004465 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 400668004466 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 400668004467 N-terminal plug; other site 400668004468 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 400668004469 ligand-binding site [chemical binding]; other site 400668004470 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 400668004471 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668004472 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 400668004473 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 400668004474 DEDDy 3'-5' exonuclease domain of WRN and similar proteins; Region: WRN_exo; cd06141 400668004475 putative active site [active] 400668004476 catalytic site [active] 400668004477 putative substrate binding site [chemical binding]; other site 400668004478 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 400668004479 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668004480 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668004481 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668004482 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 400668004483 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668004484 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 400668004485 phosphoenolpyruvate synthase; Validated; Region: PRK06464 400668004486 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 400668004487 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 400668004488 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 400668004489 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 400668004490 ribonuclease R; Region: RNase_R; TIGR02063 400668004491 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 400668004492 RNB domain; Region: RNB; pfam00773 400668004493 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 400668004494 RNA binding site [nucleotide binding]; other site 400668004495 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 400668004496 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 400668004497 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 400668004498 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 400668004499 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 400668004500 putative dimer interface [polypeptide binding]; other site 400668004501 active site pocket [active] 400668004502 putative cataytic base [active] 400668004503 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 400668004504 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 400668004505 catalytic core [active] 400668004506 Predicted membrane protein [Function unknown]; Region: COG2860 400668004507 UPF0126 domain; Region: UPF0126; pfam03458 400668004508 UPF0126 domain; Region: UPF0126; pfam03458 400668004509 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 400668004510 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 400668004511 homodimer interface [polypeptide binding]; other site 400668004512 Walker A motif; other site 400668004513 ATP binding site [chemical binding]; other site 400668004514 hydroxycobalamin binding site [chemical binding]; other site 400668004515 Walker B motif; other site 400668004516 Nickel-containing superoxide dismutase; Region: Sod_Ni; cl07609 400668004517 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cd06462 400668004518 Catalytic site [active] 400668004519 Uncharacterized conserved protein [Function unknown]; Region: COG1284 400668004520 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 400668004521 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 400668004522 Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes; Region: MAR; cd08177 400668004523 active site 400668004524 dimer interface [polypeptide binding]; other site 400668004525 metal binding site [ion binding]; metal-binding site 400668004526 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668004527 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668004528 Coenzyme A binding pocket [chemical binding]; other site 400668004529 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 400668004530 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 400668004531 RNA binding surface [nucleotide binding]; other site 400668004532 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 400668004533 active site 400668004534 uracil binding [chemical binding]; other site 400668004535 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 400668004536 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 400668004537 Helix-turn-helix domains; Region: HTH; cl00088 400668004538 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 400668004539 Sodium:solute symporter family; Region: SSF; cl00456 400668004540 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 400668004541 PAS fold; Region: PAS_7; pfam12860 400668004542 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 400668004543 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 400668004544 dimer interface [polypeptide binding]; other site 400668004545 phosphorylation site [posttranslational modification] 400668004546 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 400668004547 ATP binding site [chemical binding]; other site 400668004548 Mg2+ binding site [ion binding]; other site 400668004549 G-X-G motif; other site 400668004550 Dopa 4,5-dioxygenase family; Region: DOPA_dioxygen; cl01562 400668004551 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668004552 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668004553 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 400668004554 putative uracil binding site [chemical binding]; other site 400668004555 putative active site [active] 400668004556 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668004557 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 400668004558 Phenazine biosynthesis-like protein; Region: PhzC-PhzF; pfam02567 400668004559 Protein of unknown function (DUF962); Region: DUF962; cl01879 400668004560 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668004561 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 400668004562 putative DNA binding site [nucleotide binding]; other site 400668004563 putative Zn2+ binding site [ion binding]; other site 400668004564 Helix-turn-helix domains; Region: HTH; cl00088 400668004565 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 400668004566 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 400668004567 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668004568 catalytic residue [active] 400668004569 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 400668004570 putative FMN binding site [chemical binding]; other site 400668004571 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 400668004572 Sodium:solute symporter family; Region: SSF; cl00456 400668004573 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 400668004574 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 400668004575 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668004576 active site 400668004577 metal binding site [ion binding]; metal-binding site 400668004578 MOSC domain; Region: MOSC; pfam03473 400668004579 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 400668004580 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 400668004581 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668004582 catalytic residue [active] 400668004583 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668004584 Helix-turn-helix domains; Region: HTH; cl00088 400668004585 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 400668004586 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668004587 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 400668004588 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 400668004589 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 400668004590 HlyD family secretion protein; Region: HlyD; pfam00529 400668004591 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 400668004592 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 400668004593 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 400668004594 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668004595 DNA-binding site [nucleotide binding]; DNA binding site 400668004596 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 400668004597 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668004598 homodimer interface [polypeptide binding]; other site 400668004599 catalytic residue [active] 400668004600 LysE type translocator; Region: LysE; cl00565 400668004601 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 400668004602 GIY-YIG motif/motif A; other site 400668004603 putative active site [active] 400668004604 putative metal binding site [ion binding]; other site 400668004605 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 400668004606 dimer interface [polypeptide binding]; other site 400668004607 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668004608 metal binding site [ion binding]; metal-binding site 400668004609 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 400668004610 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 400668004611 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 400668004612 ATP binding site [chemical binding]; other site 400668004613 putative Mg++ binding site [ion binding]; other site 400668004614 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 400668004615 nucleotide binding region [chemical binding]; other site 400668004616 ATP-binding site [chemical binding]; other site 400668004617 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 400668004618 Phosphotransferase enzyme family; Region: APH; pfam01636 400668004619 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668004620 active site 400668004621 ATP binding site [chemical binding]; other site 400668004622 substrate binding site [chemical binding]; other site 400668004623 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 400668004624 active site 400668004625 phosphorylation site [posttranslational modification] 400668004626 intermolecular recognition site; other site 400668004627 TPR repeat; Region: TPR_11; pfam13414 400668004628 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 400668004629 binding surface 400668004630 TPR motif; other site 400668004631 Tetratricopeptide repeat; Region: TPR_16; pfam13432 400668004632 Response regulator receiver domain; Region: Response_reg; pfam00072 400668004633 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 400668004634 active site 400668004635 phosphorylation site [posttranslational modification] 400668004636 intermolecular recognition site; other site 400668004637 dimerization interface [polypeptide binding]; other site 400668004638 TPR repeat; Region: TPR_11; pfam13414 400668004639 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 400668004640 binding surface 400668004641 TPR motif; other site 400668004642 Biofilm formation and stress response factor; Region: BsmA; cl01794 400668004643 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668004644 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668004645 dimer interface [polypeptide binding]; other site 400668004646 putative CheW interface [polypeptide binding]; other site 400668004647 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 400668004648 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668004649 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the...; Region: ABC_MTABC3_MDL1_MDL2; cd03249 400668004650 Walker A/P-loop; other site 400668004651 ATP binding site [chemical binding]; other site 400668004652 Q-loop/lid; other site 400668004653 ABC transporter signature motif; other site 400668004654 Walker B; other site 400668004655 D-loop; other site 400668004656 H-loop/switch region; other site 400668004657 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 400668004658 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 400668004659 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 400668004660 active site 400668004661 catalytic site [active] 400668004662 glycogen branching enzyme; Provisional; Region: PRK05402 400668004663 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 400668004664 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 400668004665 active site 400668004666 catalytic site [active] 400668004667 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 400668004668 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 400668004669 Cache domain; Region: Cache_2; cl07034 400668004670 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 400668004671 dimerization interface [polypeptide binding]; other site 400668004672 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668004673 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668004674 dimer interface [polypeptide binding]; other site 400668004675 putative CheW interface [polypeptide binding]; other site 400668004676 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 400668004677 Sporulation related domain; Region: SPOR; cl10051 400668004678 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 400668004679 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339; cl15420 400668004680 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668004681 DctM-like transporters; Region: DctM; pfam06808 400668004682 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668004683 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668004684 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668004685 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 400668004686 active site 400668004687 catalytic residues [active] 400668004688 metal binding site [ion binding]; metal-binding site 400668004689 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 400668004690 CoA-transferase family III; Region: CoA_transf_3; pfam02515 400668004691 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668004692 Helix-turn-helix domains; Region: HTH; cl00088 400668004693 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 400668004694 putative dimerization interface [polypeptide binding]; other site 400668004695 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 400668004696 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 400668004697 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 400668004698 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 400668004699 MatE; Region: MatE; cl10513 400668004700 MatE; Region: MatE; cl10513 400668004701 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668004702 Helix-turn-helix domains; Region: HTH; cl00088 400668004703 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 400668004704 dimerization interface [polypeptide binding]; other site 400668004705 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 400668004706 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 400668004707 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004708 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668004709 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 400668004710 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 400668004711 transmembrane helices; other site 400668004712 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 400668004713 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004714 H+ Antiporter protein; Region: 2A0121; TIGR00900 400668004715 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 400668004716 putative substrate translocation pore; other site 400668004717 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 400668004718 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 400668004719 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004720 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668004721 GTPase RsgA; Reviewed; Region: PRK01889 400668004722 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 400668004723 GTPase/Zn-binding domain interface [polypeptide binding]; other site 400668004724 GTP/Mg2+ binding site [chemical binding]; other site 400668004725 G4 box; other site 400668004726 G5 box; other site 400668004727 G1 box; other site 400668004728 G3 box; other site 400668004729 Switch II region; other site 400668004730 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 400668004731 agmatine deiminase; Region: agmatine_aguA; TIGR03380 400668004732 transcriptional regulatory protein ZraR; Provisional; Region: PRK10365 400668004733 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 400668004734 Walker A motif; other site 400668004735 ATP binding site [chemical binding]; other site 400668004736 Walker B motif; other site 400668004737 arginine finger; other site 400668004738 Helix-turn-helix domains; Region: HTH; cl00088 400668004739 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 400668004740 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an...; Region: HisA_HisF; cd04723 400668004741 active site 400668004742 RF-1 domain; Region: RF-1; cl02875 400668004743 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 400668004744 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 400668004745 homodimer interface [polypeptide binding]; other site 400668004746 substrate-cofactor binding pocket; other site 400668004747 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668004748 catalytic residue [active] 400668004749 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 400668004750 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668004751 DinB superfamily; Region: DinB_2; pfam12867 400668004752 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 400668004753 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 400668004754 putative acyl-acceptor binding pocket; other site 400668004755 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668004756 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 400668004757 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 400668004758 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 400668004759 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 400668004760 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 400668004761 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668004762 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 400668004763 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668004764 Walker A/P-loop; other site 400668004765 ATP binding site [chemical binding]; other site 400668004766 Q-loop/lid; other site 400668004767 ABC transporter signature motif; other site 400668004768 Walker B; other site 400668004769 D-loop; other site 400668004770 H-loop/switch region; other site 400668004771 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 400668004772 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668004773 Walker A/P-loop; other site 400668004774 ATP binding site [chemical binding]; other site 400668004775 Q-loop/lid; other site 400668004776 ABC transporter signature motif; other site 400668004777 Walker B; other site 400668004778 D-loop; other site 400668004779 H-loop/switch region; other site 400668004780 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 400668004781 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 400668004782 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3779 400668004783 Protein of unknown function (DUF2185); Region: DUF2185; cl02019 400668004784 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 400668004785 active site 400668004786 NTP binding site [chemical binding]; other site 400668004787 metal binding triad [ion binding]; metal-binding site 400668004788 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668004789 classical (c) SDRs; Region: SDR_c; cd05233 400668004790 NAD(P) binding site [chemical binding]; other site 400668004791 active site 400668004792 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 400668004793 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668004794 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 400668004795 DNA binding site [nucleotide binding] 400668004796 active site 400668004797 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 400668004798 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 400668004799 non-specific DNA binding site [nucleotide binding]; other site 400668004800 salt bridge; other site 400668004801 sequence-specific DNA binding site [nucleotide binding]; other site 400668004802 AzlC protein; Region: AzlC; cl00570 400668004803 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 400668004804 thioredoxin 2; Provisional; Region: PRK10996 400668004805 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 400668004806 catalytic residues [active] 400668004807 ferredoxin; Validated; Region: PRK07118 400668004808 putative protease; Provisional; Region: PRK15452 400668004809 Peptidase family U32; Region: Peptidase_U32; cl03113 400668004810 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 400668004811 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 400668004812 N-terminal plug; other site 400668004813 ligand-binding site [chemical binding]; other site 400668004814 Protein of unknown function (DUF465); Region: DUF465; cl01070 400668004815 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 400668004816 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 400668004817 ligand binding site [chemical binding]; other site 400668004818 Protein of unknown function (DUF454); Region: DUF454; cl01063 400668004819 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 400668004820 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 400668004821 active site 400668004822 catalytic site [active] 400668004823 substrate binding site [chemical binding]; other site 400668004824 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668004825 ligand binding site [chemical binding]; other site 400668004826 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 400668004827 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 400668004828 ANP binding site [chemical binding]; other site 400668004829 Substrate Binding Site II [chemical binding]; other site 400668004830 Substrate Binding Site I [chemical binding]; other site 400668004831 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 400668004832 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 400668004833 substrate binding site [chemical binding]; other site 400668004834 dimer interface [polypeptide binding]; other site 400668004835 ATP binding site [chemical binding]; other site 400668004836 NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These...; Region: nuc_hydro_CaPnhB; cd02650 400668004837 active site 400668004838 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 400668004839 RNA/DNA binding site [nucleotide binding]; other site 400668004840 RRM dimerization site [polypeptide binding]; other site 400668004841 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 400668004842 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 400668004843 inhibitor-cofactor binding pocket; inhibition site 400668004844 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668004845 catalytic residue [active] 400668004846 endonuclease III; Provisional; Region: PRK10702 400668004847 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 400668004848 minor groove reading motif; other site 400668004849 helix-hairpin-helix signature motif; other site 400668004850 substrate binding pocket [chemical binding]; other site 400668004851 active site 400668004852 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 400668004853 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 400668004854 FMN-binding domain; Region: FMN_bind; cl01081 400668004855 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 400668004856 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 400668004857 RnfC Barrel sandwich hybrid domain; Region: RnfC_N; pfam13375 400668004858 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 400668004859 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 400668004860 electron transport complex protein RnfB; Provisional; Region: PRK05113 400668004861 Putative Fe-S cluster; Region: FeS; pfam04060 400668004862 4Fe-4S binding domain; Region: Fer4; cl02805 400668004863 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 400668004864 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 400668004865 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 400668004866 active site 400668004867 HIGH motif; other site 400668004868 KMSKS motif; other site 400668004869 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 400668004870 tRNA binding surface [nucleotide binding]; other site 400668004871 anticodon binding site; other site 400668004872 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 400668004873 dimer interface [polypeptide binding]; other site 400668004874 putative tRNA-binding site [nucleotide binding]; other site 400668004875 Domain of unknown function DUF59; Region: DUF59; cl00941 400668004876 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 400668004877 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 400668004878 nitrogenase reductase-like protein; Reviewed; Region: PRK13230 400668004879 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 400668004880 trimer interface [polypeptide binding]; other site 400668004881 active site 400668004882 putative transposase OrfB; Reviewed; Region: PHA02517 400668004883 HTH-like domain; Region: HTH_21; pfam13276 400668004884 Integrase core domain; Region: rve; cl01316 400668004885 Integrase core domain; Region: rve_3; cl15866 400668004886 Helix-turn-helix domains; Region: HTH; cl00088 400668004887 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 400668004888 nudix motif; other site 400668004889 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 400668004890 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 400668004891 putative metal binding site [ion binding]; other site 400668004892 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 400668004893 PAS domain S-box; Region: sensory_box; TIGR00229 400668004894 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 400668004895 putative active site [active] 400668004896 heme pocket [chemical binding]; other site 400668004897 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668004898 metal binding site [ion binding]; metal-binding site 400668004899 active site 400668004900 I-site; other site 400668004901 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 400668004902 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 400668004903 homodimer interface [polypeptide binding]; other site 400668004904 substrate-cofactor binding pocket; other site 400668004905 catalytic residue [active] 400668004906 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 400668004907 dimer interface [polypeptide binding]; other site 400668004908 DNA-binding transcriptional regulator CpxR; Provisional; Region: PRK10955 400668004909 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 400668004910 active site 400668004911 phosphorylation site [posttranslational modification] 400668004912 intermolecular recognition site; other site 400668004913 dimerization interface [polypeptide binding]; other site 400668004914 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 400668004915 DNA binding site [nucleotide binding] 400668004916 two-component sensor protein; Provisional; Region: cpxA; PRK09470 400668004917 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 400668004918 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 400668004919 dimer interface [polypeptide binding]; other site 400668004920 phosphorylation site [posttranslational modification] 400668004921 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 400668004922 ATP binding site [chemical binding]; other site 400668004923 Mg2+ binding site [ion binding]; other site 400668004924 G-X-G motif; other site 400668004925 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 400668004926 S-adenosylmethionine binding site [chemical binding]; other site 400668004927 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 400668004928 TraB family; Region: TraB; cl12050 400668004929 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 400668004930 Protein of unknown function, DUF481; Region: DUF481; cl01213 400668004931 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 400668004932 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668004933 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 400668004934 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 400668004935 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 400668004936 Putative acyl-CoA dehydrogenases similar to fadE5; Region: ACAD_fadE5; cd01153 400668004937 FAD binding site [chemical binding]; other site 400668004938 substrate binding site [chemical binding]; other site 400668004939 catalytic residues [active] 400668004940 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 400668004941 SCP-2 sterol transfer family; Region: SCP2; cl01225 400668004942 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK05677 400668004943 AMP-binding enzyme; Region: AMP-binding; cl15778 400668004944 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668004945 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 400668004946 enoyl-CoA hydratase; Provisional; Region: PRK06688 400668004947 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 400668004948 substrate binding site [chemical binding]; other site 400668004949 oxyanion hole (OAH) forming residues; other site 400668004950 trimer interface [polypeptide binding]; other site 400668004951 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 400668004952 Ligand binding site [chemical binding]; other site 400668004953 Electron transfer flavoprotein domain; Region: ETF; pfam01012 400668004954 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 400668004955 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 400668004956 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 400668004957 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadB; PRK11730 400668004958 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 400668004959 substrate binding site [chemical binding]; other site 400668004960 oxyanion hole (OAH) forming residues; other site 400668004961 trimer interface [polypeptide binding]; other site 400668004962 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004963 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 400668004964 3-ketoacyl-CoA thiolase; Reviewed; Region: fadA; PRK08947 400668004965 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 400668004966 dimer interface [polypeptide binding]; other site 400668004967 active site 400668004968 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 400668004969 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668004970 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668004971 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 400668004972 dimerization interface [polypeptide binding]; other site 400668004973 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668004974 dimer interface [polypeptide binding]; other site 400668004975 putative CheW interface [polypeptide binding]; other site 400668004976 cytosine deaminase; Provisional; Region: PRK09230 400668004977 Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi; Region: Bact_CD; cd01293 400668004978 active site 400668004979 Sodium:solute symporter family; Region: SSF; cl00456 400668004980 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 400668004981 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 400668004982 dimer interface [polypeptide binding]; other site 400668004983 active site 400668004984 heme binding site [chemical binding]; other site 400668004985 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 400668004986 Cache domain; Region: Cache_1; pfam02743 400668004987 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 400668004988 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 400668004989 dimerization interface [polypeptide binding]; other site 400668004990 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668004991 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668004992 dimer interface [polypeptide binding]; other site 400668004993 putative CheW interface [polypeptide binding]; other site 400668004994 Predicted membrane protein (DUF2127); Region: DUF2127; cl01785 400668004995 putative acetyltransferase; Provisional; Region: PRK03624 400668004996 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668004997 Coenzyme A binding pocket [chemical binding]; other site 400668004998 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 400668004999 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 400668005000 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 400668005001 putative active site [active] 400668005002 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_4; cd06312 400668005003 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 400668005004 putative ligand binding site [chemical binding]; other site 400668005005 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 400668005006 TM-ABC transporter signature motif; other site 400668005007 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 400668005008 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668005009 Walker A/P-loop; other site 400668005010 ATP binding site [chemical binding]; other site 400668005011 Q-loop/lid; other site 400668005012 ABC transporter signature motif; other site 400668005013 Walker B; other site 400668005014 D-loop; other site 400668005015 H-loop/switch region; other site 400668005016 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668005017 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005018 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668005019 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 400668005020 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 400668005021 substrate binding site [chemical binding]; other site 400668005022 ATP binding site [chemical binding]; other site 400668005023 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 400668005024 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 400668005025 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 400668005026 PYR/PP interface [polypeptide binding]; other site 400668005027 dimer interface [polypeptide binding]; other site 400668005028 TPP binding site [chemical binding]; other site 400668005029 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 400668005030 Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism; Region: TPP_IolD; cd02003 400668005031 TPP-binding site; other site 400668005032 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 400668005033 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 400668005034 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668005035 tetrameric interface [polypeptide binding]; other site 400668005036 NAD binding site [chemical binding]; other site 400668005037 catalytic residues [active] 400668005038 KduI/IolB family; Region: KduI; cl01508 400668005039 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668005040 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005041 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668005042 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 400668005043 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 400668005044 active site 400668005045 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668005046 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668005047 DNA binding site [nucleotide binding] 400668005048 domain linker motif; other site 400668005049 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_2; cd06278 400668005050 putative ligand binding site [chemical binding]; other site 400668005051 putative dimerization interface [polypeptide binding]; other site 400668005052 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 400668005053 active site 400668005054 catalytic residues [active] 400668005055 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 400668005056 active site 400668005057 dimerization interface [polypeptide binding]; other site 400668005058 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 400668005059 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 400668005060 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 400668005061 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668005062 Walker A/P-loop; other site 400668005063 ATP binding site [chemical binding]; other site 400668005064 Q-loop/lid; other site 400668005065 ABC transporter signature motif; other site 400668005066 Walker B; other site 400668005067 D-loop; other site 400668005068 H-loop/switch region; other site 400668005069 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 400668005070 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 400668005071 dimer interface [polypeptide binding]; other site 400668005072 conserved gate region; other site 400668005073 putative PBP binding loops; other site 400668005074 ABC-ATPase subunit interface; other site 400668005075 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668005076 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 400668005077 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 400668005078 Isochorismatase family; Region: Isochorismatase; pfam00857 400668005079 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 400668005080 catalytic triad [active] 400668005081 dimer interface [polypeptide binding]; other site 400668005082 conserved cis-peptide bond; other site 400668005083 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 400668005084 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 400668005085 metal-binding site [ion binding] 400668005086 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 400668005087 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668005088 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 400668005089 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 400668005090 Cupin domain; Region: Cupin_2; cl09118 400668005091 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668005092 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 400668005093 MFS/sugar transport protein; Region: MFS_2; pfam13347 400668005094 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 400668005095 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 400668005096 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 400668005097 enterobactin synthase subunit F; Provisional; Region: entF; PRK10252 400668005098 AMP-binding enzyme; Region: AMP-binding; cl15778 400668005099 AMP-binding enzyme; Region: AMP-binding; cl15778 400668005100 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668005101 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 400668005102 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668005103 putative substrate translocation pore; other site 400668005104 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 400668005105 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 400668005106 Walker A/P-loop; other site 400668005107 ATP binding site [chemical binding]; other site 400668005108 Q-loop/lid; other site 400668005109 ABC transporter signature motif; other site 400668005110 Walker B; other site 400668005111 D-loop; other site 400668005112 H-loop/switch region; other site 400668005113 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 400668005114 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 400668005115 putative PBP binding regions; other site 400668005116 ABC-ATPase subunit interface; other site 400668005117 chorismate binding enzyme; Region: Chorismate_bind; cl10555 400668005118 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological...; Region: isochorismatase; cd01013 400668005119 hydrophobic substrate binding pocket; other site 400668005120 Isochorismatase family; Region: Isochorismatase; pfam00857 400668005121 active site 400668005122 conserved cis-peptide bond; other site 400668005123 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668005124 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668005125 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005126 NAD(P) binding site [chemical binding]; other site 400668005127 active site 400668005128 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 400668005129 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 400668005130 N-terminal plug; other site 400668005131 ligand-binding site [chemical binding]; other site 400668005132 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 400668005133 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 400668005134 putative ligand binding residues [chemical binding]; other site 400668005135 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 400668005136 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 400668005137 Walker A/P-loop; other site 400668005138 ATP binding site [chemical binding]; other site 400668005139 Q-loop/lid; other site 400668005140 ABC transporter signature motif; other site 400668005141 Walker B; other site 400668005142 D-loop; other site 400668005143 H-loop/switch region; other site 400668005144 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 400668005145 ABC-ATPase subunit interface; other site 400668005146 dimer interface [polypeptide binding]; other site 400668005147 putative PBP binding regions; other site 400668005148 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 400668005149 ABC-ATPase subunit interface; other site 400668005150 dimer interface [polypeptide binding]; other site 400668005151 putative PBP binding regions; other site 400668005152 Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: IucD; COG3486 400668005153 Condensation domain; Region: Condensation; pfam00668 400668005154 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 400668005155 Nonribosomal peptide synthase; Region: NRPS; pfam08415 400668005156 Condensation domain; Region: Condensation; pfam00668 400668005157 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 400668005158 Nonribosomal peptide synthase; Region: NRPS; pfam08415 400668005159 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668005160 enterobactin synthase subunit E; Provisional; Region: entE; PRK10946 400668005161 AMP-binding enzyme; Region: AMP-binding; cl15778 400668005162 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668005163 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological...; Region: isochorismatase; cd01013 400668005164 hydrophobic substrate binding pocket; other site 400668005165 Isochorismatase family; Region: Isochorismatase; pfam00857 400668005166 active site 400668005167 conserved cis-peptide bond; other site 400668005168 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668005169 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 400668005170 AMP-binding enzyme; Region: AMP-binding; cl15778 400668005171 AMP-binding enzyme; Region: AMP-binding; cl15778 400668005172 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 400668005173 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668005174 Walker A/P-loop; other site 400668005175 ATP binding site [chemical binding]; other site 400668005176 Q-loop/lid; other site 400668005177 ABC transporter signature motif; other site 400668005178 Walker B; other site 400668005179 D-loop; other site 400668005180 H-loop/switch region; other site 400668005181 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 400668005182 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668005183 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668005184 Walker A/P-loop; other site 400668005185 ATP binding site [chemical binding]; other site 400668005186 Q-loop/lid; other site 400668005187 ABC transporter signature motif; other site 400668005188 Walker B; other site 400668005189 D-loop; other site 400668005190 H-loop/switch region; other site 400668005191 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 400668005192 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668005193 catalytic residue [active] 400668005194 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668005195 peptide synthase; Provisional; Region: PRK12467 400668005196 Glycosyl hydrolase family 79, N-terminal domain; Region: Glyco_hydro_79n; pfam03662 400668005197 Eukaryotic aspartyl protease; Region: Asp; pfam00026 400668005198 Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH; Region: pepsin_like; cd05471 400668005199 inhibitor binding site; inhibition site 400668005200 catalytic motif [active] 400668005201 catalytic residue [active] 400668005202 Active site flap [active] 400668005203 Avidin family; Region: Avidin; pfam01382 400668005204 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 400668005205 putative active site [active] 400668005206 heme pocket [chemical binding]; other site 400668005207 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 400668005208 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 400668005209 dimer interface [polypeptide binding]; other site 400668005210 phosphorylation site [posttranslational modification] 400668005211 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 400668005212 ATP binding site [chemical binding]; other site 400668005213 Mg2+ binding site [ion binding]; other site 400668005214 G-X-G motif; other site 400668005215 Response regulator receiver domain; Region: Response_reg; pfam00072 400668005216 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 400668005217 active site 400668005218 phosphorylation site [posttranslational modification] 400668005219 intermolecular recognition site; other site 400668005220 dimerization interface [polypeptide binding]; other site 400668005221 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 400668005222 Response regulator receiver domain; Region: Response_reg; pfam00072 400668005223 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 400668005224 active site 400668005225 phosphorylation site [posttranslational modification] 400668005226 intermolecular recognition site; other site 400668005227 dimerization interface [polypeptide binding]; other site 400668005228 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668005229 metal binding site [ion binding]; metal-binding site 400668005230 active site 400668005231 I-site; other site 400668005232 Protein of unknown function (DUF3422); Region: DUF3422; cl02073 400668005233 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 400668005234 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668005235 DNA-binding site [nucleotide binding]; DNA binding site 400668005236 UTRA domain; Region: UTRA; cl01230 400668005237 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668005238 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668005239 Walker A/P-loop; other site 400668005240 ATP binding site [chemical binding]; other site 400668005241 Q-loop/lid; other site 400668005242 ABC transporter signature motif; other site 400668005243 Walker B; other site 400668005244 D-loop; other site 400668005245 H-loop/switch region; other site 400668005246 TOBE domain; Region: TOBE_2; cl01440 400668005247 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668005248 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 400668005249 dimer interface [polypeptide binding]; other site 400668005250 conserved gate region; other site 400668005251 putative PBP binding loops; other site 400668005252 ABC-ATPase subunit interface; other site 400668005253 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668005254 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 400668005255 dimer interface [polypeptide binding]; other site 400668005256 conserved gate region; other site 400668005257 putative PBP binding loops; other site 400668005258 ABC-ATPase subunit interface; other site 400668005259 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668005260 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 400668005261 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 400668005262 active site 400668005263 trimer interface [polypeptide binding]; other site 400668005264 allosteric site; other site 400668005265 active site lid [active] 400668005266 hexamer (dimer of trimers) interface [polypeptide binding]; other site 400668005267 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 400668005268 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 400668005269 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 400668005270 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 400668005271 active site 400668005272 dimer interface [polypeptide binding]; other site 400668005273 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 400668005274 DNA-binding site [nucleotide binding]; DNA binding site 400668005275 RNA-binding motif; other site 400668005276 Fasciclin domain; Region: Fasciclin; cl02663 400668005277 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668005278 EamA-like transporter family; Region: EamA; cl01037 400668005279 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668005280 Helix-turn-helix domains; Region: HTH; cl00088 400668005281 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 400668005282 putative effector binding pocket; other site 400668005283 dimerization interface [polypeptide binding]; other site 400668005284 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 400668005285 active site 400668005286 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 400668005287 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 400668005288 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 400668005289 substrate binding site [chemical binding]; other site 400668005290 active site 400668005291 catalytic residues [active] 400668005292 heterodimer interface [polypeptide binding]; other site 400668005293 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 400668005294 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 400668005295 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668005296 catalytic residue [active] 400668005297 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668005298 Helix-turn-helix domains; Region: HTH; cl00088 400668005299 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 400668005300 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668005301 putative substrate translocation pore; other site 400668005302 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668005303 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005304 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 400668005305 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 400668005306 active site 400668005307 substrate binding site [chemical binding]; other site 400668005308 cosubstrate binding site; other site 400668005309 catalytic site [active] 400668005310 Carboxy-terminal domain of Formyltransferase and similar domains; Region: FMT_C_like; cl14785 400668005311 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 400668005312 Phage Tail Collar Domain; Region: Collar; pfam07484 400668005313 Microcystin-dependent protein [Function unknown]; Region: MdpB; COG4675 400668005314 Phage Tail Collar Domain; Region: Collar; pfam07484 400668005315 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 400668005316 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 400668005317 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 400668005318 Domain of unknown function (DUF4347); Region: DUF4347; pfam14252 400668005319 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 400668005320 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; cl15373 400668005321 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; cl15373 400668005322 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 400668005323 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005324 Ca2+ binding site [ion binding]; other site 400668005325 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005326 Ca2+ binding site [ion binding]; other site 400668005327 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005328 Ca2+ binding site [ion binding]; other site 400668005329 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005330 Ca2+ binding site [ion binding]; other site 400668005331 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005332 Ca2+ binding site [ion binding]; other site 400668005333 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005334 Ca2+ binding site [ion binding]; other site 400668005335 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005336 Ca2+ binding site [ion binding]; other site 400668005337 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005338 Ca2+ binding site [ion binding]; other site 400668005339 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005340 Ca2+ binding site [ion binding]; other site 400668005341 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005342 Ca2+ binding site [ion binding]; other site 400668005343 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005344 Ca2+ binding site [ion binding]; other site 400668005345 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005346 Ca2+ binding site [ion binding]; other site 400668005347 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 400668005348 Ca2+ binding site [ion binding]; other site 400668005349 VCBS repeat; Region: VCBS_repeat; TIGR01965 400668005350 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 400668005351 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 400668005352 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 400668005353 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 400668005354 active site 400668005355 putative substrate binding region [chemical binding]; other site 400668005356 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 400668005357 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 400668005358 guanine deaminase; Provisional; Region: PRK09228 400668005359 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 400668005360 active site 400668005361 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 400668005362 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 400668005363 ATP binding site [chemical binding]; other site 400668005364 Mg++ binding site [ion binding]; other site 400668005365 motif III; other site 400668005366 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 400668005367 nucleotide binding region [chemical binding]; other site 400668005368 DbpA RNA binding domain; Region: DbpA; pfam03880 400668005369 CHASE domain; Region: CHASE; cl01369 400668005370 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668005371 metal binding site [ion binding]; metal-binding site 400668005372 active site 400668005373 I-site; other site 400668005374 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 400668005375 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668005376 Helix-turn-helix domains; Region: HTH; cl00088 400668005377 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 400668005378 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 400668005379 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 400668005380 Walker A/P-loop; other site 400668005381 ATP binding site [chemical binding]; other site 400668005382 Q-loop/lid; other site 400668005383 ABC transporter signature motif; other site 400668005384 Walker B; other site 400668005385 D-loop; other site 400668005386 H-loop/switch region; other site 400668005387 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668005388 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 400668005389 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 400668005390 Walker A/P-loop; other site 400668005391 ATP binding site [chemical binding]; other site 400668005392 Q-loop/lid; other site 400668005393 ABC transporter signature motif; other site 400668005394 Walker B; other site 400668005395 D-loop; other site 400668005396 H-loop/switch region; other site 400668005397 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668005398 glutathione ABC transporter permease GsiD; Provisional; Region: PRK15082 400668005399 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 400668005400 dimer interface [polypeptide binding]; other site 400668005401 conserved gate region; other site 400668005402 putative PBP binding loops; other site 400668005403 ABC-ATPase subunit interface; other site 400668005404 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 400668005405 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 400668005406 dimer interface [polypeptide binding]; other site 400668005407 conserved gate region; other site 400668005408 putative PBP binding loops; other site 400668005409 ABC-ATPase subunit interface; other site 400668005410 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 400668005411 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 400668005412 Protein of unknown function, DUF479; Region: DUF479; cl01203 400668005413 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 400668005414 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 400668005415 GTP/Mg2+ binding site [chemical binding]; other site 400668005416 G4 box; other site 400668005417 G5 box; other site 400668005418 G1 box; other site 400668005419 Switch I region; other site 400668005420 G2 box; other site 400668005421 G3 box; other site 400668005422 Switch II region; other site 400668005423 Uncharacterized protein family (UPF0231); Region: UPF0231; cl11474 400668005424 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 400668005425 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 400668005426 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 400668005427 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 400668005428 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 400668005429 putative acyl-acceptor binding pocket; other site 400668005430 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668005431 ATP binding site [chemical binding]; other site 400668005432 spore coat protein, CotS family; Region: spore_CotS; TIGR02906 400668005433 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 400668005434 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 400668005435 putative active site [active] 400668005436 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; cl00246 400668005437 FAD binding site [chemical binding]; other site 400668005438 Protein of unknown function (DUF1285); Region: DUF1285; cl01571 400668005439 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 400668005440 DEAD-like helicases superfamily; Region: DEXDc; smart00487 400668005441 ATP binding site [chemical binding]; other site 400668005442 Mg++ binding site [ion binding]; other site 400668005443 motif III; other site 400668005444 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 400668005445 nucleotide binding region [chemical binding]; other site 400668005446 ATP-binding site [chemical binding]; other site 400668005447 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668005448 Helix-turn-helix domains; Region: HTH; cl00088 400668005449 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 400668005450 dimerization interface [polypeptide binding]; other site 400668005451 substrate binding pocket [chemical binding]; other site 400668005452 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 400668005453 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 400668005454 N-acetyl-D-glucosamine binding site [chemical binding]; other site 400668005455 catalytic residue [active] 400668005456 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668005457 putative peptidoglycan binding site; other site 400668005458 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668005459 putative peptidoglycan binding site; other site 400668005460 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 400668005461 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668005462 putative peptidoglycan binding site; other site 400668005463 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 400668005464 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668005465 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 400668005466 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005467 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 400668005468 RNA/DNA hybrid binding site [nucleotide binding]; other site 400668005469 active site 400668005470 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 400668005471 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 400668005472 active site 400668005473 substrate binding site [chemical binding]; other site 400668005474 catalytic site [active] 400668005475 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 400668005476 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 400668005477 putative inner membrane peptidase; Provisional; Region: PRK11778 400668005478 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 400668005479 tandem repeat interface [polypeptide binding]; other site 400668005480 oligomer interface [polypeptide binding]; other site 400668005481 active site residues [active] 400668005482 transcription-repair coupling factor; Provisional; Region: PRK10689 400668005483 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 400668005484 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 400668005485 ATP binding site [chemical binding]; other site 400668005486 putative Mg++ binding site [ion binding]; other site 400668005487 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 400668005488 nucleotide binding region [chemical binding]; other site 400668005489 ATP-binding site [chemical binding]; other site 400668005490 TRCF domain; Region: TRCF; cl04088 400668005491 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 400668005492 active site 400668005493 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 400668005494 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 400668005495 E3 interaction surface; other site 400668005496 lipoyl attachment site [posttranslational modification]; other site 400668005497 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 400668005498 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 400668005499 FMN-binding domain; Region: FMN_bind; cl01081 400668005500 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 400668005501 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 400668005502 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 400668005503 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 400668005504 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 400668005505 catalytic loop [active] 400668005506 iron binding site [ion binding]; other site 400668005507 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 400668005508 FAD binding pocket [chemical binding]; other site 400668005509 FAD binding motif [chemical binding]; other site 400668005510 phosphate binding motif [ion binding]; other site 400668005511 beta-alpha-beta structure motif; other site 400668005512 NAD binding pocket [chemical binding]; other site 400668005513 ApbE family; Region: ApbE; cl00643 400668005514 Protein of unknown function (DUF539); Region: DUF539; cl01129 400668005515 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 400668005516 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668005517 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 400668005518 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668005519 active site 400668005520 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 400668005521 trigger factor; Provisional; Region: tig; PRK01490 400668005522 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668005523 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 400668005524 Clp protease; Region: CLP_protease; pfam00574 400668005525 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 400668005526 oligomer interface [polypeptide binding]; other site 400668005527 active site residues [active] 400668005528 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 400668005529 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 400668005530 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 400668005531 Walker A motif; other site 400668005532 ATP binding site [chemical binding]; other site 400668005533 Walker B motif; other site 400668005534 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 400668005535 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 400668005536 Found in ATP-dependent protease La (LON); Region: LON; smart00464 400668005537 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 400668005538 Walker A motif; other site 400668005539 ATP binding site [chemical binding]; other site 400668005540 Walker B motif; other site 400668005541 arginine finger; other site 400668005542 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 400668005543 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 400668005544 IHF dimer interface [polypeptide binding]; other site 400668005545 IHF - DNA interface [nucleotide binding]; other site 400668005546 periplasmic folding chaperone; Provisional; Region: PRK10788 400668005547 SurA N-terminal domain; Region: SurA_N_3; cl07813 400668005548 PPIC-type PPIASE domain; Region: Rotamase; cl08278 400668005549 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 400668005550 Integrase core domain; Region: rve; cl01316 400668005551 Integrase core domain; Region: rve_3; cl15866 400668005552 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 400668005553 Oxygen tolerance; Region: BatD; pfam13584 400668005554 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 400668005555 metal ion-dependent adhesion site (MIDAS); other site 400668005556 Tetratricopeptide repeat; Region: TPR_16; pfam13432 400668005557 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 400668005558 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 400668005559 metal ion-dependent adhesion site (MIDAS); other site 400668005560 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 400668005561 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 400668005562 MoxR-like ATPases [General function prediction only]; Region: COG0714 400668005563 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 400668005564 Walker A motif; other site 400668005565 ATP binding site [chemical binding]; other site 400668005566 Walker B motif; other site 400668005567 arginine finger; other site 400668005568 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 400668005569 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 400668005570 quinone interaction residues [chemical binding]; other site 400668005571 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 400668005572 active site 400668005573 catalytic residues [active] 400668005574 FMN binding site [chemical binding]; other site 400668005575 substrate binding site [chemical binding]; other site 400668005576 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 400668005577 THUMP domain; Region: THUMP; cl12076 400668005578 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005579 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 400668005580 S-adenosylmethionine binding site [chemical binding]; other site 400668005581 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 400668005582 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 400668005583 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 400668005584 putative active site [active] 400668005585 putative substrate binding site [chemical binding]; other site 400668005586 putative cosubstrate binding site; other site 400668005587 catalytic site [active] 400668005588 Transposase; Region: DEDD_Tnp_IS110; pfam01548 400668005589 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 400668005590 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 400668005591 Transposase domain (DUF772); Region: DUF772; cl15789 400668005592 Transposase domain (DUF772); Region: DUF772; cl15789 400668005593 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 400668005594 FRG domain; Region: FRG; cl07460 400668005595 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668005596 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668005597 Protein of unknown function (DUF3549); Region: DUF3549; pfam12069 400668005598 tRNA pseudouridine synthase C; Region: DUF446; cl01187 400668005599 Domain of unknown function (DUF1853); Region: DUF1853; cl01545 400668005600 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668005601 metal binding site [ion binding]; metal-binding site 400668005602 active site 400668005603 I-site; other site 400668005604 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 400668005605 23S rRNA methyltransferase A; Provisional; Region: rrmA; PRK11088 400668005606 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 400668005607 S-adenosylmethionine binding site [chemical binding]; other site 400668005608 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 400668005609 active site clefts [active] 400668005610 zinc binding site [ion binding]; other site 400668005611 dimer interface [polypeptide binding]; other site 400668005612 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668005613 Helix-turn-helix domains; Region: HTH; cl00088 400668005614 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 400668005615 substrate binding pocket [chemical binding]; other site 400668005616 dimerization interface [polypeptide binding]; other site 400668005617 N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism]; Region: COG2942 400668005618 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cd00249 400668005619 dimerization interface [polypeptide binding]; other site 400668005620 putative active cleft [active] 400668005621 Helix-turn-helix domains; Region: HTH; cl00088 400668005622 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 400668005623 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 400668005624 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 400668005625 N-terminal ACT domain of the TyrR protein; Region: ACT_TyrR; cd04877 400668005626 putative aromatic amino acid binding site; other site 400668005627 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668005628 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 400668005629 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 400668005630 active site 400668005631 motif I; other site 400668005632 motif II; other site 400668005633 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668005634 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 400668005635 active site 400668005636 phosphorylation site [posttranslational modification] 400668005637 intermolecular recognition site; other site 400668005638 dimerization interface [polypeptide binding]; other site 400668005639 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 400668005640 Walker A motif; other site 400668005641 ATP binding site [chemical binding]; other site 400668005642 Walker B motif; other site 400668005643 arginine finger; other site 400668005644 Helix-turn-helix domains; Region: HTH; cl00088 400668005645 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668005646 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 400668005647 substrate binding pocket [chemical binding]; other site 400668005648 membrane-bound complex binding site; other site 400668005649 hinge residues; other site 400668005650 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 400668005651 dimer interface [polypeptide binding]; other site 400668005652 phosphorylation site [posttranslational modification] 400668005653 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 400668005654 ATP binding site [chemical binding]; other site 400668005655 Mg2+ binding site [ion binding]; other site 400668005656 G-X-G motif; other site 400668005657 Helix-turn-helix domains; Region: HTH; cl00088 400668005658 putative transposase OrfB; Reviewed; Region: PHA02517 400668005659 HTH-like domain; Region: HTH_21; pfam13276 400668005660 Integrase core domain; Region: rve; cl01316 400668005661 Integrase core domain; Region: rve_3; cl15866 400668005662 NMT1-like family; Region: NMT1_2; cl15260 400668005663 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 400668005664 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668005665 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668005666 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 400668005667 HopJ type III effector protein; Region: HopJ; pfam08888 400668005668 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 400668005669 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 400668005670 putative substrate translocation pore; other site 400668005671 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 400668005672 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668005673 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 400668005674 Walker A/P-loop; other site 400668005675 ATP binding site [chemical binding]; other site 400668005676 Q-loop/lid; other site 400668005677 ABC transporter signature motif; other site 400668005678 Walker B; other site 400668005679 D-loop; other site 400668005680 H-loop/switch region; other site 400668005681 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 400668005682 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 400668005683 intersubunit interface [polypeptide binding]; other site 400668005684 Alpha amylase catalytic domain found in sucrose phosphorylase-like proteins (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase); Region: AmyAc_Sucrose_phosphorylase-like_1; cd11356 400668005685 sucrose phosphorylase; Region: sucrose_gtfA; TIGR03852 400668005686 active site 400668005687 homodimer interface [polypeptide binding]; other site 400668005688 catalytic site [active] 400668005689 putative glucosyl-3-phosphoglycerate synthase; Provisional; Region: PRK13915 400668005690 mannosyl-3-phosphoglycerate phosphatase; Reviewed; Region: PRK00192 400668005691 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 400668005692 active site 400668005693 motif I; other site 400668005694 motif II; other site 400668005695 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668005696 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 400668005697 EamA-like transporter family; Region: EamA; cl01037 400668005698 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 400668005699 active site 400668005700 NTP binding site [chemical binding]; other site 400668005701 metal binding triad [ion binding]; metal-binding site 400668005702 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_31; cd04690 400668005703 nudix motif; other site 400668005704 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668005705 AAA domain; Region: AAA_28; pfam13521 400668005706 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 400668005707 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668005708 Coenzyme A binding pocket [chemical binding]; other site 400668005709 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668005710 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668005711 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 400668005712 putative active site [active] 400668005713 putative metal binding residues [ion binding]; other site 400668005714 signature motif; other site 400668005715 putative triphosphate binding site [ion binding]; other site 400668005716 dimer interface [polypeptide binding]; other site 400668005717 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 400668005718 integron integrase; Region: integrase_gron; TIGR02249 400668005719 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 400668005720 DNA binding site [nucleotide binding] 400668005721 Int/Topo IB signature motif; other site 400668005722 active site 400668005723 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 400668005724 Putative transposase; Region: Y2_Tnp; pfam04986 400668005725 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 400668005726 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 400668005727 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 400668005728 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 400668005729 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668005730 catalytic residue [active] 400668005731 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 400668005732 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 400668005733 EamA-like transporter family; Region: EamA; cl01037 400668005734 EamA-like transporter family; Region: EamA; cl01037 400668005735 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668005736 NMT1-like family; Region: NMT1_2; cl15260 400668005737 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668005738 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668005739 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668005740 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 400668005741 active site 400668005742 phosphorylation site [posttranslational modification] 400668005743 intermolecular recognition site; other site 400668005744 dimerization interface [polypeptide binding]; other site 400668005745 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 400668005746 DNA binding site [nucleotide binding] 400668005747 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 400668005748 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 400668005749 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 400668005750 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 400668005751 dimer interface [polypeptide binding]; other site 400668005752 phosphorylation site [posttranslational modification] 400668005753 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 400668005754 ATP binding site [chemical binding]; other site 400668005755 Mg2+ binding site [ion binding]; other site 400668005756 G-X-G motif; other site 400668005757 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 400668005758 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 400668005759 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668005760 Cupin domain; Region: Cupin_2; cl09118 400668005761 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668005762 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668005763 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668005764 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 400668005765 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 400668005766 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 400668005767 apolar tunnel; other site 400668005768 heme binding site [chemical binding]; other site 400668005769 dimerization interface [polypeptide binding]; other site 400668005770 Predicted permease; Region: DUF318; pfam03773 400668005771 Predicted permeases [General function prediction only]; Region: COG0701 400668005772 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 400668005773 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 400668005774 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668005775 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668005776 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668005777 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668005778 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668005779 Helix-turn-helix domains; Region: HTH; cl00088 400668005780 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 400668005781 intersubunit interface [polypeptide binding]; other site 400668005782 active site 400668005783 Zn2+ binding site [ion binding]; other site 400668005784 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 400668005785 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005786 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 400668005787 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 400668005788 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 400668005789 Walker A/P-loop; other site 400668005790 ATP binding site [chemical binding]; other site 400668005791 Q-loop/lid; other site 400668005792 ABC transporter signature motif; other site 400668005793 Walker B; other site 400668005794 D-loop; other site 400668005795 H-loop/switch region; other site 400668005796 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 400668005797 TM-ABC transporter signature motif; other site 400668005798 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 400668005799 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 400668005800 Walker A/P-loop; other site 400668005801 ATP binding site [chemical binding]; other site 400668005802 Q-loop/lid; other site 400668005803 ABC transporter signature motif; other site 400668005804 Walker B; other site 400668005805 D-loop; other site 400668005806 H-loop/switch region; other site 400668005807 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 400668005808 TM-ABC transporter signature motif; other site 400668005809 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 400668005810 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 400668005811 putative ligand binding site [chemical binding]; other site 400668005812 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 400668005813 active site 400668005814 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 400668005815 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 400668005816 iron-sulfur cluster [ion binding]; other site 400668005817 [2Fe-2S] cluster binding site [ion binding]; other site 400668005818 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 400668005819 putative alpha subunit interface [polypeptide binding]; other site 400668005820 putative active site [active] 400668005821 putative substrate binding site [chemical binding]; other site 400668005822 Fe binding site [ion binding]; other site 400668005823 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 400668005824 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 400668005825 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005826 NAD(P) binding site [chemical binding]; other site 400668005827 active site 400668005828 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 400668005829 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 400668005830 FMN-binding pocket [chemical binding]; other site 400668005831 flavin binding motif; other site 400668005832 phosphate binding motif [ion binding]; other site 400668005833 beta-alpha-beta structure motif; other site 400668005834 NAD binding pocket [chemical binding]; other site 400668005835 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 400668005836 catalytic loop [active] 400668005837 iron binding site [ion binding]; other site 400668005838 Flavin Reductases; Region: FlaRed; cl00801 400668005839 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 400668005840 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 400668005841 phosphate binding site [ion binding]; other site 400668005842 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 400668005843 Amidase; Region: Amidase; cl11426 400668005844 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668005845 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668005846 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 400668005847 NAD(P) binding site [chemical binding]; other site 400668005848 catalytic residues [active] 400668005849 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668005850 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668005851 hypothetical protein; Provisional; Region: PRK11281 400668005852 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668005853 dimer interface [polypeptide binding]; other site 400668005854 putative CheW interface [polypeptide binding]; other site 400668005855 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 400668005856 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 400668005857 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_6; cd06154 400668005858 homotrimer interaction site [polypeptide binding]; other site 400668005859 putative active site [active] 400668005860 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005861 Ornithine cyclodeaminase/mu-crystallin family; Region: OCD_Mu_crystall; pfam02423 400668005862 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 400668005863 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 400668005864 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668005865 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 400668005866 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668005867 Coenzyme A binding pocket [chemical binding]; other site 400668005868 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage...; Region: Peptidase_C39_like; cl00296 400668005869 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 400668005870 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 400668005871 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668005872 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 400668005873 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 400668005874 tetramer interface [polypeptide binding]; other site 400668005875 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668005876 catalytic residue [active] 400668005877 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 400668005878 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 400668005879 Putative addiction module component; Region: Unstab_antitox; cl09921 400668005880 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668005881 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 400668005882 putative substrate translocation pore; other site 400668005883 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668005884 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 400668005885 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005886 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 400668005887 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 400668005888 putative DNA binding site [nucleotide binding]; other site 400668005889 dimerization interface [polypeptide binding]; other site 400668005890 putative Zn2+ binding site [ion binding]; other site 400668005891 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 400668005892 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 400668005893 Ligand Binding Site [chemical binding]; other site 400668005894 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668005895 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 400668005896 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668005897 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 400668005898 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 400668005899 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005900 Calx-beta domain; Region: Calx-beta; cl02522 400668005901 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 400668005902 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005903 Calx-beta domain; Region: Calx-beta; cl02522 400668005904 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005905 Putative flagellar system-associated repeat; Region: SWM_repeat; pfam13753 400668005906 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005907 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005908 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005909 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005910 Bacterial Ig-like domain (group 3); Region: Big_3_4; pfam13754 400668005911 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 400668005912 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 400668005913 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 400668005914 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668005915 DNA binding site [nucleotide binding] 400668005916 DNA-binding transcriptional regulator CytR; Provisional; Region: PRK11041 400668005917 domain linker motif; other site 400668005918 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; Region: PBP1_LacI_like_6; cd06284 400668005919 dimerization interface [polypeptide binding]; other site 400668005920 ligand binding site [chemical binding]; other site 400668005921 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 400668005922 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 400668005923 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 400668005924 TM-ABC transporter signature motif; other site 400668005925 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 400668005926 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 400668005927 Walker A/P-loop; other site 400668005928 ATP binding site [chemical binding]; other site 400668005929 Q-loop/lid; other site 400668005930 ABC transporter signature motif; other site 400668005931 Walker B; other site 400668005932 D-loop; other site 400668005933 H-loop/switch region; other site 400668005934 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 400668005935 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668005936 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668005937 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668005938 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 400668005939 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 400668005940 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668005941 metal binding site [ion binding]; metal-binding site 400668005942 active site 400668005943 I-site; other site 400668005944 Predicted small integral membrane protein (DUF2165); Region: DUF2165; cl02290 400668005945 D-xylose transporter subunit XylF; Provisional; Region: xylF; PRK10355 400668005946 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 400668005947 putative ligand binding site [chemical binding]; other site 400668005948 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 400668005949 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 400668005950 Walker A/P-loop; other site 400668005951 ATP binding site [chemical binding]; other site 400668005952 Q-loop/lid; other site 400668005953 ABC transporter signature motif; other site 400668005954 Walker B; other site 400668005955 D-loop; other site 400668005956 H-loop/switch region; other site 400668005957 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 400668005958 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 400668005959 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 400668005960 TM-ABC transporter signature motif; other site 400668005961 xylulokinase; Provisional; Region: PRK15027 400668005962 D-xylulose kinases, Escherichia coli xylulokinase-like subgroup; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_EcXK-like; cd07808 400668005963 N- and C-terminal domain interface [polypeptide binding]; other site 400668005964 active site 400668005965 catalytic site [active] 400668005966 metal binding site [ion binding]; metal-binding site 400668005967 xylulose binding site [chemical binding]; other site 400668005968 putative ATP binding site [chemical binding]; other site 400668005969 homodimer interface [polypeptide binding]; other site 400668005970 Ligand-binding domain of DNA transcription repressor specific for xylose (XylR); Region: PBP1_XylR; cd01543 400668005971 putative dimerization interface [polypeptide binding]; other site 400668005972 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 400668005973 putative ligand binding site [chemical binding]; other site 400668005974 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668005975 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668005976 DNA-binding transcriptional repressor PurR; Provisional; Region: PRK10703 400668005977 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668005978 DNA binding site [nucleotide binding] 400668005979 domain linker motif; other site 400668005980 Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Region: PBP1_PurR; cd06275 400668005981 dimerization interface [polypeptide binding]; other site 400668005982 ligand binding site [chemical binding]; other site 400668005983 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 400668005984 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 400668005985 ligand binding site [chemical binding]; other site 400668005986 dimerization interface [polypeptide binding]; other site 400668005987 Predicted periplasmic lipoprotein (DUF2291); Region: DUF2291; cl02395 400668005988 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 400668005989 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 400668005990 Walker A/P-loop; other site 400668005991 ATP binding site [chemical binding]; other site 400668005992 Q-loop/lid; other site 400668005993 ABC transporter signature motif; other site 400668005994 Walker B; other site 400668005995 D-loop; other site 400668005996 H-loop/switch region; other site 400668005997 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 400668005998 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 400668005999 TM-ABC transporter signature motif; other site 400668006000 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 400668006001 L-rhamnose isomerase (RhaA); Region: RhaA; cl09945 400668006002 putative acetyltransferase; Provisional; Region: PRK03624 400668006003 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668006004 Coenzyme A binding pocket [chemical binding]; other site 400668006005 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668006006 DctM-like transporters; Region: DctM; pfam06808 400668006007 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 400668006008 NMT1-like family; Region: NMT1_2; cl15260 400668006009 aconitate hydratase; Validated; Region: PRK09277 400668006010 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 400668006011 substrate binding site [chemical binding]; other site 400668006012 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 400668006013 ligand binding site [chemical binding]; other site 400668006014 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 400668006015 substrate binding site [chemical binding]; other site 400668006016 YrhK-like protein; Region: YrhK; pfam14145 400668006017 Helix-turn-helix domains; Region: HTH; cl00088 400668006018 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 400668006019 metal binding site [ion binding]; metal-binding site 400668006020 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 400668006021 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 400668006022 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006023 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006024 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668006025 metal binding site [ion binding]; metal-binding site 400668006026 active site 400668006027 I-site; other site 400668006028 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668006029 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 400668006030 Walker A motif; other site 400668006031 ATP binding site [chemical binding]; other site 400668006032 Walker B motif; other site 400668006033 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668006034 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 400668006035 substrate binding pocket [chemical binding]; other site 400668006036 membrane-bound complex binding site; other site 400668006037 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668006038 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 400668006039 substrate binding pocket [chemical binding]; other site 400668006040 membrane-bound complex binding site; other site 400668006041 hinge residues; other site 400668006042 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668006043 metal binding site [ion binding]; metal-binding site 400668006044 active site 400668006045 I-site; other site 400668006046 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 400668006047 Peptidase family M23; Region: Peptidase_M23; pfam01551 400668006048 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 400668006049 DEAD-like helicases superfamily; Region: DEXDc; smart00487 400668006050 ATP binding site [chemical binding]; other site 400668006051 Mg++ binding site [ion binding]; other site 400668006052 motif III; other site 400668006053 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 400668006054 nucleotide binding region [chemical binding]; other site 400668006055 ATP-binding site [chemical binding]; other site 400668006056 Bacteriophage T holin; Region: Phage_holin_T; pfam11031 400668006057 16S rRNA pseudouridylate synthase A; Provisional; Region: PRK10839 400668006058 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 400668006059 RNA binding surface [nucleotide binding]; other site 400668006060 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 400668006061 active site 400668006062 uracil binding [chemical binding]; other site 400668006063 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 400668006064 extended (e) SDRs; Region: SDR_e; cd08946 400668006065 NAD(P) binding site [chemical binding]; other site 400668006066 active site 400668006067 substrate binding site [chemical binding]; other site 400668006068 glutamate dehydrogenase; Provisional; Region: PRK09414 400668006069 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 400668006070 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 400668006071 NAD(P) binding site [chemical binding]; other site 400668006072 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 400668006073 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 400668006074 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 400668006075 Walker A motif; other site 400668006076 ATP binding site [chemical binding]; other site 400668006077 Walker B motif; other site 400668006078 arginine finger; other site 400668006079 Helix-turn-helix domains; Region: HTH; cl00088 400668006080 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668006081 metal binding site [ion binding]; metal-binding site 400668006082 active site 400668006083 I-site; other site 400668006084 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 400668006085 Protein of unknown function (DUF3185); Region: DUF3185; pfam11381 400668006086 ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. 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...; Region: ASCH_Ef3133_like; cd06553 400668006087 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 400668006088 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668006089 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 400668006090 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 400668006091 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 400668006092 Aspartase; Region: Aspartase; cd01357 400668006093 active sites [active] 400668006094 tetramer interface [polypeptide binding]; other site 400668006095 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668006096 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 400668006097 active site 400668006098 phosphorylation site [posttranslational modification] 400668006099 intermolecular recognition site; other site 400668006100 dimerization interface [polypeptide binding]; other site 400668006101 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 400668006102 Walker A motif; other site 400668006103 ATP binding site [chemical binding]; other site 400668006104 Walker B motif; other site 400668006105 arginine finger; other site 400668006106 Helix-turn-helix domains; Region: HTH; cl00088 400668006107 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668006108 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 400668006109 substrate binding pocket [chemical binding]; other site 400668006110 membrane-bound complex binding site; other site 400668006111 hinge residues; other site 400668006112 sensory histidine kinase AtoS; Provisional; Region: PRK11360 400668006113 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 400668006114 ATP binding site [chemical binding]; other site 400668006115 Mg2+ binding site [ion binding]; other site 400668006116 G-X-G motif; other site 400668006117 DsrE/DsrF-like family; Region: DrsE; cl00672 400668006118 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 400668006119 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 400668006120 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668006121 NMT1-like family; Region: NMT1_2; cl15260 400668006122 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 400668006123 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 400668006124 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668006125 Helix-turn-helix domains; Region: HTH; cl00088 400668006126 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 400668006127 putative dimerization interface [polypeptide binding]; other site 400668006128 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 400668006129 S-adenosylmethionine binding site [chemical binding]; other site 400668006130 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 400668006131 Sulfatase; Region: Sulfatase; cl10460 400668006132 putative metal dependent hydrolase; Provisional; Region: PRK11598 400668006133 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 400668006134 Sulfatase; Region: Sulfatase; cl10460 400668006135 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 400668006136 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 400668006137 S-adenosylmethionine binding site [chemical binding]; other site 400668006138 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 400668006139 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 400668006140 PepSY-associated TM helix; Region: PepSY_TM_2; cl15813 400668006141 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 400668006142 Protein of unknown function (DUF2750); Region: DUF2750; pfam11042 400668006143 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 400668006144 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 400668006145 active site 400668006146 purine riboside binding site [chemical binding]; other site 400668006147 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 400668006148 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 400668006149 putative ligand binding site [chemical binding]; other site 400668006150 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 400668006151 TM-ABC transporter signature motif; other site 400668006152 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 400668006153 TM-ABC transporter signature motif; other site 400668006154 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 400668006155 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 400668006156 Walker A/P-loop; other site 400668006157 ATP binding site [chemical binding]; other site 400668006158 Q-loop/lid; other site 400668006159 ABC transporter signature motif; other site 400668006160 Walker B; other site 400668006161 D-loop; other site 400668006162 H-loop/switch region; other site 400668006163 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 400668006164 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668006165 metal binding site [ion binding]; metal-binding site 400668006166 active site 400668006167 I-site; other site 400668006168 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 400668006169 active site 400668006170 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 400668006171 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668006172 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 400668006173 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 400668006174 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 400668006175 Flagellin N-methylase; Region: FliB; cl00497 400668006176 response regulator PleD; Reviewed; Region: pleD; PRK09581 400668006177 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 400668006178 active site 400668006179 phosphorylation site [posttranslational modification] 400668006180 intermolecular recognition site; other site 400668006181 dimerization interface [polypeptide binding]; other site 400668006182 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 400668006183 active site 400668006184 phosphorylation site [posttranslational modification] 400668006185 intermolecular recognition site; other site 400668006186 dimerization interface [polypeptide binding]; other site 400668006187 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668006188 metal binding site [ion binding]; metal-binding site 400668006189 active site 400668006190 I-site; other site 400668006191 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 400668006192 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 400668006193 GatB domain; Region: GatB_Yqey; cl11497 400668006194 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 400668006195 Amidase; Region: Amidase; cl11426 400668006196 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 400668006197 rod shape-determining protein MreB; Provisional; Region: PRK13927 400668006198 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 400668006199 ATP binding site [chemical binding]; other site 400668006200 Cell division protein FtsA; Region: FtsA; cl11496 400668006201 rod shape-determining protein MreC; Provisional; Region: PRK13922 400668006202 rod shape-determining protein MreC; Region: MreC; pfam04085 400668006203 rod shape-determining protein MreD; Region: MreD; cl01087 400668006204 Maf-like protein; Region: Maf; pfam02545 400668006205 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 400668006206 active site 400668006207 dimer interface [polypeptide binding]; other site 400668006208 ribonuclease G; Provisional; Region: PRK11712 400668006209 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 400668006210 homodimer interface [polypeptide binding]; other site 400668006211 oligonucleotide binding site [chemical binding]; other site 400668006212 TIGR02099 family protein; Region: TIGR02099 400668006213 AsmA-like C-terminal region; Region: AsmA_2; cl15864 400668006214 Predicted amidohydrolase [General function prediction only]; Region: COG0388 400668006215 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 400668006216 putative active site [active] 400668006217 catalytic triad [active] 400668006218 dimer interface [polypeptide binding]; other site 400668006219 Cyclophilin-like; Region: Cyclophil_like; cl00950 400668006220 ribonucleoside transporter; Reviewed; Region: nepI; PRK10213 400668006221 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 400668006222 putative substrate translocation pore; other site 400668006223 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 400668006224 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 400668006225 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668006226 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668006227 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668006228 Endonuclease I; Region: Endonuclease_1; cl01003 400668006229 Short C-terminal domain; Region: SHOCT; cl01373 400668006230 putative phosphoketolase; Provisional; Region: PRK05261 400668006231 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 400668006232 TPP-binding site; other site 400668006233 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; Region: XFP; pfam03894 400668006234 XFP C-terminal domain; Region: XFP_C; pfam09363 400668006235 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 400668006236 catalytic residue [active] 400668006237 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 400668006238 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 400668006239 putative active site [active] 400668006240 transaldolase; Provisional; Region: PRK03903 400668006241 catalytic residue [active] 400668006242 alternate F1F0 ATPase, F1 subunit beta; Region: alt_F1F0_F1_bet; TIGR03305 400668006243 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 400668006244 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 400668006245 alpha subunit interaction interface [polypeptide binding]; other site 400668006246 Walker A motif; other site 400668006247 ATP binding site [chemical binding]; other site 400668006248 Walker B motif; other site 400668006249 inhibitor binding site; inhibition site 400668006250 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 400668006251 F0F1 ATP synthase subunit epsilon; Validated; Region: PRK06228 400668006252 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 400668006253 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 400668006254 N-ATPase, AtpR subunit; Region: AtpR; cl11871 400668006255 ATP synthase A chain; Region: ATP-synt_A; cl00413 400668006256 ATP synthase subunit C; Region: ATP-synt_C; cl00466 400668006257 Plant ATP synthase F0; Region: YMF19; cl07975 400668006258 alternate F1F0 ATPase, F0 subunit B; Region: alt_F1F0_F0_B; TIGR03321 400668006259 alternate F1F0 ATPase, F1 subunit alpha; Region: alt_F1F0_F1_al; TIGR03324 400668006260 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 400668006261 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 400668006262 beta subunit interaction interface [polypeptide binding]; other site 400668006263 Walker A motif; other site 400668006264 ATP binding site [chemical binding]; other site 400668006265 Walker B motif; other site 400668006266 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 400668006267 ATP synthase; Region: ATP-synt; cl00365 400668006268 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 400668006269 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 400668006270 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; cl00047 400668006271 Helix-turn-helix domains; Region: HTH; cl00088 400668006272 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 400668006273 HSP70 interaction site [polypeptide binding]; other site 400668006274 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 400668006275 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 400668006276 putative substrate binding site [chemical binding]; other site 400668006277 putative ATP binding site [chemical binding]; other site 400668006278 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 400668006279 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 400668006280 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 400668006281 NAD binding site [chemical binding]; other site 400668006282 substrate binding site [chemical binding]; other site 400668006283 catalytic Zn binding site [ion binding]; other site 400668006284 tetramer interface [polypeptide binding]; other site 400668006285 structural Zn binding site [ion binding]; other site 400668006286 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 400668006287 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 400668006288 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 400668006289 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 400668006290 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 400668006291 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006292 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668006293 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 400668006294 NAD(P) binding site [chemical binding]; other site 400668006295 catalytic residues [active] 400668006296 Domain of unknown function (DUF4398); Region: DUF4398; pfam14346 400668006297 hypothetical protein; Provisional; Region: PRK12472 400668006298 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668006299 ligand binding site [chemical binding]; other site 400668006300 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668006301 Amidinotransferase; Region: Amidinotransf; cl12043 400668006302 ornithine carbamoyltransferase; Validated; Region: PRK02102 400668006303 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 400668006304 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006305 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 400668006306 Cation efflux family; Region: Cation_efflux; cl00316 400668006307 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 400668006308 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 400668006309 Catalytic site [active] 400668006310 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 400668006311 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 400668006312 active site 400668006313 DNA binding site [nucleotide binding] 400668006314 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 400668006315 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 400668006316 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668006317 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668006318 DNA binding site [nucleotide binding] 400668006319 domain linker motif; other site 400668006320 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 400668006321 dimerization interface [polypeptide binding]; other site 400668006322 ligand binding site [chemical binding]; other site 400668006323 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_11; cd06321 400668006324 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 400668006325 putative ligand binding site [chemical binding]; other site 400668006326 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 400668006327 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 400668006328 Walker A/P-loop; other site 400668006329 ATP binding site [chemical binding]; other site 400668006330 Q-loop/lid; other site 400668006331 ABC transporter signature motif; other site 400668006332 Walker B; other site 400668006333 D-loop; other site 400668006334 H-loop/switch region; other site 400668006335 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 400668006336 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 400668006337 TM-ABC transporter signature motif; other site 400668006338 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 400668006339 uncharacterized xylulose kinase-like proteins, subgroup 1; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_XK_like_1; cd07804 400668006340 N- and C-terminal domain interface [polypeptide binding]; other site 400668006341 putative active site [active] 400668006342 catalytic site [active] 400668006343 metal binding site [ion binding]; metal-binding site 400668006344 putative xylulose binding site [chemical binding]; other site 400668006345 putative ATP binding site [chemical binding]; other site 400668006346 putative homodimer interface [polypeptide binding]; other site 400668006347 D-xylulose kinases, subgroup 1; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_D-XK_1; cd07809 400668006348 N- and C-terminal domain interface [polypeptide binding]; other site 400668006349 D-xylulose kinase; Region: XylB; TIGR01312 400668006350 active site 400668006351 catalytic site [active] 400668006352 metal binding site [ion binding]; metal-binding site 400668006353 xylulose binding site [chemical binding]; other site 400668006354 ATP binding site [chemical binding]; other site 400668006355 putative homodimer interface [polypeptide binding]; other site 400668006356 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006357 short chain dehydrogenase; Provisional; Region: PRK07060 400668006358 NAD(P) binding site [chemical binding]; other site 400668006359 active site 400668006360 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 400668006361 classical (c) SDRs; Region: SDR_c; cd05233 400668006362 NAD(P) binding site [chemical binding]; other site 400668006363 active site 400668006364 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 400668006365 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 400668006366 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668006367 putative substrate translocation pore; other site 400668006368 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 400668006369 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 400668006370 DNA binding residues [nucleotide binding] 400668006371 magnesium Mg(2+) and cobalt Co(2+) transport protein (corA); Region: corA; TIGR00383 400668006372 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 400668006373 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 400668006374 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 400668006375 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 400668006376 Helix-turn-helix domains; Region: HTH; cl00088 400668006377 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 400668006378 dimerization interface [polypeptide binding]; other site 400668006379 diaminopimelate decarboxylase; Provisional; Region: PRK11165 400668006380 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 400668006381 active site 400668006382 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668006383 substrate binding site [chemical binding]; other site 400668006384 catalytic residues [active] 400668006385 dimer interface [polypeptide binding]; other site 400668006386 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 400668006387 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 400668006388 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 400668006389 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 400668006390 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 400668006391 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 400668006392 LysR family transcriptional regulator; Provisional; Region: PRK14997 400668006393 Helix-turn-helix domains; Region: HTH; cl00088 400668006394 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 400668006395 dimerization interface [polypeptide binding]; other site 400668006396 maltose/maltodextrin transporter ATP-binding protein; Provisional; Region: PRK11000 400668006397 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668006398 Walker A/P-loop; other site 400668006399 ATP binding site [chemical binding]; other site 400668006400 Q-loop/lid; other site 400668006401 ABC transporter signature motif; other site 400668006402 Walker B; other site 400668006403 D-loop; other site 400668006404 H-loop/switch region; other site 400668006405 TOBE domain; Region: TOBE_2; cl01440 400668006406 Transcriptional regulator [Transcription]; Region: IclR; COG1414 400668006407 Helix-turn-helix domains; Region: HTH; cl00088 400668006408 Bacterial transcriptional regulator; Region: IclR; pfam01614 400668006409 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 400668006410 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 400668006411 dimer interface [polypeptide binding]; other site 400668006412 conserved gate region; other site 400668006413 putative PBP binding loops; other site 400668006414 ABC-ATPase subunit interface; other site 400668006415 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 400668006416 dimer interface [polypeptide binding]; other site 400668006417 conserved gate region; other site 400668006418 putative PBP binding loops; other site 400668006419 ABC-ATPase subunit interface; other site 400668006420 Alpha-galactosidase [Carbohydrate transport and metabolism]; Region: GalA; COG3345 400668006421 The enzymes of glycosyl hydrolase family 31 (GH31) occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase; Region: GH31; cl11402 400668006422 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 400668006423 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 400668006424 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 400668006425 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed; Region: PRK09140 400668006426 active site 400668006427 intersubunit interface [polypeptide binding]; other site 400668006428 catalytic residue [active] 400668006429 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 400668006430 Beta-galactosidase [Carbohydrate transport and metabolism]; Region: LacA; COG1874 400668006431 Beta-galactosidase; Region: Glyco_hydro_42; cl03154 400668006432 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 400668006433 Beta-galactosidase C-terminal domain; Region: Glyco_hydro_42C; pfam08533 400668006434 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668006435 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 400668006436 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 400668006437 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_3; cd08490 400668006438 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 400668006439 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 400668006440 dimer interface [polypeptide binding]; other site 400668006441 conserved gate region; other site 400668006442 putative PBP binding loops; other site 400668006443 ABC-ATPase subunit interface; other site 400668006444 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 400668006445 dimer interface [polypeptide binding]; other site 400668006446 conserved gate region; other site 400668006447 putative PBP binding loops; other site 400668006448 ABC-ATPase subunit interface; other site 400668006449 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 400668006450 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 400668006451 Walker A/P-loop; other site 400668006452 ATP binding site [chemical binding]; other site 400668006453 Q-loop/lid; other site 400668006454 ABC transporter signature motif; other site 400668006455 Walker B; other site 400668006456 D-loop; other site 400668006457 H-loop/switch region; other site 400668006458 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668006459 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 400668006460 Walker A/P-loop; other site 400668006461 ATP binding site [chemical binding]; other site 400668006462 Q-loop/lid; other site 400668006463 ABC transporter signature motif; other site 400668006464 Walker B; other site 400668006465 D-loop; other site 400668006466 H-loop/switch region; other site 400668006467 GAF domain; Region: GAF_2; pfam13185 400668006468 GAF domain; Region: GAF; cl15785 400668006469 PAS domain S-box; Region: sensory_box; TIGR00229 400668006470 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 400668006471 putative active site [active] 400668006472 heme pocket [chemical binding]; other site 400668006473 PAS fold; Region: PAS_3; pfam08447 400668006474 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 400668006475 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 400668006476 dimer interface [polypeptide binding]; other site 400668006477 phosphorylation site [posttranslational modification] 400668006478 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 400668006479 ATP binding site [chemical binding]; other site 400668006480 Mg2+ binding site [ion binding]; other site 400668006481 G-X-G motif; other site 400668006482 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 400668006483 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 400668006484 active site 400668006485 phosphorylation site [posttranslational modification] 400668006486 intermolecular recognition site; other site 400668006487 dimerization interface [polypeptide binding]; other site 400668006488 Response regulator receiver domain; Region: Response_reg; pfam00072 400668006489 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 400668006490 active site 400668006491 phosphorylation site [posttranslational modification] 400668006492 intermolecular recognition site; other site 400668006493 dimerization interface [polypeptide binding]; other site 400668006494 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 400668006495 Response regulator receiver domain; Region: Response_reg; pfam00072 400668006496 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 400668006497 active site 400668006498 phosphorylation site [posttranslational modification] 400668006499 intermolecular recognition site; other site 400668006500 dimerization interface [polypeptide binding]; other site 400668006501 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668006502 metal binding site [ion binding]; metal-binding site 400668006503 active site 400668006504 I-site; other site 400668006505 2-isopropylmalate synthase; Validated; Region: PRK03739 400668006506 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 400668006507 active site 400668006508 catalytic residues [active] 400668006509 metal binding site [ion binding]; metal-binding site 400668006510 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 400668006511 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668006512 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 400668006513 putative DNA binding site [nucleotide binding]; other site 400668006514 putative Zn2+ binding site [ion binding]; other site 400668006515 Helix-turn-helix domains; Region: HTH; cl00088 400668006516 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 400668006517 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 400668006518 dimerization interface [polypeptide binding]; other site 400668006519 active site 400668006520 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 400668006521 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668006522 putative substrate translocation pore; other site 400668006523 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 400668006524 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668006525 Helix-turn-helix domains; Region: HTH; cl00088 400668006526 helicase 45; Provisional; Region: PTZ00424 400668006527 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 400668006528 ATP binding site [chemical binding]; other site 400668006529 Mg++ binding site [ion binding]; other site 400668006530 motif III; other site 400668006531 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 400668006532 nucleotide binding region [chemical binding]; other site 400668006533 ATP-binding site [chemical binding]; other site 400668006534 Protein of unknown function (DUF1415); Region: DUF1415; cl01301 400668006535 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 400668006536 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 400668006537 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 400668006538 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006539 2-dehydropantoate 2-reductase; Region: apbA_panE; TIGR00745 400668006540 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 400668006541 Protein of unknown function (DUF520); Region: DUF520; cl00723 400668006542 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 400668006543 DNA binding site [nucleotide binding] 400668006544 active site 400668006545 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 400668006546 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 400668006547 oligomerisation interface [polypeptide binding]; other site 400668006548 mobile loop; other site 400668006549 roof hairpin; other site 400668006550 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 400668006551 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 400668006552 ring oligomerisation interface [polypeptide binding]; other site 400668006553 ATP/Mg binding site [chemical binding]; other site 400668006554 stacking interactions; other site 400668006555 hinge regions; other site 400668006556 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 400668006557 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 400668006558 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 400668006559 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 400668006560 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 400668006561 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 400668006562 dimerization interface 3.5A [polypeptide binding]; other site 400668006563 active site 400668006564 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 400668006565 active site 400668006566 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 400668006567 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 400668006568 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668006569 catalytic residue [active] 400668006570 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 400668006571 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 400668006572 substrate binding site [chemical binding]; other site 400668006573 active site 400668006574 catalytic residues [active] 400668006575 heterodimer interface [polypeptide binding]; other site 400668006576 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 400668006577 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 400668006578 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 400668006579 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 400668006580 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 400668006581 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 400668006582 Sporulation related domain; Region: SPOR; cl10051 400668006583 Colicin V production protein; Region: Colicin_V; cl00567 400668006584 amidophosphoribosyltransferase; Provisional; Region: PRK09246 400668006585 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 400668006586 active site 400668006587 tetramer interface [polypeptide binding]; other site 400668006588 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668006589 active site 400668006590 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 400668006591 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 400668006592 homodimer interface [polypeptide binding]; other site 400668006593 substrate-cofactor binding pocket; other site 400668006594 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668006595 catalytic residue [active] 400668006596 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 400668006597 Protein export membrane protein; Region: SecD_SecF; cl14618 400668006598 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 400668006599 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 400668006600 ABC transporter ATPase component; Reviewed; Region: PRK11147 400668006601 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668006602 Walker A/P-loop; other site 400668006603 ATP binding site [chemical binding]; other site 400668006604 Q-loop/lid; other site 400668006605 ABC transporter signature motif; other site 400668006606 Walker B; other site 400668006607 D-loop; other site 400668006608 H-loop/switch region; other site 400668006609 ABC transporter; Region: ABC_tran_2; pfam12848 400668006610 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 400668006611 Domain of unknown function (DUF2760); Region: DUF2760; pfam10816 400668006612 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 400668006613 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 400668006614 DNA-K related protein; Region: DUF3731; pfam12531 400668006615 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 400668006616 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 400668006617 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 400668006618 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 400668006619 putative PBP binding loops; other site 400668006620 dimer interface [polypeptide binding]; other site 400668006621 ABC-ATPase subunit interface; other site 400668006622 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 400668006623 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 400668006624 dimer interface [polypeptide binding]; other site 400668006625 conserved gate region; other site 400668006626 ABC-ATPase subunit interface; other site 400668006627 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 400668006628 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 400668006629 Walker A/P-loop; other site 400668006630 ATP binding site [chemical binding]; other site 400668006631 Q-loop/lid; other site 400668006632 ABC transporter signature motif; other site 400668006633 Walker B; other site 400668006634 D-loop; other site 400668006635 H-loop/switch region; other site 400668006636 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 400668006637 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 400668006638 Walker A/P-loop; other site 400668006639 ATP binding site [chemical binding]; other site 400668006640 Q-loop/lid; other site 400668006641 ABC transporter signature motif; other site 400668006642 Walker B; other site 400668006643 D-loop; other site 400668006644 H-loop/switch region; other site 400668006645 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 400668006646 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 400668006647 Walker A/P-loop; other site 400668006648 ATP binding site [chemical binding]; other site 400668006649 Q-loop/lid; other site 400668006650 ABC transporter signature motif; other site 400668006651 Walker B; other site 400668006652 D-loop; other site 400668006653 H-loop/switch region; other site 400668006654 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 400668006655 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 400668006656 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 400668006657 ABC-ATPase subunit interface; other site 400668006658 dimer interface [polypeptide binding]; other site 400668006659 putative PBP binding regions; other site 400668006660 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 400668006661 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 400668006662 ABC-ATPase subunit interface; other site 400668006663 dimer interface [polypeptide binding]; other site 400668006664 putative PBP binding regions; other site 400668006665 ABC-type Fe3+-citrate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FecB; COG4594 400668006666 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 400668006667 siderophore binding site; other site 400668006668 Lipase (class 3). 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...; Region: Lipase_3; cd00519 400668006669 active site flap/lid [active] 400668006670 nucleophilic elbow; other site 400668006671 catalytic triad [active] 400668006672 Putative ParB-like nuclease; Region: ParBc_2; pfam08857 400668006673 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 400668006674 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668006675 Coenzyme A binding pocket [chemical binding]; other site 400668006676 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 400668006677 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 400668006678 putative NAD(P) binding site [chemical binding]; other site 400668006679 catalytic Zn binding site [ion binding]; other site 400668006680 MarC family integral membrane protein; Region: MarC; cl00919 400668006681 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 400668006682 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 400668006683 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 400668006684 putative active site [active] 400668006685 Zn binding site [ion binding]; other site 400668006686 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 400668006687 elongation factor P; Provisional; Region: PRK04542 400668006688 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 400668006689 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 400668006690 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 400668006691 RNA binding site [nucleotide binding]; other site 400668006692 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional; Region: PRK15114 400668006693 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 400668006694 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 400668006695 HSP70 interaction site [polypeptide binding]; other site 400668006696 Bacterial SH3 domain; Region: SH3_3; cl02551 400668006697 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 400668006698 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 400668006699 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 400668006700 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 400668006701 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 400668006702 trimer interface [polypeptide binding]; other site 400668006703 dimer interface [polypeptide binding]; other site 400668006704 putative active site [active] 400668006705 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 400668006706 MoaE interaction surface [polypeptide binding]; other site 400668006707 MoeB interaction surface [polypeptide binding]; other site 400668006708 thiocarboxylated glycine; other site 400668006709 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 400668006710 MoaE homodimer interface [polypeptide binding]; other site 400668006711 MoaD interaction [polypeptide binding]; other site 400668006712 active site residues [active] 400668006713 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 400668006714 Int/Topo IB signature motif; other site 400668006715 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 400668006716 Peptidase family M48; Region: Peptidase_M48; cl12018 400668006717 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 400668006718 CPxP motif; other site 400668006719 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 400668006720 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 400668006721 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 400668006722 active site 400668006723 catalytic site [active] 400668006724 MFS_1 like family; Region: MFS_1_like; pfam12832 400668006725 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 400668006726 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668006727 Helix-turn-helix domains; Region: HTH; cl00088 400668006728 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 400668006729 dimerization interface [polypeptide binding]; other site 400668006730 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 400668006731 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 400668006732 substrate binding site [chemical binding]; other site 400668006733 ligand binding site [chemical binding]; other site 400668006734 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 400668006735 substrate binding site [chemical binding]; other site 400668006736 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 400668006737 tartrate dehydrogenase; Provisional; Region: PRK08194 400668006738 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 400668006739 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006740 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 400668006741 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 400668006742 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 400668006743 30S subunit binding site; other site 400668006744 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 400668006745 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 400668006746 substrate binding site [chemical binding]; other site 400668006747 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 400668006748 substrate binding site [chemical binding]; other site 400668006749 ligand binding site [chemical binding]; other site 400668006750 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668006751 active site 400668006752 ATP binding site [chemical binding]; other site 400668006753 substrate binding site [chemical binding]; other site 400668006754 activation loop (A-loop); other site 400668006755 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl15394 400668006756 MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain; Region: MiaE; cd07910 400668006757 active site 400668006758 dinuclear metal binding site [ion binding]; other site 400668006759 dimerization interface [polypeptide binding]; other site 400668006760 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 400668006761 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 400668006762 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 400668006763 putative active site [active] 400668006764 putative metal binding site [ion binding]; other site 400668006765 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 400668006766 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 400668006767 substrate binding site [chemical binding]; other site 400668006768 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 400668006769 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 400668006770 FeS/SAM binding site; other site 400668006771 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 400668006772 Ligand Binding Site [chemical binding]; other site 400668006773 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668006774 Helix-turn-helix domains; Region: HTH; cl00088 400668006775 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 400668006776 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668006777 Coenzyme A binding pocket [chemical binding]; other site 400668006778 AzlC protein; Region: AzlC; cl00570 400668006779 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 400668006780 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 400668006781 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668006782 active site 400668006783 HIGH motif; other site 400668006784 nucleotide binding site [chemical binding]; other site 400668006785 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 400668006786 KMSKS motif; other site 400668006787 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 400668006788 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 400668006789 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 400668006790 active site 400668006791 HIGH motif; other site 400668006792 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 400668006793 KMSKS motif; other site 400668006794 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 400668006795 tRNA binding surface [nucleotide binding]; other site 400668006796 anticodon binding site; other site 400668006797 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 400668006798 Ligand Binding Site [chemical binding]; other site 400668006799 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 400668006800 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 400668006801 active site 400668006802 interdomain interaction site; other site 400668006803 putative metal-binding site [ion binding]; other site 400668006804 nucleotide binding site [chemical binding]; other site 400668006805 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 400668006806 domain I; other site 400668006807 DNA binding groove [nucleotide binding] 400668006808 phosphate binding site [ion binding]; other site 400668006809 domain II; other site 400668006810 domain III; other site 400668006811 nucleotide binding site [chemical binding]; other site 400668006812 catalytic site [active] 400668006813 domain IV; other site 400668006814 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 400668006815 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 400668006816 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 400668006817 Topoisomerase I zinc-ribbon-like; Region: Topo_Zn_Ribbon; pfam08272 400668006818 LexA repressor; Validated; Region: PRK00215 400668006819 Helix-turn-helix domains; Region: HTH; cl00088 400668006820 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard...; Region: Maf_Ham1; cl00276 400668006821 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 400668006822 Catalytic site [active] 400668006823 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 400668006824 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668006825 DEAD_2; Region: DEAD_2; pfam06733 400668006826 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668006827 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 400668006828 DEAD-like helicases superfamily; Region: DEXDc; smart00487 400668006829 ATP binding site [chemical binding]; other site 400668006830 Mg++ binding site [ion binding]; other site 400668006831 motif III; other site 400668006832 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 400668006833 nucleotide binding region [chemical binding]; other site 400668006834 ATP-binding site [chemical binding]; other site 400668006835 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 400668006836 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 400668006837 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 400668006838 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668006839 NAD(P) binding site [chemical binding]; other site 400668006840 active site 400668006841 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 400668006842 Domain of unknown function (DUF4389); Region: DUF4389; pfam14333 400668006843 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 400668006844 catalytic core [active] 400668006845 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 400668006846 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668006847 hypothetical protein; Provisional; Region: PRK10279 400668006848 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 400668006849 active site 400668006850 nucleophile elbow; other site 400668006851 Maf-like protein; Region: Maf; pfam02545 400668006852 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 400668006853 active site 400668006854 dimer interface [polypeptide binding]; other site 400668006855 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 400668006856 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 400668006857 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 400668006858 Acyl transferase domain; Region: Acyl_transf_1; cl08282 400668006859 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 400668006860 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 400668006861 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 400668006862 NAD(P) binding site [chemical binding]; other site 400668006863 homotetramer interface [polypeptide binding]; other site 400668006864 homodimer interface [polypeptide binding]; other site 400668006865 active site 400668006866 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668006867 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 400668006868 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 400668006869 dimer interface [polypeptide binding]; other site 400668006870 active site 400668006871 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 400668006872 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668006873 Walker A/P-loop; other site 400668006874 ATP binding site [chemical binding]; other site 400668006875 Q-loop/lid; other site 400668006876 ABC transporter signature motif; other site 400668006877 Walker B; other site 400668006878 D-loop; other site 400668006879 H-loop/switch region; other site 400668006880 ABC-2 type transporter; Region: ABC2_membrane; cl11417 400668006881 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 400668006882 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 400668006883 Membrane transport protein; Region: Mem_trans; cl09117 400668006884 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668006885 Helix-turn-helix domains; Region: HTH; cl00088 400668006886 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 400668006887 putative effector binding pocket; other site 400668006888 dimerization interface [polypeptide binding]; other site 400668006889 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 400668006890 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 400668006891 active site 400668006892 catalytic tetrad [active] 400668006893 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 400668006894 catalytic triad [active] 400668006895 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 400668006896 dihydrodipicolinate synthase; Region: dapA; TIGR00674 400668006897 dimer interface [polypeptide binding]; other site 400668006898 active site 400668006899 catalytic residue [active] 400668006900 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 400668006901 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 400668006902 ATP binding site [chemical binding]; other site 400668006903 active site 400668006904 substrate binding site [chemical binding]; other site 400668006905 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 400668006906 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 400668006907 FtsX-like permease family; Region: FtsX; cl15850 400668006908 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 400668006909 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 400668006910 Walker A/P-loop; other site 400668006911 ATP binding site [chemical binding]; other site 400668006912 Q-loop/lid; other site 400668006913 ABC transporter signature motif; other site 400668006914 Walker B; other site 400668006915 D-loop; other site 400668006916 H-loop/switch region; other site 400668006917 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 400668006918 Competence protein; Region: Competence; cl00471 400668006919 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 400668006920 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 400668006921 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 400668006922 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 400668006923 Trm112p-like protein; Region: Trm112p; cl01066 400668006924 Low molecular weight phosphatase family; Region: LMWPc; cd00115 400668006925 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 400668006926 active site 400668006927 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 400668006928 FAD binding domain; Region: FAD_binding_4; pfam01565 400668006929 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 400668006930 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 400668006931 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 400668006932 active site 400668006933 nucleophile elbow; other site 400668006934 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 400668006935 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 400668006936 dimer interface [polypeptide binding]; other site 400668006937 active site 400668006938 CoA binding pocket [chemical binding]; other site 400668006939 phosphoglucomutase; Validated; Region: PRK07564 400668006940 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 400668006941 active site 400668006942 substrate binding site [chemical binding]; other site 400668006943 metal binding site [ion binding]; metal-binding site 400668006944 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668006945 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 400668006946 FAD binding domain; Region: FAD_binding_4; pfam01565 400668006947 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 400668006948 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 400668006949 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 400668006950 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668006951 catalytic residue [active] 400668006952 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 400668006953 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 400668006954 Rhomboid family; Region: Rhomboid; cl11446 400668006955 Protein of unknown function (DUF1315); Region: DUF1315; cl01215 400668006956 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 400668006957 aminopeptidase N; Provisional; Region: pepN; PRK14015 400668006958 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 400668006959 active site 400668006960 Zn binding site [ion binding]; other site 400668006961 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 400668006962 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 400668006963 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 400668006964 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 400668006965 substrate binding pocket [chemical binding]; other site 400668006966 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 400668006967 B12 binding site [chemical binding]; other site 400668006968 cobalt ligand [ion binding]; other site 400668006969 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 400668006970 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 400668006971 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 400668006972 homodimer interface [polypeptide binding]; other site 400668006973 Walker A motif; other site 400668006974 ATP binding site [chemical binding]; other site 400668006975 hydroxycobalamin binding site [chemical binding]; other site 400668006976 Walker B motif; other site 400668006977 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 400668006978 homotrimer interaction site [polypeptide binding]; other site 400668006979 putative active site [active] 400668006980 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 400668006981 ligand binding site [chemical binding]; other site 400668006982 flexible hinge region; other site 400668006983 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 400668006984 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668006985 Walker A/P-loop; other site 400668006986 ATP binding site [chemical binding]; other site 400668006987 Q-loop/lid; other site 400668006988 ABC transporter signature motif; other site 400668006989 Walker B; other site 400668006990 D-loop; other site 400668006991 H-loop/switch region; other site 400668006992 ABC transporter; Region: ABC_tran_2; pfam12848 400668006993 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 400668006994 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 400668006995 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 400668006996 MOSC domain; Region: MOSC; pfam03473 400668006997 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 400668006998 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 400668006999 dimer interface [polypeptide binding]; other site 400668007000 active site 400668007001 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668007002 catalytic residues [active] 400668007003 substrate binding site [chemical binding]; other site 400668007004 Predicted transporter component [General function prediction only]; Region: COG2391 400668007005 Sulphur transport; Region: Sulf_transp; cl01018 400668007006 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 400668007007 Sulphur transport; Region: Sulf_transp; cl01018 400668007008 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 400668007009 putative metal binding site [ion binding]; other site 400668007010 superoxide dismutase; Provisional; Region: PRK10543 400668007011 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 400668007012 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 400668007013 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 400668007014 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 400668007015 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 400668007016 Active Sites [active] 400668007017 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 400668007018 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 400668007019 CysD dimerization site [polypeptide binding]; other site 400668007020 G1 box; other site 400668007021 putative GEF interaction site [polypeptide binding]; other site 400668007022 GTP/Mg2+ binding site [chemical binding]; other site 400668007023 Switch I region; other site 400668007024 G2 box; other site 400668007025 G3 box; other site 400668007026 Switch II region; other site 400668007027 G4 box; other site 400668007028 G5 box; other site 400668007029 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 400668007030 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 400668007031 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 400668007032 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 400668007033 FAD binding pocket [chemical binding]; other site 400668007034 FAD binding motif [chemical binding]; other site 400668007035 phosphate binding motif [ion binding]; other site 400668007036 NAD binding pocket [chemical binding]; other site 400668007037 Helix-turn-helix domains; Region: HTH; cl00088 400668007038 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 400668007039 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 400668007040 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 400668007041 dimer interface [polypeptide binding]; other site 400668007042 anticodon binding site; other site 400668007043 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 400668007044 homodimer interface [polypeptide binding]; other site 400668007045 motif 1; other site 400668007046 active site 400668007047 motif 2; other site 400668007048 GAD domain; Region: GAD; pfam02938 400668007049 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 400668007050 active site 400668007051 motif 3; other site 400668007052 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 400668007053 active site 400668007054 putative DNA-binding cleft [nucleotide binding]; other site 400668007055 dimer interface [polypeptide binding]; other site 400668007056 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 400668007057 RuvA N terminal domain; Region: RuvA_N; pfam01330 400668007058 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 400668007059 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 400668007060 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 400668007061 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 400668007062 Walker A motif; other site 400668007063 ATP binding site [chemical binding]; other site 400668007064 Walker B motif; other site 400668007065 arginine finger; other site 400668007066 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 400668007067 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 400668007068 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 400668007069 Gram-negative bacterial tonB protein; Region: TonB; cl10048 400668007070 translocation protein TolB; Provisional; Region: tolB; PRK00178 400668007071 TolB amino-terminal domain; Region: TolB_N; cl00639 400668007072 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 400668007073 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 400668007074 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 400668007075 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668007076 ligand binding site [chemical binding]; other site 400668007077 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 400668007078 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 400668007079 binding surface 400668007080 TPR motif; other site 400668007081 Quinolinate synthetase A protein; Region: NadA; cl00420 400668007082 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 400668007083 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 400668007084 putative FMN binding site [chemical binding]; other site 400668007085 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 400668007086 metal binding site [ion binding]; metal-binding site 400668007087 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 400668007088 putative active site [active] 400668007089 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 400668007090 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 400668007091 active site 400668007092 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668007093 active site 400668007094 I-site; other site 400668007095 metal binding site [ion binding]; metal-binding site 400668007096 translation initiation factor Sui1; Validated; Region: PRK06824 400668007097 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two...; Region: SUI1_eIF1; cl00229 400668007098 Predicted RNA interaction site [nucleotide binding]; other site 400668007099 putative binding site; other site 400668007100 Mutations affecting start-site selection; other site 400668007101 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 400668007102 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668007103 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 400668007104 active site 400668007105 glycerate dehydrogenase; Provisional; Region: PRK06932 400668007106 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668007107 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 400668007108 active site 400668007109 catalytic triad [active] 400668007110 oxyanion hole [active] 400668007111 switch loop; other site 400668007112 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 400668007113 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 400668007114 Walker A/P-loop; other site 400668007115 ATP binding site [chemical binding]; other site 400668007116 Q-loop/lid; other site 400668007117 ABC transporter signature motif; other site 400668007118 Walker B; other site 400668007119 D-loop; other site 400668007120 H-loop/switch region; other site 400668007121 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 400668007122 FtsX-like permease family; Region: FtsX; cl15850 400668007123 DNA polymerase II; Reviewed; Region: PRK05762 400668007124 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases; Region: DNA_polB_II_exo; cd05784 400668007125 active site 400668007126 catalytic site [active] 400668007127 substrate binding site [chemical binding]; other site 400668007128 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 400668007129 active site 400668007130 metal-binding site 400668007131 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 400668007132 active site 400668007133 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 400668007134 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 400668007135 Response regulator receiver domain; Region: Response_reg; pfam00072 400668007136 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 400668007137 active site 400668007138 phosphorylation site [posttranslational modification] 400668007139 intermolecular recognition site; other site 400668007140 dimerization interface [polypeptide binding]; other site 400668007141 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668007142 ferrochelatase; Reviewed; Region: hemH; PRK00035 400668007143 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 400668007144 C-terminal domain interface [polypeptide binding]; other site 400668007145 active site 400668007146 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 400668007147 active site 400668007148 N-terminal domain interface [polypeptide binding]; other site 400668007149 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 400668007150 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668007151 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 400668007152 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 400668007153 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 400668007154 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 400668007155 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668007156 TIGR01777 family protein; Region: yfcH 400668007157 NAD(P) binding site [chemical binding]; other site 400668007158 active site 400668007159 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 400668007160 putative active site [active] 400668007161 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 400668007162 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007163 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 400668007164 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 400668007165 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 400668007166 BolA-like protein; Region: BolA; cl00386 400668007167 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 400668007168 anti sigma factor interaction site; other site 400668007169 regulatory phosphorylation site [posttranslational modification]; other site 400668007170 Response regulator receiver domain; Region: Response_reg; pfam00072 400668007171 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 400668007172 active site 400668007173 phosphorylation site [posttranslational modification] 400668007174 intermolecular recognition site; other site 400668007175 dimerization interface [polypeptide binding]; other site 400668007176 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 400668007177 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 400668007178 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 400668007179 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 400668007180 ATP binding site [chemical binding]; other site 400668007181 putative Mg++ binding site [ion binding]; other site 400668007182 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 400668007183 nucleotide binding region [chemical binding]; other site 400668007184 ATP-binding site [chemical binding]; other site 400668007185 RQC domain; Region: RQC; cl09632 400668007186 HRDC domain; Region: HRDC; cl02578 400668007187 hypothetical protein; Provisional; Region: PRK04860 400668007188 SprT homologues; Region: SprT; cl01182 400668007189 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 400668007190 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 400668007191 Ligand Binding Site [chemical binding]; other site 400668007192 YfaZ precursor; Region: YfaZ; pfam07437 400668007193 Adenine/guanine phosphoribosyltransferases and related PRPP-binding proteins [Nucleotide transport and metabolism]; Region: Apt; COG0503 400668007194 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668007195 active site 400668007196 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 400668007197 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 400668007198 ligand binding site [chemical binding]; other site 400668007199 flexible hinge region; other site 400668007200 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 400668007201 putative switch regulator; other site 400668007202 non-specific DNA interactions [nucleotide binding]; other site 400668007203 DNA binding site [nucleotide binding] 400668007204 sequence specific DNA binding site [nucleotide binding]; other site 400668007205 putative cAMP binding site [chemical binding]; other site 400668007206 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 400668007207 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 400668007208 FeS/SAM binding site; other site 400668007209 HemN C-terminal domain; Region: HemN_C; pfam06969 400668007210 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 400668007211 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 400668007212 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 400668007213 CPxP motif; other site 400668007214 FOG: CBS domain [General function prediction only]; Region: COG0517 400668007215 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 400668007216 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 400668007217 dimer interaction site [polypeptide binding]; other site 400668007218 substrate-binding tunnel; other site 400668007219 active site 400668007220 catalytic site [active] 400668007221 substrate binding site [chemical binding]; other site 400668007222 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 400668007223 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 400668007224 motif II; other site 400668007225 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 400668007226 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 400668007227 tandem repeat interface [polypeptide binding]; other site 400668007228 oligomer interface [polypeptide binding]; other site 400668007229 active site residues [active] 400668007230 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 400668007231 HemK family putative methylases; Region: hemK_fam; TIGR00536 400668007232 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 400668007233 S-adenosylmethionine binding site [chemical binding]; other site 400668007234 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 400668007235 Tetramer interface [polypeptide binding]; other site 400668007236 active site 400668007237 FMN-binding site [chemical binding]; other site 400668007238 Protein of unknown function DUF84; Region: NTPase_I-T; cl00866 400668007239 dUMP phosphatase; Provisional; Region: PRK09449 400668007240 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 400668007241 motif II; other site 400668007242 His-Xaa-Ser system putative quinone modification maturase; Region: SAM_quin_mod; TIGR03981 400668007243 His-Xaa-Ser system protein, TIGR03982 family; Region: TIGR03982 400668007244 His-Xaa-Ser repeat protein HxsA; Region: His_Ser_Rich; TIGR03979 400668007245 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 400668007246 His-Xaa-Ser system radical SAM maturase HsxC; Region: rSAM_paired_2; TIGR03977 400668007247 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 400668007248 FeS/SAM binding site; other site 400668007249 His-Xaa-Ser system radical SAM maturase HsxB; Region: rSAM_paired_1; TIGR03978 400668007250 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 400668007251 FeS/SAM binding site; other site 400668007252 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; cl01544 400668007253 Cache domain; Region: Cache_1; pfam02743 400668007254 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 400668007255 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668007256 metal binding site [ion binding]; metal-binding site 400668007257 active site 400668007258 I-site; other site 400668007259 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 400668007260 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 400668007261 putative substrate translocation pore; other site 400668007262 copper exporting ATPase; Provisional; Region: copA; PRK10671 400668007263 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 400668007264 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 400668007265 metal-binding site [ion binding] 400668007266 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 400668007267 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668007268 Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR_unk; cd04787 400668007269 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 400668007270 DNA binding residues [nucleotide binding] 400668007271 dimer interface [polypeptide binding]; other site 400668007272 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 400668007273 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668007274 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 400668007275 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 400668007276 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668007277 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 400668007278 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 400668007279 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 400668007280 active site 400668007281 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 400668007282 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 400668007283 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668007284 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668007285 AAA domain; Region: AAA_32; pfam13654 400668007286 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 400668007287 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 400668007288 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 400668007289 active site 400668007290 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 400668007291 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007292 thymidylate kinase; Validated; Region: tmk; PRK00698 400668007293 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 400668007294 TMP-binding site; other site 400668007295 ATP-binding site [chemical binding]; other site 400668007296 YceG-like family; Region: YceG; pfam02618 400668007297 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 400668007298 dimerization interface [polypeptide binding]; other site 400668007299 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 400668007300 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668007301 catalytic residue [active] 400668007302 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 400668007303 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 400668007304 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668007305 homodimer interface [polypeptide binding]; other site 400668007306 catalytic residue [active] 400668007307 Peptidase family M48; Region: Peptidase_M48; cl12018 400668007308 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 400668007309 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 400668007310 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 400668007311 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 400668007312 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 400668007313 [4Fe-4S] binding site [ion binding]; other site 400668007314 molybdopterin cofactor binding site; other site 400668007315 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 400668007316 molybdopterin cofactor binding site; other site 400668007317 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 400668007318 putative dimer interface [polypeptide binding]; other site 400668007319 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 400668007320 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 400668007321 SLBB domain; Region: SLBB; pfam10531 400668007322 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 400668007323 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 400668007324 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a...; Region: TRX_Fd_NuoE_FDH_gamma; cd03081 400668007325 putative dimer interface [polypeptide binding]; other site 400668007326 [2Fe-2S] cluster binding site [ion binding]; other site 400668007327 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 400668007328 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 400668007329 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668007330 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 400668007331 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 400668007332 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 400668007333 Flagellar protein YcgR; Region: YcgR_2; pfam12945 400668007334 erythronate-4-phosphate dehydrogenase; Validated; Region: PRK00257 400668007335 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668007336 Domain of unknown function (DUF3410); Region: DUF3410; pfam11890 400668007337 Protein of unknown function, DUF462; Region: DUF462; cl01190 400668007338 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 400668007339 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 400668007340 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 400668007341 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 400668007342 dimer interface [polypeptide binding]; other site 400668007343 glycine-pyridoxal phosphate binding site [chemical binding]; other site 400668007344 active site 400668007345 folate binding site [chemical binding]; other site 400668007346 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 400668007347 lipoyl attachment site [posttranslational modification]; other site 400668007348 glycine dehydrogenase; Provisional; Region: PRK05367 400668007349 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 400668007350 tetramer interface [polypeptide binding]; other site 400668007351 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668007352 catalytic residue [active] 400668007353 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 400668007354 tetramer interface [polypeptide binding]; other site 400668007355 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668007356 catalytic residue [active] 400668007357 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668007358 Helix-turn-helix domains; Region: HTH; cl00088 400668007359 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 400668007360 putative effector binding pocket; other site 400668007361 dimerization interface [polypeptide binding]; other site 400668007362 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 400668007363 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 400668007364 putative substrate translocation pore; other site 400668007365 Glucosyl transferase GtrII; Region: Glucos_trans_II; cl10304 400668007366 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668007367 metal binding site [ion binding]; metal-binding site 400668007368 active site 400668007369 I-site; other site 400668007370 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668007371 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 400668007372 dimer interface [polypeptide binding]; other site 400668007373 NADP binding site [chemical binding]; other site 400668007374 catalytic residues [active] 400668007375 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 400668007376 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 400668007377 active site 400668007378 NAD binding site [chemical binding]; other site 400668007379 metal binding site [ion binding]; metal-binding site 400668007380 DctM-like transporters; Region: DctM; pfam06808 400668007381 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668007382 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668007383 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668007384 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668007385 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668007386 Helix-turn-helix domains; Region: HTH; cl00088 400668007387 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 400668007388 dimerization interface [polypeptide binding]; other site 400668007389 Bacterial protein of unknown function (DUF839); Region: DUF839; pfam05787 400668007390 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 400668007391 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 400668007392 LysE type translocator; Region: LysE; cl00565 400668007393 Cupin domain; Region: Cupin_2; cl09118 400668007394 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668007395 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668007396 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668007397 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 400668007398 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 400668007399 dimerization interface [polypeptide binding]; other site 400668007400 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668007401 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668007402 dimer interface [polypeptide binding]; other site 400668007403 putative CheW interface [polypeptide binding]; other site 400668007404 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 400668007405 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 400668007406 transmembrane helices; other site 400668007407 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 400668007408 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 400668007409 RNA binding surface [nucleotide binding]; other site 400668007410 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 400668007411 active site 400668007412 ribonuclease E; Reviewed; Region: rne; PRK10811 400668007413 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 400668007414 homodimer interface [polypeptide binding]; other site 400668007415 oligonucleotide binding site [chemical binding]; other site 400668007416 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668007417 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 400668007418 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668007419 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 400668007420 pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated; Region: aceF; PRK11854 400668007421 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 400668007422 E3 interaction surface; other site 400668007423 lipoyl attachment site [posttranslational modification]; other site 400668007424 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 400668007425 E3 interaction surface; other site 400668007426 lipoyl attachment site [posttranslational modification]; other site 400668007427 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 400668007428 E3 interaction surface; other site 400668007429 lipoyl attachment site [posttranslational modification]; other site 400668007430 e3 binding domain; Region: E3_binding; pfam02817 400668007431 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 400668007432 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 400668007433 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 400668007434 dimer interface [polypeptide binding]; other site 400668007435 TPP-binding site [chemical binding]; other site 400668007436 quinolinate phosphoribosyltransferase; Validated; Region: PRK09016 400668007437 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 400668007438 dimerization interface [polypeptide binding]; other site 400668007439 active site 400668007440 Acetokinase family; Region: Acetate_kinase; cl01029 400668007441 propionate/acetate kinase; Provisional; Region: PRK12379 400668007442 phosphate acetyltransferase; Reviewed; Region: PRK05632 400668007443 DRTGG domain; Region: DRTGG; cl12147 400668007444 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 400668007445 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 400668007446 Pilin (bacterial filament); Region: Pilin; pfam00114 400668007447 Type II/IV secretion system protein; Region: T2SE; pfam00437 400668007448 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007449 Walker A motif; other site 400668007450 ATP binding site [chemical binding]; other site 400668007451 Walker B motif; other site 400668007452 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 400668007453 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 400668007454 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 400668007455 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 400668007456 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 400668007457 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 400668007458 CoA-binding site [chemical binding]; other site 400668007459 ATP-binding [chemical binding]; other site 400668007460 Domain of unknown function (DUF329); Region: DUF329; cl01144 400668007461 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 400668007462 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 400668007463 active site 400668007464 phosphorylation site [posttranslational modification] 400668007465 intermolecular recognition site; other site 400668007466 dimerization interface [polypeptide binding]; other site 400668007467 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 400668007468 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 400668007469 TPR motif; other site 400668007470 binding surface 400668007471 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 400668007472 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 400668007473 ATP binding site [chemical binding]; other site 400668007474 Mg2+ binding site [ion binding]; other site 400668007475 G-X-G motif; other site 400668007476 Transcriptional regulators [Transcription]; Region: FadR; COG2186 400668007477 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668007478 DNA-binding site [nucleotide binding]; DNA binding site 400668007479 FCD domain; Region: FCD; cl11656 400668007480 benzoate transporter; Region: benE; TIGR00843 400668007481 Benzoate membrane transport protein; Region: BenE; pfam03594 400668007482 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 400668007483 ectoine/hydroxyectoine ABC transporter, ATP-binding protein; Region: ectoine_ehuA; TIGR03005 400668007484 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 400668007485 Walker A/P-loop; other site 400668007486 ATP binding site [chemical binding]; other site 400668007487 Q-loop/lid; other site 400668007488 ABC transporter signature motif; other site 400668007489 Walker B; other site 400668007490 D-loop; other site 400668007491 H-loop/switch region; other site 400668007492 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668007493 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 400668007494 dimer interface [polypeptide binding]; other site 400668007495 conserved gate region; other site 400668007496 putative PBP binding loops; other site 400668007497 ABC-ATPase subunit interface; other site 400668007498 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668007499 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 400668007500 dimer interface [polypeptide binding]; other site 400668007501 conserved gate region; other site 400668007502 putative PBP binding loops; other site 400668007503 ABC-ATPase subunit interface; other site 400668007504 ectoine/hydroxyectoine ABC transporter solute-binding protein; Region: ectoine_ehuB; TIGR02995 400668007505 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 400668007506 substrate binding pocket [chemical binding]; other site 400668007507 membrane-bound complex binding site; other site 400668007508 hinge residues; other site 400668007509 sensor protein QseC; Provisional; Region: PRK10337 400668007510 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 400668007511 dimer interface [polypeptide binding]; other site 400668007512 phosphorylation site [posttranslational modification] 400668007513 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 400668007514 ATP binding site [chemical binding]; other site 400668007515 Mg2+ binding site [ion binding]; other site 400668007516 G-X-G motif; other site 400668007517 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 400668007518 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 400668007519 active site 400668007520 phosphorylation site [posttranslational modification] 400668007521 intermolecular recognition site; other site 400668007522 dimerization interface [polypeptide binding]; other site 400668007523 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 400668007524 DNA binding site [nucleotide binding] 400668007525 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 400668007526 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 400668007527 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 400668007528 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 400668007529 thiol:disulfide interchange protein DsbE; Provisional; Region: PRK15412 400668007530 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 400668007531 catalytic residues [active] 400668007532 Domain of unknown function (DUF4266); Region: DUF4266; pfam14086 400668007533 Protein of unknown function (DUF3570); Region: DUF3570; pfam12094 400668007534 ApbE family; Region: ApbE; cl00643 400668007535 putative fumarate hydratase; Provisional; Region: PRK15392 400668007536 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 400668007537 Fumarase C-terminus; Region: Fumerase_C; cl00795 400668007538 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 400668007539 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 400668007540 prolyl-tRNA synthetase; Provisional; Region: PRK09194 400668007541 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 400668007542 dimer interface [polypeptide binding]; other site 400668007543 motif 1; other site 400668007544 active site 400668007545 motif 2; other site 400668007546 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 400668007547 putative deacylase active site [active] 400668007548 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 400668007549 active site 400668007550 motif 3; other site 400668007551 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 400668007552 anticodon binding site; other site 400668007553 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 400668007554 ArsC family; Region: ArsC; pfam03960 400668007555 catalytic residues [active] 400668007556 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668007557 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 400668007558 Helix-turn-helix domains; Region: HTH; cl00088 400668007559 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 400668007560 substrate binding site [chemical binding]; other site 400668007561 dimerization interface [polypeptide binding]; other site 400668007562 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668007563 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668007564 NeuB family; Region: NeuB; cl00496 400668007565 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 400668007566 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 400668007567 IscR-regulated protein YhgI; Region: YhgI_GntY; TIGR03341 400668007568 NifU-like domain; Region: NifU; cl00484 400668007569 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 400668007570 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 400668007571 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 400668007572 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 400668007573 SH3 domain-containing protein; Provisional; Region: PRK10884 400668007574 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 400668007575 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 400668007576 elongation factor G; Reviewed; Region: PRK00007 400668007577 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 400668007578 G1 box; other site 400668007579 putative GEF interaction site [polypeptide binding]; other site 400668007580 GTP/Mg2+ binding site [chemical binding]; other site 400668007581 Switch I region; other site 400668007582 G2 box; other site 400668007583 G3 box; other site 400668007584 Switch II region; other site 400668007585 G4 box; other site 400668007586 G5 box; other site 400668007587 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 400668007588 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 400668007589 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 400668007590 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 400668007591 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 400668007592 active site 400668007593 catalytic tetrad [active] 400668007594 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 400668007595 Septum formation topological specificity factor MinE; Region: MinE; cl00538 400668007596 cell division inhibitor MinD; Provisional; Region: PRK10818 400668007597 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 400668007598 Switch I; other site 400668007599 Switch II; other site 400668007600 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 400668007601 septum formation inhibitor; Reviewed; Region: minC; PRK00339 400668007602 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 400668007603 exonuclease subunit SbcC; Provisional; Region: PRK10246 400668007604 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007605 Walker A/P-loop; other site 400668007606 ATP binding site [chemical binding]; other site 400668007607 Q-loop/lid; other site 400668007608 exonuclease subunit SbcC; Provisional; Region: PRK10246 400668007609 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007610 ABC transporter signature motif; other site 400668007611 Walker B; other site 400668007612 D-loop; other site 400668007613 H-loop/switch region; other site 400668007614 exonuclease subunit SbcD; Provisional; Region: PRK10966 400668007615 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 400668007616 active site 400668007617 metal binding site [ion binding]; metal-binding site 400668007618 DNA binding site [nucleotide binding] 400668007619 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 400668007620 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 400668007621 catalytic loop [active] 400668007622 iron binding site [ion binding]; other site 400668007623 short chain dehydrogenase; Provisional; Region: PRK06180 400668007624 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 400668007625 NADP binding site [chemical binding]; other site 400668007626 active site 400668007627 steroid binding site; other site 400668007628 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 400668007629 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668007630 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 400668007631 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 400668007632 metal binding site [ion binding]; metal-binding site 400668007633 dimer interface [polypeptide binding]; other site 400668007634 Periplasmic pectate lyase; Region: Pectate_lyase_2; pfam06917 400668007635 glutathione reductase; Validated; Region: PRK06116 400668007636 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668007637 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 400668007638 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 400668007639 putative phosphate binding site [ion binding]; other site 400668007640 putative catalytic site [active] 400668007641 active site 400668007642 metal binding site A [ion binding]; metal-binding site 400668007643 DNA binding site [nucleotide binding] 400668007644 putative AP binding site [nucleotide binding]; other site 400668007645 putative metal binding site B [ion binding]; other site 400668007646 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 400668007647 dimerization interface [polypeptide binding]; other site 400668007648 putative DNA binding site [nucleotide binding]; other site 400668007649 putative Zn2+ binding site [ion binding]; other site 400668007650 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668007651 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 400668007652 DNA ligase; Provisional; Region: PRK09125 400668007653 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 400668007654 DNA binding site [nucleotide binding] 400668007655 active site 400668007656 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 400668007657 DNA binding site [nucleotide binding] 400668007658 heat shock protein 90; Provisional; Region: PRK05218 400668007659 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 400668007660 ATP binding site [chemical binding]; other site 400668007661 Mg2+ binding site [ion binding]; other site 400668007662 G-X-G motif; other site 400668007663 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 400668007664 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4727 400668007665 Uncharacterized protein conserved in bacteria (DUF2145); Region: DUF2145; pfam09916 400668007666 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668007667 O-methyltransferase; Region: Methyltransf_3; pfam01596 400668007668 Protein of unknown function, DUF599; Region: DUF599; cl01575 400668007669 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 400668007670 active site 400668007671 substrate binding pocket [chemical binding]; other site 400668007672 dimer interface [polypeptide binding]; other site 400668007673 Sulfatase; Region: Sulfatase; cl10460 400668007674 ATP-dependent RNA helicase DeaD; Provisional; Region: PRK11634 400668007675 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 400668007676 ATP binding site [chemical binding]; other site 400668007677 Mg++ binding site [ion binding]; other site 400668007678 motif III; other site 400668007679 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 400668007680 nucleotide binding region [chemical binding]; other site 400668007681 ATP-binding site [chemical binding]; other site 400668007682 DbpA RNA binding domain; Region: DbpA; pfam03880 400668007683 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 400668007684 Domain of unknown function DUF20; Region: UPF0118; pfam01594 400668007685 exonuclease I; Provisional; Region: sbcB; PRK11779 400668007686 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 400668007687 active site 400668007688 substrate binding site [chemical binding]; other site 400668007689 catalytic site [active] 400668007690 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 400668007691 hypothetical protein; Provisional; Region: PRK01617 400668007692 SEC-C motif; Region: SEC-C; pfam02810 400668007693 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 400668007694 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 400668007695 active site 400668007696 phosphorylation site [posttranslational modification] 400668007697 intermolecular recognition site; other site 400668007698 dimerization interface [polypeptide binding]; other site 400668007699 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 400668007700 Zn2+ binding site [ion binding]; other site 400668007701 Mg2+ binding site [ion binding]; other site 400668007702 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 400668007703 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 400668007704 dimer interface [polypeptide binding]; other site 400668007705 phosphorylation site [posttranslational modification] 400668007706 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 400668007707 ATP binding site [chemical binding]; other site 400668007708 Mg2+ binding site [ion binding]; other site 400668007709 G-X-G motif; other site 400668007710 Response regulator receiver domain; Region: Response_reg; pfam00072 400668007711 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 400668007712 active site 400668007713 phosphorylation site [posttranslational modification] 400668007714 intermolecular recognition site; other site 400668007715 dimerization interface [polypeptide binding]; other site 400668007716 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 400668007717 metal coordination site [ion binding]; other site 400668007718 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 400668007719 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 400668007720 active site 400668007721 catalytic tetrad [active] 400668007722 3-phosphoshikimate 1-carboxyvinyltransferase; Region: PLN02338 400668007723 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 400668007724 hinge; other site 400668007725 active site 400668007726 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 400668007727 dimer interface [polypeptide binding]; other site 400668007728 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 400668007729 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 400668007730 FeS/SAM binding site; other site 400668007731 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 400668007732 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 400668007733 ThiS interaction site; other site 400668007734 putative active site [active] 400668007735 tetramer interface [polypeptide binding]; other site 400668007736 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 400668007737 thiS-thiF/thiG interaction site; other site 400668007738 HMP-P kinase/thiamin-monophosphate pyrophosphorylase; Region: PLN02898 400668007739 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 400668007740 dimer interface [polypeptide binding]; other site 400668007741 substrate binding site [chemical binding]; other site 400668007742 ATP binding site [chemical binding]; other site 400668007743 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 400668007744 thiamine phosphate binding site [chemical binding]; other site 400668007745 active site 400668007746 pyrophosphate binding site [ion binding]; other site 400668007747 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 400668007748 ThiC-associated domain; Region: ThiC-associated; pfam13667 400668007749 ThiC family; Region: ThiC; cl08031 400668007750 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional; Region: PRK14994 400668007751 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 400668007752 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 400668007753 putative ligand binding site [chemical binding]; other site 400668007754 Restriction endonuclease; Region: Mrr_cat; cl00516 400668007755 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 400668007756 dimer interface [polypeptide binding]; other site 400668007757 active site 400668007758 Stringent starvation protein B; Region: SspB; cl01120 400668007759 stringent starvation protein A; Provisional; Region: sspA; PRK09481 400668007760 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 400668007761 C-terminal domain interface [polypeptide binding]; other site 400668007762 putative GSH binding site (G-site) [chemical binding]; other site 400668007763 dimer interface [polypeptide binding]; other site 400668007764 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 400668007765 dimer interface [polypeptide binding]; other site 400668007766 N-terminal domain interface [polypeptide binding]; other site 400668007767 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 400668007768 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 400668007769 23S rRNA interface [nucleotide binding]; other site 400668007770 L3 interface [polypeptide binding]; other site 400668007771 Predicted ATPase [General function prediction only]; Region: COG1485 400668007772 Uncharacterized conserved protein [Function unknown]; Region: COG0327 400668007773 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 400668007774 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 400668007775 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 400668007776 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 400668007777 protein binding site [polypeptide binding]; other site 400668007778 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 400668007779 hydrophobic ligand binding site; other site 400668007780 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 400668007781 histidinol dehydrogenase; Region: hisD; TIGR00069 400668007782 NAD binding site [chemical binding]; other site 400668007783 dimerization interface [polypeptide binding]; other site 400668007784 product binding site; other site 400668007785 substrate binding site [chemical binding]; other site 400668007786 zinc binding site [ion binding]; other site 400668007787 catalytic residues [active] 400668007788 ATP phosphoribosyltransferase; Region: HisG; cl15266 400668007789 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 400668007790 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 400668007791 hinge; other site 400668007792 active site 400668007793 BolA-like protein; Region: BolA; cl00386 400668007794 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 400668007795 mce related protein; Region: MCE; pfam02470 400668007796 Permease; Region: Permease; cl00510 400668007797 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 400668007798 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 400668007799 Walker A/P-loop; other site 400668007800 ATP binding site [chemical binding]; other site 400668007801 Q-loop/lid; other site 400668007802 ABC transporter signature motif; other site 400668007803 Walker B; other site 400668007804 D-loop; other site 400668007805 H-loop/switch region; other site 400668007806 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 400668007807 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 400668007808 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 400668007809 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 400668007810 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 400668007811 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 400668007812 OstA-like protein; Region: OstA; cl00844 400668007813 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 400668007814 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 400668007815 Walker A/P-loop; other site 400668007816 ATP binding site [chemical binding]; other site 400668007817 Q-loop/lid; other site 400668007818 ABC transporter signature motif; other site 400668007819 Walker B; other site 400668007820 D-loop; other site 400668007821 H-loop/switch region; other site 400668007822 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 400668007823 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 400668007824 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 400668007825 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 400668007826 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 400668007827 active site 400668007828 phosphorylation site [posttranslational modification] 400668007829 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 400668007830 dimerization domain swap beta strand [polypeptide binding]; other site 400668007831 regulatory protein interface [polypeptide binding]; other site 400668007832 active site 400668007833 regulatory phosphorylation site [posttranslational modification]; other site 400668007834 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 400668007835 MgtE intracellular N domain; Region: MgtE_N; cl15244 400668007836 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 400668007837 Divalent cation transporter; Region: MgtE; cl00786 400668007838 Protein of unknown function (DUF615); Region: DUF615; cl01147 400668007839 methionine sulfoxide reductase B; Provisional; Region: PRK05508 400668007840 methionine sulfoxide reductase B; Provisional; Region: PRK00222; cl15841 400668007841 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 400668007842 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 400668007843 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668007844 Reverse transcriptase (RNA-dependent DNA polymerase); Region: RVT_1; pfam00078 400668007845 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 400668007846 putative active site [active] 400668007847 putative NTP binding site [chemical binding]; other site 400668007848 putative nucleic acid binding site [nucleotide binding]; other site 400668007849 Helix-turn-helix domains; Region: HTH; cl00088 400668007850 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 400668007851 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 400668007852 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 400668007853 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668007854 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668007855 dimer interface [polypeptide binding]; other site 400668007856 putative CheW interface [polypeptide binding]; other site 400668007857 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 400668007858 putative active site [active] 400668007859 putative dimer interface [polypeptide binding]; other site 400668007860 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668007861 classical (c) SDRs; Region: SDR_c; cd05233 400668007862 NAD(P) binding site [chemical binding]; other site 400668007863 active site 400668007864 oxidase reductase; Provisional; Region: PTZ00273 400668007865 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 400668007866 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668007867 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 400668007868 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007869 Family description; Region: UvrD_C_2; cl15862 400668007870 DNA helicase II; Region: uvrD; TIGR01075 400668007871 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO; Region: M14_PaAOTO_like; cd06250 400668007872 active site 400668007873 Zn binding site [ion binding]; other site 400668007874 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 400668007875 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 400668007876 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4135 400668007877 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 400668007878 dimer interface [polypeptide binding]; other site 400668007879 putative PBP binding loops; other site 400668007880 ABC-ATPase subunit interface; other site 400668007881 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668007882 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4136 400668007883 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007884 Walker A/P-loop; other site 400668007885 ATP binding site [chemical binding]; other site 400668007886 Q-loop/lid; other site 400668007887 ABC transporter signature motif; other site 400668007888 Walker B; other site 400668007889 D-loop; other site 400668007890 H-loop/switch region; other site 400668007891 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007892 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007893 TPR repeat; Region: TPR_11; pfam13414 400668007894 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 400668007895 binding surface 400668007896 TPR motif; other site 400668007897 TPR repeat; Region: TPR_11; pfam13414 400668007898 Cupin domain; Region: Cupin_2; cl09118 400668007899 Helix-turn-helix domain; Region: HTH_18; pfam12833 400668007900 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668007901 LysE type translocator; Region: LysE; cl00565 400668007902 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 400668007903 active site 400668007904 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 400668007905 DctM-like transporters; Region: DctM; pfam06808 400668007906 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668007907 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668007908 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668007909 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668007910 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668007911 Helix-turn-helix domains; Region: HTH; cl00088 400668007912 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 400668007913 dimerization interface [polypeptide binding]; other site 400668007914 Domain of unknown function (DUF4336); Region: DUF4336; pfam14234 400668007915 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 400668007916 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 400668007917 metal binding site [ion binding]; metal-binding site 400668007918 dimer interface [polypeptide binding]; other site 400668007919 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 400668007920 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 400668007921 inhibitor-cofactor binding pocket; inhibition site 400668007922 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668007923 catalytic residue [active] 400668007924 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 400668007925 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 400668007926 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 400668007927 active site 400668007928 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668007929 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 400668007930 NAD(P) binding site [chemical binding]; other site 400668007931 catalytic residues [active] 400668007932 Predicted ATPase [General function prediction only]; Region: COG3910 400668007933 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668007934 Walker A/P-loop; other site 400668007935 ATP binding site [chemical binding]; other site 400668007936 Q-loop/lid; other site 400668007937 ABC transporter signature motif; other site 400668007938 Walker B; other site 400668007939 D-loop; other site 400668007940 H-loop/switch region; other site 400668007941 FOG: CBS domain [General function prediction only]; Region: COG0517 400668007942 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_27; cd04640 400668007943 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 400668007944 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 400668007945 catalytic residues [active] 400668007946 dimer interface [polypeptide binding]; other site 400668007947 Helix-turn-helix domain; Region: HTH_18; pfam12833 400668007948 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668007949 Uncharacterized conserved protein [Function unknown]; Region: COG2128 400668007950 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 400668007951 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 400668007952 Nucleoside recognition; Region: Gate; cl00486 400668007953 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 400668007954 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 400668007955 YaeQ protein; Region: YaeQ; cl01913 400668007956 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 400668007957 Catalytic site [active] 400668007958 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 400668007959 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 400668007960 non-specific DNA binding site [nucleotide binding]; other site 400668007961 salt bridge; other site 400668007962 sequence-specific DNA binding site [nucleotide binding]; other site 400668007963 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 400668007964 Catalytic site [active] 400668007965 Global regulator protein family; Region: CsrA; cl00670 400668007966 atypical (a) SDRs, subgroup 5; Region: SDR_a5; cd05243 400668007967 NADH(P)-binding; Region: NAD_binding_10; pfam13460 400668007968 NAD(P) binding site [chemical binding]; other site 400668007969 putative active site [active] 400668007970 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668007971 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668007972 tetramerization interface [polypeptide binding]; other site 400668007973 NAD(P) binding site [chemical binding]; other site 400668007974 catalytic residues [active] 400668007975 BCCT family transporter; Region: BCCT; cl00569 400668007976 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668007977 Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like; Region: ALDH_DhaS; cd07114 400668007978 NAD(P) binding site [chemical binding]; other site 400668007979 catalytic residues [active] 400668007980 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 400668007981 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 400668007982 Flavin Reductases; Region: FlaRed; cl00801 400668007983 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668007984 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 400668007985 Amino acid synthesis; Region: AA_synth; pfam06684 400668007986 Transcriptional regulators [Transcription]; Region: GntR; COG1802 400668007987 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668007988 DNA-binding site [nucleotide binding]; DNA binding site 400668007989 FCD domain; Region: FCD; cl11656 400668007990 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 400668007991 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 400668007992 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 400668007993 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 400668007994 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 400668007995 dimer interface [polypeptide binding]; other site 400668007996 conserved gate region; other site 400668007997 putative PBP binding loops; other site 400668007998 ABC-ATPase subunit interface; other site 400668007999 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668008000 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 400668008001 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668008002 Walker A/P-loop; other site 400668008003 ATP binding site [chemical binding]; other site 400668008004 Q-loop/lid; other site 400668008005 ABC transporter signature motif; other site 400668008006 Walker B; other site 400668008007 D-loop; other site 400668008008 H-loop/switch region; other site 400668008009 TOBE domain; Region: TOBE_2; cl01440 400668008010 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 400668008011 sequence-specific DNA binding site [nucleotide binding]; other site 400668008012 salt bridge; other site 400668008013 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 400668008014 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668008015 Protein of unknown function (DUF1778); Region: DUF1778; cl01845 400668008016 Cupin domain; Region: Cupin_2; cl09118 400668008017 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668008018 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668008019 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668008020 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 400668008021 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 400668008022 NADP binding site [chemical binding]; other site 400668008023 dimer interface [polypeptide binding]; other site 400668008024 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 400668008025 Phage Tail Protein X; Region: Phage_tail_X; cl02088 400668008026 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 400668008027 chromosome segregation protein; Provisional; Region: PRK02224 400668008028 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668008029 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 400668008030 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 400668008031 AAA domain; Region: AAA_21; pfam13304 400668008032 Nuclear pore complex subunit [Intracellular trafficking and secretion]; Region: NUP170; COG5308 400668008033 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 400668008034 Phage Tail Protein X; Region: Phage_tail_X; cl02088 400668008035 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 400668008036 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 400668008037 Toxin YafO, type II toxin-antitoxin system; Region: YafO_toxin; cl08066 400668008038 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 400668008039 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 400668008040 FMN binding site [chemical binding]; other site 400668008041 active site 400668008042 catalytic residues [active] 400668008043 substrate binding site [chemical binding]; other site 400668008044 transaldolase-like protein; Provisional; Region: PTZ00411 400668008045 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 400668008046 active site 400668008047 dimer interface [polypeptide binding]; other site 400668008048 catalytic residue [active] 400668008049 maltose O-acetyltransferase; Provisional; Region: PRK10092 400668008050 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 400668008051 trimer interface [polypeptide binding]; other site 400668008052 active site 400668008053 substrate binding site [chemical binding]; other site 400668008054 CoA binding site [chemical binding]; other site 400668008055 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 400668008056 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 400668008057 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668008058 metal binding site [ion binding]; metal-binding site 400668008059 active site 400668008060 I-site; other site 400668008061 VacJ like lipoprotein; Region: VacJ; cl01073 400668008062 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 400668008063 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 400668008064 ATP binding site [chemical binding]; other site 400668008065 putative Mg++ binding site [ion binding]; other site 400668008066 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 400668008067 nucleotide binding region [chemical binding]; other site 400668008068 ATP-binding site [chemical binding]; other site 400668008069 Helicase associated domain (HA2); Region: HA2; cl04503 400668008070 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 400668008071 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 400668008072 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 400668008073 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 400668008074 dimer interface [polypeptide binding]; other site 400668008075 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668008076 catalytic residue [active] 400668008077 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 400668008078 S-adenosylmethionine binding site [chemical binding]; other site 400668008079 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 400668008080 active site 400668008081 metal binding site [ion binding]; metal-binding site 400668008082 Protein of unknown function (DUF1706); Region: DUF1706; cl01748 400668008083 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668008084 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 400668008085 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 400668008086 DNA binding residues [nucleotide binding] 400668008087 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 400668008088 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 400668008089 putative active site [active] 400668008090 putative dimer interface [polypeptide binding]; other site 400668008091 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 400668008092 metal ion-dependent adhesion site (MIDAS); other site 400668008093 TIGR03503 family protein; Region: TIGR03503 400668008094 Flagellin N-methylase; Region: FliB; cl00497 400668008095 YcgL domain; Region: YcgL; cl01189 400668008096 ribonuclease D; Region: rnd; TIGR01388 400668008097 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 400668008098 putative active site [active] 400668008099 catalytic site [active] 400668008100 putative substrate binding site [chemical binding]; other site 400668008101 HRDC domain; Region: HRDC; cl02578 400668008102 recombination protein RecR; Reviewed; Region: recR; PRK00076 400668008103 RecR protein; Region: RecR; pfam02132 400668008104 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 400668008105 putative active site [active] 400668008106 putative metal-binding site [ion binding]; other site 400668008107 tetramer interface [polypeptide binding]; other site 400668008108 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 400668008109 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 400668008110 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 400668008111 Walker A motif; other site 400668008112 ATP binding site [chemical binding]; other site 400668008113 Walker B motif; other site 400668008114 arginine finger; other site 400668008115 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 400668008116 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 400668008117 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 400668008118 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 400668008119 active site residue [active] 400668008120 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 400668008121 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668008122 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 400668008123 ATP binding site [chemical binding]; other site 400668008124 putative Mg++ binding site [ion binding]; other site 400668008125 acetylornithine aminotransferase; Provisional; Region: argD; PRK03244 400668008126 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 400668008127 nucleotide binding region [chemical binding]; other site 400668008128 ATP-binding site [chemical binding]; other site 400668008129 Double zinc ribbon; Region: DZR; pfam12773 400668008130 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668008131 Helix-turn-helix domains; Region: HTH; cl00088 400668008132 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 400668008133 DTW domain; Region: DTW; cl01221 400668008134 Protein of unknown function (DUF2947); Region: DUF2947; pfam11163 400668008135 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 400668008136 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 400668008137 motif II; other site 400668008138 Nucleoid-associated protein [General function prediction only]; Region: COG3081 400668008139 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 400668008140 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668008141 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 400668008142 dimer interface [polypeptide binding]; other site 400668008143 active site 400668008144 metal binding site [ion binding]; metal-binding site 400668008145 glutathione binding site [chemical binding]; other site 400668008146 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668008147 ligand binding site [chemical binding]; other site 400668008148 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 400668008149 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008150 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 400668008151 Helix-turn-helix domains; Region: HTH; cl00088 400668008152 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 400668008153 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 400668008154 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008155 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 400668008156 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 400668008157 intersubunit interface [polypeptide binding]; other site 400668008158 active site 400668008159 Zn2+ binding site [ion binding]; other site 400668008160 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 400668008161 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 400668008162 Metal-binding active site; metal-binding site 400668008163 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 400668008164 Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs; Region: Gne_like_SDR_e; cd05238 400668008165 putative NAD(P) binding site [chemical binding]; other site 400668008166 active site 400668008167 putative substrate binding site [chemical binding]; other site 400668008168 GntP family permease; Region: GntP_permease; pfam02447 400668008169 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 400668008170 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008171 flavoprotein, HI0933 family; Region: TIGR00275 400668008172 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008173 Imelysin; Region: Peptidase_M75; cl09159 400668008174 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 400668008175 Imelysin; Region: Peptidase_M75; cl09159 400668008176 Protein of unknown function (DUF1513); Region: DUF1513; pfam07433 400668008177 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668008178 metal binding site [ion binding]; metal-binding site 400668008179 active site 400668008180 I-site; other site 400668008181 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 400668008182 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 400668008183 HTH-like domain; Region: HTH_21; pfam13276 400668008184 Integrase core domain; Region: rve; cl01316 400668008185 DDE domain; Region: DDE_Tnp_IS240; pfam13610 400668008186 Integrase core domain; Region: rve_3; cl15866 400668008187 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668008188 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 400668008189 D-alanine--poly(phosphoribitol) ligase subunit 1; Provisional; Region: PRK04813 400668008190 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008191 peptide synthase; Validated; Region: PRK05691 400668008192 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008193 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 400668008194 Condensation domain; Region: Condensation; pfam00668 400668008195 Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntF; COG1020 400668008196 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 400668008197 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008198 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 400668008199 S-adenosylmethionine binding site [chemical binding]; other site 400668008200 peptide synthase; Provisional; Region: PRK12467 400668008201 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008202 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008203 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 400668008204 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008205 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008206 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008207 D-alanine--poly(phosphoribitol) ligase subunit 1; Provisional; Region: PRK04813 400668008208 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008209 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008210 peptide synthase; Provisional; Region: PRK12467 400668008211 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 400668008212 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008213 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008214 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008215 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008216 ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]; Region: PvdE; COG4615 400668008217 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668008218 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 400668008219 Walker A/P-loop; other site 400668008220 ATP binding site [chemical binding]; other site 400668008221 Q-loop/lid; other site 400668008222 ABC transporter signature motif; other site 400668008223 Walker B; other site 400668008224 D-loop; other site 400668008225 H-loop/switch region; other site 400668008226 Predicted ATPase [General function prediction only]; Region: COG3910 400668008227 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668008228 Walker A/P-loop; other site 400668008229 ATP binding site [chemical binding]; other site 400668008230 Q-loop/lid; other site 400668008231 ABC transporter signature motif; other site 400668008232 Walker B; other site 400668008233 D-loop; other site 400668008234 H-loop/switch region; other site 400668008235 peptide synthase; Provisional; Region: PRK12467 400668008236 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 400668008237 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008238 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008239 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3319 400668008240 peptide synthase; Provisional; Region: PRK12316 400668008241 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 400668008242 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008243 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008244 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008245 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 400668008246 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008247 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008248 peptide synthase; Provisional; Region: PRK12467 400668008249 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008250 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008251 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008252 HxxPF-repeated domain; Region: HxxPF_rpt; pfam13745 400668008253 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008254 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008255 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008256 non-ribosomal peptide synthase domain TIGR01720; Region: NRPS-para261 400668008257 AMP-binding enzyme; Region: AMP-binding; cl15778 400668008258 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668008259 HTH-like domain; Region: HTH_21; pfam13276 400668008260 Integrase core domain; Region: rve; cl01316 400668008261 DDE domain; Region: DDE_Tnp_IS240; pfam13610 400668008262 Integrase core domain; Region: rve_3; cl15866 400668008263 Integrase core domain; Region: rve; cl01316 400668008264 holo-(acyl carrier protein) synthase 2; Provisional; Region: PRK10351 400668008265 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 400668008266 Transposase [DNA replication, recombination, and repair]; Region: COG5433 400668008267 Transposase [DNA replication, recombination, and repair]; Region: COG5433 400668008268 Predicted thioesterase involved in non-ribosomal peptide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: GrsT; COG3208 400668008269 Integrase core domain; Region: rve_3; cl15866 400668008270 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 400668008271 Integrase core domain; Region: rve; cl01316 400668008272 Integrase core domain; Region: rve_3; cl15866 400668008273 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 400668008274 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 400668008275 IHF dimer interface [polypeptide binding]; other site 400668008276 IHF - DNA interface [nucleotide binding]; other site 400668008277 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 400668008278 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 400668008279 putative tRNA-binding site [nucleotide binding]; other site 400668008280 B3/4 domain; Region: B3_4; cl11458 400668008281 tRNA synthetase B5 domain; Region: B5; cl08394 400668008282 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 400668008283 dimer interface [polypeptide binding]; other site 400668008284 motif 1; other site 400668008285 motif 3; other site 400668008286 motif 2; other site 400668008287 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 400668008288 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 400668008289 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 400668008290 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 400668008291 dimer interface [polypeptide binding]; other site 400668008292 motif 1; other site 400668008293 active site 400668008294 motif 2; other site 400668008295 motif 3; other site 400668008296 ribosomal protein L20; Region: rpl20; CHL00068 400668008297 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 400668008298 23S rRNA binding site [nucleotide binding]; other site 400668008299 L21 binding site [polypeptide binding]; other site 400668008300 L13 binding site [polypeptide binding]; other site 400668008301 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 400668008302 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 400668008303 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 400668008304 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 400668008305 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 400668008306 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 400668008307 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 400668008308 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 400668008309 active site 400668008310 dimer interface [polypeptide binding]; other site 400668008311 motif 1; other site 400668008312 motif 2; other site 400668008313 motif 3; other site 400668008314 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 400668008315 anticodon binding site; other site 400668008316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008317 O-methyltransferase; Region: Methyltransf_3; pfam01596 400668008318 GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria; Region: GIY-YIG_HE_Tlr8p_PBC-V_like; cd10443 400668008319 GIY-YIG motif/motif A; other site 400668008320 putative active site [active] 400668008321 putative metal binding site [ion binding]; other site 400668008322 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 400668008323 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 400668008324 non-specific DNA binding site [nucleotide binding]; other site 400668008325 salt bridge; other site 400668008326 sequence-specific DNA binding site [nucleotide binding]; other site 400668008327 Cupin domain; Region: Cupin_2; cl09118 400668008328 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 400668008329 PPIC-type PPIASE domain; Region: Rotamase; cl08278 400668008330 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 400668008331 Response regulator receiver domain; Region: Response_reg; pfam00072 400668008332 active site 400668008333 phosphorylation site [posttranslational modification] 400668008334 intermolecular recognition site; other site 400668008335 dimerization interface [polypeptide binding]; other site 400668008336 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 400668008337 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 400668008338 active site 400668008339 phosphorylation site [posttranslational modification] 400668008340 intermolecular recognition site; other site 400668008341 dimerization interface [polypeptide binding]; other site 400668008342 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 400668008343 active site 400668008344 8-oxo-dGMP binding site [chemical binding]; other site 400668008345 nudix motif; other site 400668008346 metal binding site [ion binding]; metal-binding site 400668008347 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 400668008348 heterotetramer interface [polypeptide binding]; other site 400668008349 active site pocket [active] 400668008350 cleavage site 400668008351 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 400668008352 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668008353 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 400668008354 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 400668008355 nucleotide binding region [chemical binding]; other site 400668008356 ATP-binding site [chemical binding]; other site 400668008357 SEC-C motif; Region: SEC-C; pfam02810 400668008358 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 400668008359 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 400668008360 cell division protein FtsZ; Validated; Region: PRK09330 400668008361 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 400668008362 nucleotide binding site [chemical binding]; other site 400668008363 SulA interaction site; other site 400668008364 cell division protein FtsA; Region: ftsA; TIGR01174 400668008365 Cell division protein FtsA; Region: FtsA; cl11496 400668008366 Cell division protein FtsA; Region: FtsA; cl11496 400668008367 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 400668008368 Cell division protein FtsQ; Region: FtsQ; pfam03799 400668008369 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 400668008370 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 400668008371 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668008372 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 400668008373 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 400668008374 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 400668008375 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 400668008376 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 400668008377 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 400668008378 active site 400668008379 homodimer interface [polypeptide binding]; other site 400668008380 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 400668008381 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008382 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 400668008383 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 400668008384 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 400668008385 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 400668008386 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 400668008387 Mg++ binding site [ion binding]; other site 400668008388 putative catalytic motif [active] 400668008389 putative substrate binding site [chemical binding]; other site 400668008390 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 400668008391 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 400668008392 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 400668008393 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 400668008394 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 400668008395 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 400668008396 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 400668008397 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 400668008398 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 400668008399 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 400668008400 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668008401 Septum formation initiator; Region: DivIC; cl11433 400668008402 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 400668008403 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008404 cell division protein MraZ; Reviewed; Region: PRK00326 400668008405 MraZ protein; Region: MraZ; pfam02381 400668008406 MraZ protein; Region: MraZ; pfam02381 400668008407 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 400668008408 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 400668008409 dimer interface [polypeptide binding]; other site 400668008410 phosphorylation site [posttranslational modification] 400668008411 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 400668008412 ATP binding site [chemical binding]; other site 400668008413 Mg2+ binding site [ion binding]; other site 400668008414 G-X-G motif; other site 400668008415 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668008416 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 400668008417 active site 400668008418 phosphorylation site [posttranslational modification] 400668008419 intermolecular recognition site; other site 400668008420 dimerization interface [polypeptide binding]; other site 400668008421 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 400668008422 DNA binding site [nucleotide binding] 400668008423 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 400668008424 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 400668008425 GDP-binding site [chemical binding]; other site 400668008426 ACT binding site; other site 400668008427 IMP binding site; other site 400668008428 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 400668008429 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 400668008430 dimer interface [polypeptide binding]; other site 400668008431 motif 1; other site 400668008432 active site 400668008433 motif 2; other site 400668008434 motif 3; other site 400668008435 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 400668008436 FtsH protease regulator HflC; Provisional; Region: PRK11029 400668008437 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 400668008438 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 400668008439 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 400668008440 HflK protein; Region: hflK; TIGR01933 400668008441 GTPase HflX; Provisional; Region: PRK11058 400668008442 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 400668008443 HflX GTPase family; Region: HflX; cd01878 400668008444 G1 box; other site 400668008445 GTP/Mg2+ binding site [chemical binding]; other site 400668008446 Switch I region; other site 400668008447 G2 box; other site 400668008448 G3 box; other site 400668008449 Switch II region; other site 400668008450 G4 box; other site 400668008451 G5 box; other site 400668008452 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 400668008453 Sm1 motif; other site 400668008454 intra - hexamer interaction site; other site 400668008455 inter - hexamer interaction site [polypeptide binding]; other site 400668008456 nucleotide binding pocket [chemical binding]; other site 400668008457 Sm2 motif; other site 400668008458 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668008459 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 400668008460 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 400668008461 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 400668008462 ATP binding site [chemical binding]; other site 400668008463 Mg2+ binding site [ion binding]; other site 400668008464 G-X-G motif; other site 400668008465 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 400668008466 ATP binding site [chemical binding]; other site 400668008467 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 400668008468 N-acetylmuramoyl-l-alanine amidase II; Provisional; Region: PRK10431 400668008469 AMIN domain; Region: AMIN; pfam11741 400668008470 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 400668008471 active site 400668008472 metal binding site [ion binding]; metal-binding site 400668008473 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 400668008474 putative peptidoglycan binding site; other site 400668008475 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 400668008476 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668008477 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668008478 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 400668008479 putative active site [active] 400668008480 putative substrate binding site [chemical binding]; other site 400668008481 catalytic site [active] 400668008482 dimer interface [polypeptide binding]; other site 400668008483 GTPase RsgA; Reviewed; Region: PRK12288 400668008484 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 400668008485 RNA binding site [nucleotide binding]; other site 400668008486 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 400668008487 GTPase/Zn-binding domain interface [polypeptide binding]; other site 400668008488 GTP/Mg2+ binding site [chemical binding]; other site 400668008489 G4 box; other site 400668008490 G5 box; other site 400668008491 G1 box; other site 400668008492 Switch I region; other site 400668008493 G2 box; other site 400668008494 G3 box; other site 400668008495 Switch II region; other site 400668008496 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 400668008497 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 400668008498 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 400668008499 ligand binding site [chemical binding]; other site 400668008500 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 400668008501 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 400668008502 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 400668008503 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 400668008504 Protein export membrane protein; Region: SecD_SecF; cl14618 400668008505 SecD export protein N-terminal TM region; Region: SecD-TM1; cl08136 400668008506 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 400668008507 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 400668008508 Protein export membrane protein; Region: SecD_SecF; cl14618 400668008509 Preprotein translocase subunit; Region: YajC; cl00806 400668008510 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 400668008511 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 400668008512 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 400668008513 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 400668008514 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 400668008515 sequence-specific DNA binding site [nucleotide binding]; other site 400668008516 salt bridge; other site 400668008517 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 400668008518 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 400668008519 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 400668008520 Aspartase; Region: Aspartase; cd01357 400668008521 active sites [active] 400668008522 tetramer interface [polypeptide binding]; other site 400668008523 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 400668008524 active site 400668008525 homodimer interface [polypeptide binding]; other site 400668008526 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668008527 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 400668008528 Nitronate monooxygenase; Region: NMO; pfam03060 400668008529 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 400668008530 FMN binding site [chemical binding]; other site 400668008531 substrate binding site [chemical binding]; other site 400668008532 putative catalytic residue [active] 400668008533 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668008534 GtrA-like protein; Region: GtrA; cl00971 400668008535 Cupin domain; Region: Cupin_2; cl09118 400668008536 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 400668008537 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 400668008538 dimer interface [polypeptide binding]; other site 400668008539 phosphorylation site [posttranslational modification] 400668008540 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 400668008541 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668008542 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 400668008543 active site 400668008544 phosphorylation site [posttranslational modification] 400668008545 intermolecular recognition site; other site 400668008546 dimerization interface [polypeptide binding]; other site 400668008547 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 400668008548 DNA binding site [nucleotide binding] 400668008549 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 400668008550 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 400668008551 Ligand binding site; other site 400668008552 Putative Catalytic site; other site 400668008553 DXD motif; other site 400668008554 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 400668008555 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 400668008556 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 400668008557 conserved cys residue [active] 400668008558 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668008559 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 400668008560 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 400668008561 FAD binding pocket [chemical binding]; other site 400668008562 FAD binding motif [chemical binding]; other site 400668008563 phosphate binding motif [ion binding]; other site 400668008564 beta-alpha-beta structure motif; other site 400668008565 NAD binding pocket [chemical binding]; other site 400668008566 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 400668008567 catalytic loop [active] 400668008568 iron binding site [ion binding]; other site 400668008569 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 400668008570 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 400668008571 [2Fe-2S] cluster binding site [ion binding]; other site 400668008572 C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_GbcA-like; cd08884 400668008573 putative alpha subunit interface [polypeptide binding]; other site 400668008574 putative active site [active] 400668008575 putative substrate binding site [chemical binding]; other site 400668008576 Fe binding site [ion binding]; other site 400668008577 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 400668008578 Helix-turn-helix domains; Region: HTH; cl00088 400668008579 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 400668008580 substrate binding pocket [chemical binding]; other site 400668008581 dimerization interface [polypeptide binding]; other site 400668008582 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 400668008583 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 400668008584 catalytic loop [active] 400668008585 iron binding site [ion binding]; other site 400668008586 The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S]...; Region: O2ase_reductase_like; cd06187 400668008587 FAD binding pocket [chemical binding]; other site 400668008588 FAD binding motif [chemical binding]; other site 400668008589 phosphate binding motif [ion binding]; other site 400668008590 beta-alpha-beta structure motif; other site 400668008591 NAD binding pocket [chemical binding]; other site 400668008592 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 400668008593 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 400668008594 iron-sulfur cluster [ion binding]; other site 400668008595 [2Fe-2S] cluster binding site [ion binding]; other site 400668008596 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 400668008597 putative alpha subunit interface [polypeptide binding]; other site 400668008598 putative active site [active] 400668008599 putative substrate binding site [chemical binding]; other site 400668008600 Fe binding site [ion binding]; other site 400668008601 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 400668008602 inter-subunit interface; other site 400668008603 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 400668008604 [2Fe-2S] cluster binding site [ion binding]; other site 400668008605 NMT1-like family; Region: NMT1_2; cl15260 400668008606 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 400668008607 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668008608 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 400668008609 maleylacetoacetate isomerase; Region: maiA; TIGR01262 400668008610 C-terminal domain interface [polypeptide binding]; other site 400668008611 GSH binding site (G-site) [chemical binding]; other site 400668008612 putative dimer interface [polypeptide binding]; other site 400668008613 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 400668008614 dimer interface [polypeptide binding]; other site 400668008615 N-terminal domain interface [polypeptide binding]; other site 400668008616 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 400668008617 gentisate 1,2-dioxygenase; Region: gentisate_1_2; TIGR02272 400668008618 Cupin domain; Region: Cupin_2; cl09118 400668008619 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668008620 phosphatidylserine synthase; Provisional; Region: pssA; PRK09428 400668008621 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_1; cd09134 400668008622 domain interface [polypeptide binding]; other site 400668008623 putative active site [active] 400668008624 catalytic site [active] 400668008625 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria; Region: PLDc_PSS_G_neg_2; cd09136 400668008626 domain interface [polypeptide binding]; other site 400668008627 putative active site [active] 400668008628 catalytic site [active] 400668008629 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668008630 Helix-turn-helix domains; Region: HTH; cl00088 400668008631 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 400668008632 dimerization interface [polypeptide binding]; other site 400668008633 substrate binding pocket [chemical binding]; other site 400668008634 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 400668008635 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668008636 Helix-turn-helix domains; Region: HTH; cl00088 400668008637 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 400668008638 dimerization interface [polypeptide binding]; other site 400668008639 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 400668008640 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 400668008641 inhibitor site; inhibition site 400668008642 active site 400668008643 dimer interface [polypeptide binding]; other site 400668008644 catalytic residue [active] 400668008645 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 400668008646 NMT1-like family; Region: NMT1_2; cl15260 400668008647 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668008648 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 400668008649 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 400668008650 CRISPR/Cas system-associated protein Cmr5; Region: Cmr5_III-B; cd09749 400668008651 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 400668008652 CRISPR-associated protein (Cas_Cmr3); Region: Cas_Cmr3; pfam09700 400668008653 CRISPR/Cas system-associated RAMP superfamily protein Cmr3; Region: Cmr3_III-B; cd09748 400668008654 CRISPR/Cas system-associated protein Cas10; Region: Cas10_III; cl13853 400668008655 CRISPR-associated protein Cas10/Cmr2, subtype III-B; Region: cas_TM1794_Cmr2; TIGR02577 400668008656 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 400668008657 GIY-YIG domain of uncharacterized proteins from bacteria and their eukaryotic homologs; Region: GIY-YIG_COG3680; cd10440 400668008658 GIY-YIG motif/motif A; other site 400668008659 putative active site [active] 400668008660 putative metal binding site [ion binding]; other site 400668008661 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668008662 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668008663 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 400668008664 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 400668008665 XdhC Rossmann domain; Region: XdhC_C; pfam13478 400668008666 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 400668008667 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 400668008668 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 400668008669 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 400668008670 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 400668008671 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 400668008672 Predicted membrane protein (DUF2127); Region: DUF2127; cl01785 400668008673 NMT1/THI5 like; Region: NMT1; pfam09084 400668008674 NMT1-like family; Region: NMT1_2; cl15260 400668008675 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 400668008676 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 400668008677 Walker A/P-loop; other site 400668008678 ATP binding site [chemical binding]; other site 400668008679 Q-loop/lid; other site 400668008680 ABC transporter signature motif; other site 400668008681 Walker B; other site 400668008682 D-loop; other site 400668008683 H-loop/switch region; other site 400668008684 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 400668008685 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668008686 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 400668008687 nucleoside/Zn binding site; other site 400668008688 dimer interface [polypeptide binding]; other site 400668008689 catalytic motif [active] 400668008690 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; cl14733 400668008691 oxidase reductase; Provisional; Region: PTZ00273 400668008692 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668008693 YcfA-like protein; Region: YcfA; cl00752 400668008694 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 400668008695 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 400668008696 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 400668008697 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 400668008698 active site 400668008699 homotetramer interface [polypeptide binding]; other site 400668008700 salicylate hydroxylase; Provisional; Region: PRK08163 400668008701 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008702 Predicted transcriptional regulator [Transcription]; Region: COG4189 400668008703 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 400668008704 dimerization interface [polypeptide binding]; other site 400668008705 putative DNA binding site [nucleotide binding]; other site 400668008706 putative Zn2+ binding site [ion binding]; other site 400668008707 Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]; Region: AbfA; COG3534 400668008708 Alpha-L-arabinofuranosidase C-terminus; Region: Alpha-L-AF_C; cl01412 400668008709 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668008710 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668008711 Walker A/P-loop; other site 400668008712 ATP binding site [chemical binding]; other site 400668008713 Q-loop/lid; other site 400668008714 ABC transporter signature motif; other site 400668008715 Walker B; other site 400668008716 D-loop; other site 400668008717 H-loop/switch region; other site 400668008718 TOBE domain; Region: TOBE_2; cl01440 400668008719 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 400668008720 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 400668008721 dimer interface [polypeptide binding]; other site 400668008722 conserved gate region; other site 400668008723 putative PBP binding loops; other site 400668008724 ABC-ATPase subunit interface; other site 400668008725 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668008726 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 400668008727 dimer interface [polypeptide binding]; other site 400668008728 conserved gate region; other site 400668008729 putative PBP binding loops; other site 400668008730 ABC-ATPase subunit interface; other site 400668008731 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 400668008732 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 400668008733 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 400668008734 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 400668008735 active site 400668008736 catalytic residues [active] 400668008737 ferrichrome/ferrioxamine B periplasmic transporter; Provisional; Region: PRK14048 400668008738 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 400668008739 intersubunit interface [polypeptide binding]; other site 400668008740 Cache domain; Region: Cache_1; pfam02743 400668008741 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668008742 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 400668008743 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668008744 dimer interface [polypeptide binding]; other site 400668008745 putative CheW interface [polypeptide binding]; other site 400668008746 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 400668008747 Ligand Binding Site [chemical binding]; other site 400668008748 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 400668008749 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 400668008750 Ligand Binding Site [chemical binding]; other site 400668008751 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 400668008752 Domain of unknown function (DUF3483); Region: DUF3483; pfam11982 400668008753 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 400668008754 Cysteine-rich domain; Region: CCG; pfam02754 400668008755 Cysteine-rich domain; Region: CCG; pfam02754 400668008756 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 400668008757 Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_3_FMN; cd04734 400668008758 putative active site [active] 400668008759 putative FMN binding site [chemical binding]; other site 400668008760 putative substrate binding site [chemical binding]; other site 400668008761 putative catalytic residue [active] 400668008762 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668008763 Heme NO binding; Region: HNOB; cl15268 400668008764 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 400668008765 dimer interface [polypeptide binding]; other site 400668008766 active site 400668008767 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 400668008768 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 400668008769 active site 400668008770 dimer interface [polypeptide binding]; other site 400668008771 motif 1; other site 400668008772 motif 2; other site 400668008773 motif 3; other site 400668008774 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 400668008775 anticodon binding site; other site 400668008776 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668008777 metal binding site [ion binding]; metal-binding site 400668008778 active site 400668008779 I-site; other site 400668008780 Peptidase family M48; Region: Peptidase_M48; cl12018 400668008781 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG3292 400668008782 Two component regulator propeller; Region: Reg_prop; pfam07494 400668008783 Two component regulator propeller; Region: Reg_prop; pfam07494 400668008784 Two component regulator propeller; Region: Reg_prop; pfam07494 400668008785 Two component regulator propeller; Region: Reg_prop; pfam07494 400668008786 Y_Y_Y domain; Region: Y_Y_Y; pfam07495 400668008787 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668008788 metal binding site [ion binding]; metal-binding site 400668008789 active site 400668008790 I-site; other site 400668008791 beta-D-glucuronidase; Provisional; Region: PRK10150 400668008792 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; cl08371 400668008793 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 400668008794 Cellulase (glycosyl hydrolase family 5); Region: Cellulase; cl15381 400668008795 fumarylacetoacetase; Region: fum_ac_acetase; TIGR01266 400668008796 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 400668008797 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668008798 maleylacetoacetate isomerase; Region: maiA; TIGR01262 400668008799 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 400668008800 C-terminal domain interface [polypeptide binding]; other site 400668008801 GSH binding site (G-site) [chemical binding]; other site 400668008802 putative dimer interface [polypeptide binding]; other site 400668008803 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 400668008804 dimer interface [polypeptide binding]; other site 400668008805 N-terminal domain interface [polypeptide binding]; other site 400668008806 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 400668008807 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 400668008808 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 400668008809 dimer interface [polypeptide binding]; other site 400668008810 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 400668008811 active site 400668008812 Fe binding site [ion binding]; other site 400668008813 Cupin domain; Region: Cupin_2; cl09118 400668008814 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668008815 Helix-turn-helix domains; Region: HTH; cl00088 400668008816 mechanosensitive channel MscS; Provisional; Region: PRK10334 400668008817 Mechanosensitive ion channel; Region: MS_channel; pfam00924 400668008818 Uncharacterized protein family (UPF0160); Region: UPF0160; cl01749 400668008819 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 400668008820 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 400668008821 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668008822 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668008823 dimer interface [polypeptide binding]; other site 400668008824 putative CheW interface [polypeptide binding]; other site 400668008825 Bacterial protein of unknown function (DUF925); Region: DUF925; cl01435 400668008826 Protein of unknown function (DUF523); Region: DUF523; cl00733 400668008827 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 400668008828 sporadically distributed protein, TIGR04141 family; Region: TIGR04141 400668008829 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 400668008830 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 400668008831 active site 400668008832 Zn binding site [ion binding]; other site 400668008833 D-lactate dehydrogenase; Provisional; Region: PRK11183 400668008834 FAD binding domain; Region: FAD_binding_4; pfam01565 400668008835 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 400668008836 Sensors of blue-light using FAD; Region: BLUF; cl04855 400668008837 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 400668008838 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 400668008839 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 400668008840 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 400668008841 FAD binding domain; Region: FAD_binding_4; pfam01565 400668008842 formyltetrahydrofolate deformylase; Reviewed; Region: PRK13011 400668008843 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 400668008844 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 400668008845 putative active site [active] 400668008846 putative substrate binding site [chemical binding]; other site 400668008847 putative cosubstrate binding site; other site 400668008848 catalytic site [active] 400668008849 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 400668008850 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 400668008851 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 400668008852 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 400668008853 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 400668008854 Sarcosine oxidase, delta subunit family; Region: SoxD; cl01767 400668008855 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 400668008856 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008857 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 400668008858 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 400668008859 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 400668008860 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 400668008861 Fibronectin type III-like domain; Region: Fn3-like; cl15273 400668008862 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 400668008863 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 400668008864 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 400668008865 dimer interface [polypeptide binding]; other site 400668008866 conserved gate region; other site 400668008867 putative PBP binding loops; other site 400668008868 ABC-ATPase subunit interface; other site 400668008869 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668008870 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 400668008871 dimer interface [polypeptide binding]; other site 400668008872 conserved gate region; other site 400668008873 putative PBP binding loops; other site 400668008874 ABC-ATPase subunit interface; other site 400668008875 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668008876 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668008877 Walker A/P-loop; other site 400668008878 ATP binding site [chemical binding]; other site 400668008879 Q-loop/lid; other site 400668008880 ABC transporter signature motif; other site 400668008881 Walker B; other site 400668008882 D-loop; other site 400668008883 H-loop/switch region; other site 400668008884 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 400668008885 putative active site pocket [active] 400668008886 dimerization interface [polypeptide binding]; other site 400668008887 putative catalytic residue [active] 400668008888 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668008889 Helix-turn-helix domains; Region: HTH; cl00088 400668008890 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 400668008891 dimerization interface [polypeptide binding]; other site 400668008892 LysE type translocator; Region: LysE; cl00565 400668008893 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 400668008894 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 400668008895 putative substrate translocation pore; other site 400668008896 Cupin domain; Region: Cupin_2; cl09118 400668008897 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668008898 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668008899 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668008900 ApbE family; Region: ApbE; cl00643 400668008901 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 400668008902 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668008903 Walker A/P-loop; other site 400668008904 ATP binding site [chemical binding]; other site 400668008905 ABC transporter signature motif; other site 400668008906 Walker B; other site 400668008907 D-loop; other site 400668008908 H-loop/switch region; other site 400668008909 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 400668008910 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 400668008911 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 400668008912 dimerization interface [polypeptide binding]; other site 400668008913 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668008914 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668008915 dimer interface [polypeptide binding]; other site 400668008916 putative CheW interface [polypeptide binding]; other site 400668008917 Helix-turn-helix domains; Region: HTH; cl00088 400668008918 WYL domain; Region: WYL; cl14852 400668008919 Protein of unknown function (DUF3024); Region: DUF3024; pfam11225 400668008920 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 400668008921 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 400668008922 mannonate dehydratase; Provisional; Region: PRK03906 400668008923 mannonate dehydratase; Region: uxuA; TIGR00695 400668008924 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 400668008925 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 400668008926 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 400668008927 Glucuronate isomerase; Region: UxaC; cl00829 400668008928 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 400668008929 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 400668008930 Glycosyl hydrolase family 31 (GH31) domain of a bacterial protein family represented by Escherichia coli protein Aec37. The gene encoding Aec37 (aec-37) is located within a genomic island (AGI-3) isolated from the extraintestinal avian pathogenic...; Region: GH31_glycosidase_Aec37; cd06599 400668008931 putative active site [active] 400668008932 putative catalytic site [active] 400668008933 DctM-like transporters; Region: DctM; pfam06808 400668008934 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668008935 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668008936 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668008937 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668008938 DNA-binding transcriptional repressor UxuR; Provisional; Region: PRK10225 400668008939 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668008940 DNA-binding site [nucleotide binding]; DNA binding site 400668008941 FCD domain; Region: FCD; cl11656 400668008942 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 400668008943 PAS domain; Region: PAS_9; pfam13426 400668008944 putative active site [active] 400668008945 heme pocket [chemical binding]; other site 400668008946 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 400668008947 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 400668008948 putative active site [active] 400668008949 heme pocket [chemical binding]; other site 400668008950 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 400668008951 dimer interface [polypeptide binding]; other site 400668008952 phosphorylation site [posttranslational modification] 400668008953 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 400668008954 ATP binding site [chemical binding]; other site 400668008955 Mg2+ binding site [ion binding]; other site 400668008956 G-X-G motif; other site 400668008957 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 400668008958 active site 400668008959 phosphorylation site [posttranslational modification] 400668008960 intermolecular recognition site; other site 400668008961 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 400668008962 active site 400668008963 phosphorylation site [posttranslational modification] 400668008964 intermolecular recognition site; other site 400668008965 dimerization interface [polypeptide binding]; other site 400668008966 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668008967 metal binding site [ion binding]; metal-binding site 400668008968 active site 400668008969 I-site; other site 400668008970 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 400668008971 2-hydroxycarboxylate transporter family; Region: 2HCT; cl01386 400668008972 Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]; Region: CitA; COG3290 400668008973 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 400668008974 ATP binding site [chemical binding]; other site 400668008975 Mg2+ binding site [ion binding]; other site 400668008976 G-X-G motif; other site 400668008977 Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]; Region: CitB; COG4565 400668008978 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 400668008979 active site 400668008980 phosphorylation site [posttranslational modification] 400668008981 intermolecular recognition site; other site 400668008982 dimerization interface [polypeptide binding]; other site 400668008983 Transcriptional regulator; Region: CitT; pfam12431 400668008984 Helix-turn-helix domains; Region: HTH; cl00088 400668008985 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 400668008986 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008987 hydroxyglutarate oxidase; Provisional; Region: PRK11728 400668008988 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 400668008989 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668008990 CoA-ligase; Region: Ligase_CoA; cl02894 400668008991 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 400668008992 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668008993 CoA-ligase; Region: Ligase_CoA; cl02894 400668008994 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 400668008995 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668008996 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 400668008997 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 400668008998 E3 interaction surface; other site 400668008999 lipoyl attachment site [posttranslational modification]; other site 400668009000 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 400668009001 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 400668009002 E3 interaction surface; other site 400668009003 lipoyl attachment site [posttranslational modification]; other site 400668009004 e3 binding domain; Region: E3_binding; pfam02817 400668009005 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 400668009006 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 400668009007 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 400668009008 TPP-binding site [chemical binding]; other site 400668009009 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 400668009010 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 400668009011 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 400668009012 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009013 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK05675 400668009014 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 400668009015 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 400668009016 SdhC subunit interface [polypeptide binding]; other site 400668009017 proximal heme binding site [chemical binding]; other site 400668009018 cardiolipin binding site; other site 400668009019 Iron-sulfur protein interface; other site 400668009020 proximal quinone binding site [chemical binding]; other site 400668009021 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 400668009022 proximal quinone binding site [chemical binding]; other site 400668009023 SdhD (CybS) interface [polypeptide binding]; other site 400668009024 proximal heme binding site [chemical binding]; other site 400668009025 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 400668009026 dimer interface [polypeptide binding]; other site 400668009027 Citrate synthase; Region: Citrate_synt; pfam00285 400668009028 active site 400668009029 citrylCoA binding site [chemical binding]; other site 400668009030 NADH binding [chemical binding]; other site 400668009031 cationic pore residues; other site 400668009032 oxalacetate/citrate binding site [chemical binding]; other site 400668009033 coenzyme A binding site [chemical binding]; other site 400668009034 catalytic triad [active] 400668009035 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 400668009036 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 400668009037 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 400668009038 dimerization interface [polypeptide binding]; other site 400668009039 putative ATP binding site [chemical binding]; other site 400668009040 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 400668009041 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 400668009042 active site 400668009043 substrate binding site [chemical binding]; other site 400668009044 cosubstrate binding site; other site 400668009045 catalytic site [active] 400668009046 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 400668009047 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 400668009048 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 400668009049 GTP binding site; other site 400668009050 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 400668009051 hypothetical protein; Validated; Region: PRK09071 400668009052 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 400668009053 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 400668009054 [4Fe-4S] binding site [ion binding]; other site 400668009055 molybdopterin cofactor binding site; other site 400668009056 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 400668009057 molybdopterin cofactor binding site; other site 400668009058 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 400668009059 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 400668009060 nitrite reductase subunit NirD; Provisional; Region: PRK14989 400668009061 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668009062 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 400668009063 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 400668009064 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 400668009065 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668009066 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 400668009067 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 400668009068 Walker A/P-loop; other site 400668009069 ATP binding site [chemical binding]; other site 400668009070 Q-loop/lid; other site 400668009071 ABC transporter signature motif; other site 400668009072 Walker B; other site 400668009073 D-loop; other site 400668009074 H-loop/switch region; other site 400668009075 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 400668009076 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 400668009077 dimer interface [polypeptide binding]; other site 400668009078 conserved gate region; other site 400668009079 putative PBP binding loops; other site 400668009080 ABC-ATPase subunit interface; other site 400668009081 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 400668009082 NMT1-like family; Region: NMT1_2; cl15260 400668009083 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 400668009084 NMT1-like family; Region: NMT1_2; cl15260 400668009085 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 400668009086 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 400668009087 active site 400668009088 phosphorylation site [posttranslational modification] 400668009089 intermolecular recognition site; other site 400668009090 dimerization interface [polypeptide binding]; other site 400668009091 ANTAR domain; Region: ANTAR; cl04297 400668009092 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 400668009093 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 400668009094 DNA binding residues [nucleotide binding] 400668009095 dimerization interface [polypeptide binding]; other site 400668009096 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 400668009097 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 400668009098 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 400668009099 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 400668009100 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 400668009101 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668009102 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 400668009103 Walker A/P-loop; other site 400668009104 ATP binding site [chemical binding]; other site 400668009105 Q-loop/lid; other site 400668009106 ABC transporter signature motif; other site 400668009107 Walker B; other site 400668009108 D-loop; other site 400668009109 H-loop/switch region; other site 400668009110 biofilm formation regulator HmsP; Provisional; Region: PRK11829 400668009111 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 400668009112 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668009113 metal binding site [ion binding]; metal-binding site 400668009114 active site 400668009115 I-site; other site 400668009116 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 400668009117 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 400668009118 Protein of unknown function (DUF1244); Region: DUF1244; cl01385 400668009119 DTW domain; Region: DTW; cl01221 400668009120 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 400668009121 active site 400668009122 hydrophilic channel; other site 400668009123 dimerization interface [polypeptide binding]; other site 400668009124 catalytic residues [active] 400668009125 active site lid [active] 400668009126 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 400668009127 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 400668009128 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 400668009129 catalytic residues [active] 400668009130 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 400668009131 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 400668009132 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 400668009133 heme binding site [chemical binding]; other site 400668009134 ferroxidase pore; other site 400668009135 ferroxidase diiron center [ion binding]; other site 400668009136 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 400668009137 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 400668009138 heme binding site [chemical binding]; other site 400668009139 ferroxidase pore; other site 400668009140 ferroxidase diiron center [ion binding]; other site 400668009141 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 400668009142 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 400668009143 CAP-like domain; other site 400668009144 active site 400668009145 primary dimer interface [polypeptide binding]; other site 400668009146 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 400668009147 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 400668009148 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668009149 N-carbamolyputrescine amidase; Region: PLN02747 400668009150 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 400668009151 putative active site; other site 400668009152 catalytic triad [active] 400668009153 putative dimer interface [polypeptide binding]; other site 400668009154 arginine decarboxylase; Provisional; Region: PRK05354 400668009155 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 400668009156 active site 400668009157 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668009158 catalytic residues [active] 400668009159 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 400668009160 lipoyl synthase; Provisional; Region: PRK05481 400668009161 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 400668009162 FeS/SAM binding site; other site 400668009163 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 400668009164 Protein of unknown function (DUF493); Region: DUF493; cl01102 400668009165 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 400668009166 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668009167 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 400668009168 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 400668009169 rare lipoprotein A; Region: rlpA; TIGR00413 400668009170 Sporulation related domain; Region: SPOR; cl10051 400668009171 Transglycosylase SLT domain; Region: SLT_2; pfam13406 400668009172 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 400668009173 N-acetyl-D-glucosamine binding site [chemical binding]; other site 400668009174 catalytic residue [active] 400668009175 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 400668009176 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 400668009177 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 400668009178 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668009179 Uncharacterized conserved protein [Function unknown]; Region: COG1576; cl00679 400668009180 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; pfam02590 400668009181 Oligomerisation domain; Region: Oligomerisation; cl00519 400668009182 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 400668009183 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 400668009184 active site 400668009185 (T/H)XGH motif; other site 400668009186 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 400668009187 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 400668009188 putative catalytic cysteine [active] 400668009189 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 400668009190 homodimer interaction site [polypeptide binding]; other site 400668009191 cofactor binding site; other site 400668009192 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 400668009193 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 400668009194 RNA binding site [nucleotide binding]; other site 400668009195 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 400668009196 RNA binding site [nucleotide binding]; other site 400668009197 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 400668009198 RNA binding site [nucleotide binding]; other site 400668009199 S1_RPS1_repeat_ec4: 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_ec4; cd05689 400668009200 RNA binding site [nucleotide binding]; other site 400668009201 S1_RPS1_repeat_ec5: 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_ec5; cd05690 400668009202 RNA binding site [nucleotide binding]; other site 400668009203 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 400668009204 RNA binding site [nucleotide binding]; other site 400668009205 cytidylate kinase; Provisional; Region: cmk; PRK00023 400668009206 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 400668009207 CMP-binding site; other site 400668009208 The sites determining sugar specificity; other site 400668009209 bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK14806 400668009210 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009211 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a...; Region: EPT_RTPC-like; cl00288 400668009212 putative active site [active] 400668009213 Chorismate mutase type II; Region: CM_2; cl00693 400668009214 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 400668009215 Prephenate dehydratase; Region: PDT; pfam00800 400668009216 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 400668009217 putative L-Phe binding site [chemical binding]; other site 400668009218 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 400668009219 homodimer interface [polypeptide binding]; other site 400668009220 substrate-cofactor binding pocket; other site 400668009221 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 400668009222 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668009223 catalytic residue [active] 400668009224 DNA gyrase subunit A; Validated; Region: PRK05560 400668009225 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 400668009226 CAP-like domain; other site 400668009227 active site 400668009228 primary dimer interface [polypeptide binding]; other site 400668009229 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 400668009230 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 400668009231 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 400668009232 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 400668009233 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 400668009234 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 400668009235 S-adenosylmethionine binding site [chemical binding]; other site 400668009236 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009237 short chain dehydrogenase; Provisional; Region: PRK08703 400668009238 NAD(P) binding site [chemical binding]; other site 400668009239 active site 400668009240 Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]; Region: Ptr; COG1025 400668009241 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 400668009242 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 400668009243 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 400668009244 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 400668009245 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 400668009246 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009247 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 400668009248 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 400668009249 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 400668009250 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 400668009251 Transcriptional regulator; Region: Transcrip_reg; cl00361 400668009252 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 400668009253 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 400668009254 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668009255 homodimer interface [polypeptide binding]; other site 400668009256 catalytic residue [active] 400668009257 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 400668009258 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 400668009259 putative acyl-acceptor binding pocket; other site 400668009260 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 400668009261 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 400668009262 dimerization interface [polypeptide binding]; other site 400668009263 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 400668009264 dimer interface [polypeptide binding]; other site 400668009265 phosphorylation site [posttranslational modification] 400668009266 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 400668009267 ATP binding site [chemical binding]; other site 400668009268 Mg2+ binding site [ion binding]; other site 400668009269 G-X-G motif; other site 400668009270 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 400668009271 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 400668009272 active site 400668009273 phosphorylation site [posttranslational modification] 400668009274 intermolecular recognition site; other site 400668009275 dimerization interface [polypeptide binding]; other site 400668009276 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 400668009277 DNA binding site [nucleotide binding] 400668009278 Membrane transport protein; Region: Mem_trans; cl09117 400668009279 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 400668009280 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 400668009281 putative active site [active] 400668009282 heme pocket [chemical binding]; other site 400668009283 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 400668009284 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 400668009285 dimer interface [polypeptide binding]; other site 400668009286 phosphorylation site [posttranslational modification] 400668009287 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 400668009288 ATP binding site [chemical binding]; other site 400668009289 Mg2+ binding site [ion binding]; other site 400668009290 G-X-G motif; other site 400668009291 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668009292 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 400668009293 active site 400668009294 phosphorylation site [posttranslational modification] 400668009295 intermolecular recognition site; other site 400668009296 dimerization interface [polypeptide binding]; other site 400668009297 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 400668009298 Walker A motif; other site 400668009299 ATP binding site [chemical binding]; other site 400668009300 Walker B motif; other site 400668009301 arginine finger; other site 400668009302 Helix-turn-helix domains; Region: HTH; cl00088 400668009303 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668009304 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668009305 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 400668009306 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668009307 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668009308 dimer interface [polypeptide binding]; other site 400668009309 putative CheW interface [polypeptide binding]; other site 400668009310 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 400668009311 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 400668009312 HIGH motif; other site 400668009313 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 400668009314 active site 400668009315 KMSKS motif; other site 400668009316 flap endonuclease-like protein; Provisional; Region: PRK09482 400668009317 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 400668009318 active site 400668009319 metal binding site 1 [ion binding]; metal-binding site 400668009320 putative 5' ssDNA interaction site; other site 400668009321 metal binding site 3; metal-binding site 400668009322 metal binding site 2 [ion binding]; metal-binding site 400668009323 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 400668009324 putative DNA binding site [nucleotide binding]; other site 400668009325 putative metal binding site [ion binding]; other site 400668009326 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 400668009327 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 400668009328 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 400668009329 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 400668009330 active site 400668009331 metal binding site [ion binding]; metal-binding site 400668009332 carboxy-terminal protease; Provisional; Region: PRK11186 400668009333 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 400668009334 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 400668009335 protein binding site [polypeptide binding]; other site 400668009336 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 400668009337 Catalytic dyad [active] 400668009338 C-terminal domain of tail specific protease (DUF3340); Region: DUF3340; pfam11818 400668009339 LexA regulated protein; Provisional; Region: PRK11675 400668009340 thymidine kinase; Provisional; Region: PRK04296 400668009341 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668009342 ATP binding site [chemical binding]; other site 400668009343 Walker A motif; other site 400668009344 Walker B motif; other site 400668009345 Putative exonuclease, RdgC; Region: RdgC; cl01122 400668009346 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 400668009347 Cation efflux family; Region: Cation_efflux; cl00316 400668009348 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 400668009349 RmuC family; Region: RmuC; pfam02646 400668009350 hypothetical protein; Provisional; Region: PRK11568 400668009351 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 400668009352 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 400668009353 ATP-dependent helicase HepA; Validated; Region: PRK04914 400668009354 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 400668009355 ATP binding site [chemical binding]; other site 400668009356 putative Mg++ binding site [ion binding]; other site 400668009357 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 400668009358 nucleotide binding region [chemical binding]; other site 400668009359 ATP-binding site [chemical binding]; other site 400668009360 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 400668009361 active site 400668009362 Putative mono-oxygenase ydhR; Region: ydhR; cl07420 400668009363 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668009364 Helix-turn-helix domains; Region: HTH; cl00088 400668009365 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 400668009366 dimer interface [polypeptide binding]; other site 400668009367 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668009368 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 400668009369 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_7; cd03862 400668009370 putative active site [active] 400668009371 Zn binding site [ion binding]; other site 400668009372 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 400668009373 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 400668009374 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 400668009375 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 400668009376 putative binding surface; other site 400668009377 active site 400668009378 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 400668009379 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668009380 EVE domain; Region: EVE; cl00728 400668009381 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 400668009382 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 400668009383 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 400668009384 FeS/SAM binding site; other site 400668009385 TRAM domain; Region: TRAM; cl01282 400668009386 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 400668009387 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668009388 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 400668009389 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 400668009390 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 400668009391 Transporter associated domain; Region: CorC_HlyC; cl08393 400668009392 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 400668009393 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 400668009394 putative active site [active] 400668009395 catalytic triad [active] 400668009396 putative dimer interface [polypeptide binding]; other site 400668009397 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 400668009398 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 400668009399 HIGH motif; other site 400668009400 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 400668009401 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 400668009402 active site 400668009403 KMSKS motif; other site 400668009404 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 400668009405 tRNA binding surface [nucleotide binding]; other site 400668009406 Lipopolysaccharide-assembly; Region: LptE; cl01125 400668009407 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 400668009408 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 400668009409 FIST N domain; Region: FIST; cl10701 400668009410 Uncharacterized conserved protein [Function unknown]; Region: COG3287 400668009411 FIST C domain; Region: FIST_C; pfam10442 400668009412 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668009413 dimer interface [polypeptide binding]; other site 400668009414 putative CheW interface [polypeptide binding]; other site 400668009415 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668009416 Flavin Reductases; Region: FlaRed; cl00801 400668009417 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 400668009418 ligand binding site [chemical binding]; other site 400668009419 flexible hinge region; other site 400668009420 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 400668009421 ligand binding site [chemical binding]; other site 400668009422 flexible hinge region; other site 400668009423 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668009424 putative acyl-acceptor binding pocket; other site 400668009425 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase_like_7; cd04502 400668009426 active site 400668009427 catalytic triad [active] 400668009428 oxyanion hole [active] 400668009429 LysE type translocator; Region: LysE; cl00565 400668009430 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 400668009431 dihydrodipicolinate synthase; Region: dapA; TIGR00674 400668009432 dimer interface [polypeptide binding]; other site 400668009433 active site 400668009434 catalytic residue [active] 400668009435 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668009436 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 400668009437 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 400668009438 tetramer interface [polypeptide binding]; other site 400668009439 active site 400668009440 Mg2+/Mn2+ binding site [ion binding]; other site 400668009441 Tannase and feruloyl esterase; Region: Tannase; pfam07519 400668009442 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 400668009443 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668009444 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 400668009445 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 400668009446 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 400668009447 Protein of unknown function (DUF330); Region: DUF330; cl01135 400668009448 paraquat-inducible protein B; Provisional; Region: PRK10807 400668009449 mce related protein; Region: MCE; pfam02470 400668009450 mce related protein; Region: MCE; pfam02470 400668009451 mce related protein; Region: MCE; pfam02470 400668009452 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 400668009453 Paraquat-inducible protein A; Region: PqiA; pfam04403 400668009454 Paraquat-inducible protein A; Region: PqiA; pfam04403 400668009455 Protein of unknown function (DUF2867); Region: DUF2867; pfam11066 400668009456 Late embryogenesis abundant protein; Region: LEA_2; cl12118 400668009457 Late embryogenesis abundant protein; Region: LEA_2; cl12118 400668009458 Protein of unknown function, DUF486; Region: DUF486; cl01236 400668009459 23S rRNA pseudouridine synthase F; Provisional; Region: PRK10475 400668009460 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 400668009461 RNA binding surface [nucleotide binding]; other site 400668009462 PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluF; cd02554 400668009463 probable active site [active] 400668009464 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 400668009465 Ribbon-helix-helix domain; Region: RHH_4; cl01775 400668009466 intracellular protease, PfpI family; Region: PfpI; TIGR01382 400668009467 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 400668009468 conserved cys residue [active] 400668009469 Mechanosensitive ion channel; Region: MS_channel; pfam00924 400668009470 MarC family integral membrane protein; Region: MarC; cl00919 400668009471 LysE type translocator; Region: LysE; cl00565 400668009472 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668009473 NIPSNAP; Region: NIPSNAP; pfam07978 400668009474 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668009475 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 400668009476 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668009477 Coenzyme A binding pocket [chemical binding]; other site 400668009478 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 400668009479 trimer interface [polypeptide binding]; other site 400668009480 active site 400668009481 substrate binding site [chemical binding]; other site 400668009482 CoA binding site [chemical binding]; other site 400668009483 putative transposase OrfB; Reviewed; Region: PHA02517 400668009484 HTH-like domain; Region: HTH_21; pfam13276 400668009485 Integrase core domain; Region: rve; cl01316 400668009486 Integrase core domain; Region: rve_3; cl15866 400668009487 Helix-turn-helix domains; Region: HTH; cl00088 400668009488 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668009489 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 400668009490 active site 400668009491 metal binding site [ion binding]; metal-binding site 400668009492 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; cl01747 400668009493 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 400668009494 Putative transposase; Region: Y2_Tnp; pfam04986 400668009495 integron integrase; Region: integrase_gron; TIGR02249 400668009496 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 400668009497 DNA binding site [nucleotide binding] 400668009498 Int/Topo IB signature motif; other site 400668009499 active site 400668009500 NAD synthetase; Provisional; Region: PRK13981 400668009501 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 400668009502 multimer interface [polypeptide binding]; other site 400668009503 active site 400668009504 catalytic triad [active] 400668009505 protein interface 1 [polypeptide binding]; other site 400668009506 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 400668009507 homodimer interface [polypeptide binding]; other site 400668009508 NAD binding pocket [chemical binding]; other site 400668009509 ATP binding pocket [chemical binding]; other site 400668009510 Mg binding site [ion binding]; other site 400668009511 active-site loop [active] 400668009512 LIM is a small protein-protein interaction domain, containing two zinc fingers; Region: LIM; cl02475 400668009513 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 400668009514 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 400668009515 Type II transport protein GspH; Region: GspH; pfam12019 400668009516 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668009517 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 400668009518 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 400668009519 chorismate binding enzyme; Region: Chorismate_bind; cl10555 400668009520 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 400668009521 putative active site [active] 400668009522 putative CoA binding site [chemical binding]; other site 400668009523 nudix motif; other site 400668009524 metal binding site [ion binding]; metal-binding site 400668009525 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 400668009526 Active Sites [active] 400668009527 Helix-turn-helix domains; Region: HTH; cl00088 400668009528 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK05318 400668009529 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668009530 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 400668009531 Helix-turn-helix domains; Region: HTH; cl00088 400668009532 putative transposase OrfB; Reviewed; Region: PHA02517 400668009533 HTH-like domain; Region: HTH_21; pfam13276 400668009534 Integrase core domain; Region: rve; cl01316 400668009535 Integrase core domain; Region: rve_3; cl15866 400668009536 multidrug efflux pump VmrA; Reviewed; Region: vmrA; PRK09575 400668009537 MatE; Region: MatE; cl10513 400668009538 MatE; Region: MatE; cl10513 400668009539 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668009540 Helix-turn-helix domains; Region: HTH; cl00088 400668009541 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 400668009542 dimerization interface [polypeptide binding]; other site 400668009543 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 400668009544 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668009545 Coenzyme A binding pocket [chemical binding]; other site 400668009546 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 400668009547 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 400668009548 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 400668009549 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 400668009550 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 400668009551 DsbD alpha interface [polypeptide binding]; other site 400668009552 catalytic residues [active] 400668009553 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 400668009554 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 400668009555 carboxyltransferase (CT) interaction site; other site 400668009556 biotinylation site [posttranslational modification]; other site 400668009557 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 400668009558 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 400668009559 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668009560 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 400668009561 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 400668009562 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009563 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 400668009564 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 400668009565 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 400668009566 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 400668009567 FMN binding site [chemical binding]; other site 400668009568 active site 400668009569 catalytic residues [active] 400668009570 substrate binding site [chemical binding]; other site 400668009571 Helix-turn-helix domains; Region: HTH; cl00088 400668009572 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 400668009573 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 400668009574 purine monophosphate binding site [chemical binding]; other site 400668009575 dimer interface [polypeptide binding]; other site 400668009576 putative catalytic residues [active] 400668009577 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 400668009578 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 400668009579 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 400668009580 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 400668009581 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668009582 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 400668009583 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 400668009584 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 400668009585 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 400668009586 nucleotide binding site/active site [active] 400668009587 HIT family signature motif; other site 400668009588 catalytic residue [active] 400668009589 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 400668009590 diiron binding motif [ion binding]; other site 400668009591 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 400668009592 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 400668009593 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 400668009594 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl15773 400668009595 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 400668009596 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 400668009597 ATP cone domain; Region: ATP-cone; pfam03477 400668009598 Class I ribonucleotide reductase; Region: RNR_I; cd01679 400668009599 active site 400668009600 dimer interface [polypeptide binding]; other site 400668009601 catalytic residues [active] 400668009602 effector binding site; other site 400668009603 R2 peptide binding site; other site 400668009604 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 400668009605 dimer interface [polypeptide binding]; other site 400668009606 putative radical transfer pathway; other site 400668009607 diiron center [ion binding]; other site 400668009608 tyrosyl radical; other site 400668009609 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 400668009610 catalytic loop [active] 400668009611 iron binding site [ion binding]; other site 400668009612 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 400668009613 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 400668009614 acyl-CoA esterase; Provisional; Region: PRK10673 400668009615 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 400668009616 N-terminal plug; other site 400668009617 ligand-binding site [chemical binding]; other site 400668009618 prephenate dehydratase; Provisional; Region: PRK11899 400668009619 Prephenate dehydratase; Region: PDT; pfam00800 400668009620 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 400668009621 putative L-Phe binding site [chemical binding]; other site 400668009622 Haemolytic domain; Region: Haemolytic; cl00506 400668009623 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 400668009624 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 400668009625 active site 400668009626 phosphorylation site [posttranslational modification] 400668009627 intermolecular recognition site; other site 400668009628 dimerization interface [polypeptide binding]; other site 400668009629 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 400668009630 DNA binding residues [nucleotide binding] 400668009631 dimerization interface [polypeptide binding]; other site 400668009632 acetyl-CoA synthetase; Provisional; Region: PRK00174 400668009633 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 400668009634 AMP-binding enzyme; Region: AMP-binding; cl15778 400668009635 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668009636 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 400668009637 S-adenosylmethionine binding site [chemical binding]; other site 400668009638 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 400668009639 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 400668009640 motif II; other site 400668009641 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 400668009642 NMT1-like family; Region: NMT1_2; cl15260 400668009643 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668009644 putative peptidase; Provisional; Region: PRK11649 400668009645 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 400668009646 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 400668009647 Cation transport protein; Region: TrkH; cl10514 400668009648 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 400668009649 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 400668009650 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 400668009651 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 400668009652 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 400668009653 Ligand binding site [chemical binding]; other site 400668009654 Electron transfer flavoprotein domain; Region: ETF; pfam01012 400668009655 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 400668009656 active site 400668009657 feruloyl-CoA synthase; Reviewed; Region: PRK08180 400668009658 AMP-binding enzyme; Region: AMP-binding; cl15778 400668009659 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 400668009660 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 400668009661 active site 400668009662 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 400668009663 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 400668009664 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 400668009665 NAD binding site [chemical binding]; other site 400668009666 homotetramer interface [polypeptide binding]; other site 400668009667 homodimer interface [polypeptide binding]; other site 400668009668 active site 400668009669 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 400668009670 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 400668009671 substrate binding site [chemical binding]; other site 400668009672 oxyanion hole (OAH) forming residues; other site 400668009673 trimer interface [polypeptide binding]; other site 400668009674 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 400668009675 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 400668009676 dimer interface [polypeptide binding]; other site 400668009677 active site 400668009678 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 400668009679 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 400668009680 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 400668009681 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668009682 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668009683 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668009684 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668009685 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668009686 DctM-like transporters; Region: DctM; pfam06808 400668009687 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668009688 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668009689 Helix-turn-helix domains; Region: HTH; cl00088 400668009690 CHASE domain; Region: CHASE; cl01369 400668009691 PAS domain S-box; Region: sensory_box; TIGR00229 400668009692 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 400668009693 putative active site [active] 400668009694 heme pocket [chemical binding]; other site 400668009695 PAS domain S-box; Region: sensory_box; TIGR00229 400668009696 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 400668009697 putative active site [active] 400668009698 heme pocket [chemical binding]; other site 400668009699 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 400668009700 PAS fold; Region: PAS_3; pfam08447 400668009701 putative active site [active] 400668009702 heme pocket [chemical binding]; other site 400668009703 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 400668009704 dimer interface [polypeptide binding]; other site 400668009705 phosphorylation site [posttranslational modification] 400668009706 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 400668009707 ATP binding site [chemical binding]; other site 400668009708 Mg2+ binding site [ion binding]; other site 400668009709 G-X-G motif; other site 400668009710 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 400668009711 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 400668009712 active site 400668009713 phosphorylation site [posttranslational modification] 400668009714 intermolecular recognition site; other site 400668009715 dimerization interface [polypeptide binding]; other site 400668009716 Response regulator receiver domain; Region: Response_reg; pfam00072 400668009717 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 400668009718 active site 400668009719 phosphorylation site [posttranslational modification] 400668009720 intermolecular recognition site; other site 400668009721 dimerization interface [polypeptide binding]; other site 400668009722 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 400668009723 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 400668009724 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009725 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 400668009726 active site 400668009727 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 400668009728 active site 400668009729 NTP binding site [chemical binding]; other site 400668009730 metal binding triad [ion binding]; metal-binding site 400668009731 antibiotic binding site [chemical binding]; other site 400668009732 Protein of unknown function DUF86; Region: DUF86; cl01031 400668009733 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 400668009734 FeS/SAM binding site; other site 400668009735 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668009736 Helix-turn-helix domains; Region: HTH; cl00088 400668009737 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 400668009738 putative effector binding pocket; other site 400668009739 dimerization interface [polypeptide binding]; other site 400668009740 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 400668009741 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 400668009742 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 400668009743 catalytic residues [active] 400668009744 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 400668009745 Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of...; Region: 1,2-CTD; cd03460 400668009746 dimer interface [polypeptide binding]; other site 400668009747 active site 400668009748 Muconolactone delta-isomerase; Region: MIase; cl01992 400668009749 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 400668009750 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 400668009751 octamer interface [polypeptide binding]; other site 400668009752 active site 400668009753 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668009754 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668009755 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 400668009756 Helix-turn-helix domains; Region: HTH; cl00088 400668009757 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; Region: PBP2_BenM_CatM_CatR; cd08445 400668009758 dimerizarion interface [polypeptide binding]; other site 400668009759 CrgA pocket; other site 400668009760 substrate binding pocket [chemical binding]; other site 400668009761 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 400668009762 Helix-turn-helix domains; Region: HTH; cl00088 400668009763 Bacterial transcriptional regulator; Region: IclR; pfam01614 400668009764 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 400668009765 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 400668009766 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 400668009767 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 400668009768 dimer interface [polypeptide binding]; other site 400668009769 active site 400668009770 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 400668009771 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 400668009772 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 400668009773 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; cl01409 400668009774 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668009775 putative acyltransferase; Provisional; Region: PRK05790 400668009776 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 400668009777 dimer interface [polypeptide binding]; other site 400668009778 active site 400668009779 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 400668009780 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 400668009781 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668009782 Helix-turn-helix domains; Region: HTH; cl00088 400668009783 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 400668009784 putative dimerization interface [polypeptide binding]; other site 400668009785 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668009786 The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold; Region: PBP2_NodD; cd08462 400668009787 putative substrate binding pocket [chemical binding]; other site 400668009788 putative dimerization interface [polypeptide binding]; other site 400668009789 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 400668009790 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 400668009791 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 400668009792 formaldehyde dehydrogenase, glutathione-independent; Region: fdhA_non_GSH; TIGR02819 400668009793 Pseudomonas putida aldehyde-dismutating formaldehyde dehydrogenase (PFDH); Region: PFDH_like; cd08282 400668009794 NAD binding site [chemical binding]; other site 400668009795 catalytic Zn binding site [ion binding]; other site 400668009796 structural Zn binding site [ion binding]; other site 400668009797 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 400668009798 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 400668009799 Surface antigen; Region: Bac_surface_Ag; cl03097 400668009800 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 400668009801 haemagglutination activity domain; Region: Haemagg_act; cl05436 400668009802 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 400668009803 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 400668009804 putative substrate binding site [chemical binding]; other site 400668009805 putative ATP binding site [chemical binding]; other site 400668009806 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 400668009807 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009808 hypothetical protein; Provisional; Region: PRK05965 400668009809 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 400668009810 inhibitor-cofactor binding pocket; inhibition site 400668009811 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668009812 catalytic residue [active] 400668009813 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668009814 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 400668009815 putative DNA binding site [nucleotide binding]; other site 400668009816 putative Zn2+ binding site [ion binding]; other site 400668009817 Helix-turn-helix domains; Region: HTH; cl00088 400668009818 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668009819 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668009820 tetramerization interface [polypeptide binding]; other site 400668009821 NAD(P) binding site [chemical binding]; other site 400668009822 catalytic residues [active] 400668009823 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_7; cd06910 400668009824 putative active site [active] 400668009825 Zn binding site [ion binding]; other site 400668009826 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 400668009827 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009828 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668009829 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668009830 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 400668009831 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 400668009832 Walker A/P-loop; other site 400668009833 ATP binding site [chemical binding]; other site 400668009834 Q-loop/lid; other site 400668009835 ABC transporter signature motif; other site 400668009836 Walker B; other site 400668009837 D-loop; other site 400668009838 H-loop/switch region; other site 400668009839 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 400668009840 Walker A/P-loop; other site 400668009841 ATP binding site [chemical binding]; other site 400668009842 Q-loop/lid; other site 400668009843 ABC transporter signature motif; other site 400668009844 Walker B; other site 400668009845 D-loop; other site 400668009846 H-loop/switch region; other site 400668009847 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668009848 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 400668009849 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668009850 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 400668009851 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 400668009852 dimer interface [polypeptide binding]; other site 400668009853 conserved gate region; other site 400668009854 putative PBP binding loops; other site 400668009855 ABC-ATPase subunit interface; other site 400668009856 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 400668009857 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_17; cd08503 400668009858 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 400668009859 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009860 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 400668009861 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 400668009862 motif II; other site 400668009863 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 400668009864 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668009865 NAD(P) binding site [chemical binding]; other site 400668009866 catalytic residues [active] 400668009867 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668009868 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 400668009869 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668009870 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668009871 Coenzyme A binding pocket [chemical binding]; other site 400668009872 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 400668009873 tartrate dehydrogenase; Provisional; Region: PRK08194 400668009874 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 400668009875 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 400668009876 tetramer interface [polypeptide binding]; other site 400668009877 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668009878 catalytic residue [active] 400668009879 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 400668009880 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009881 Cupin domain; Region: Cupin_2; cl09118 400668009882 Cupin domain; Region: Cupin_2; cl09118 400668009883 Uncharacterized conserved protein (DUF2132); Region: DUF2132; cl01894 400668009884 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668009885 Helix-turn-helix domains; Region: HTH; cl00088 400668009886 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 400668009887 dimerization interface [polypeptide binding]; other site 400668009888 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 400668009889 intersubunit interface [polypeptide binding]; other site 400668009890 active site 400668009891 Zn2+ binding site [ion binding]; other site 400668009892 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668009893 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668009894 DctM-like transporters; Region: DctM; pfam06808 400668009895 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668009896 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668009897 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase; Provisional; Region: PRK11563 400668009898 N-terminal domain of the monoamine oxidase C dehydratase; Region: ALDH_MaoC-N; cd07128 400668009899 substrate binding site [chemical binding]; other site 400668009900 dimer interface [polypeptide binding]; other site 400668009901 NADP binding site [chemical binding]; other site 400668009902 catalytic residues [active] 400668009903 MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid...; Region: MaoC_C; cd03452 400668009904 substrate binding site [chemical binding]; other site 400668009905 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 400668009906 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 400668009907 FAD binding pocket [chemical binding]; other site 400668009908 FAD binding motif [chemical binding]; other site 400668009909 phosphate binding motif [ion binding]; other site 400668009910 beta-alpha-beta structure motif; other site 400668009911 NAD(p) ribose binding residues [chemical binding]; other site 400668009912 NAD binding pocket [chemical binding]; other site 400668009913 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 400668009914 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 400668009915 catalytic loop [active] 400668009916 iron binding site [ion binding]; other site 400668009917 Domain of unknown function DUF59; Region: DUF59; cl00941 400668009918 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 400668009919 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 400668009920 Phenylacetic acid degradation B; Region: PaaB; cl01371 400668009921 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; cl01346 400668009922 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 400668009923 AMP-binding enzyme; Region: AMP-binding; cl15778 400668009924 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 400668009925 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 400668009926 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 400668009927 dimer interface [polypeptide binding]; other site 400668009928 active site 400668009929 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 400668009930 CoenzymeA binding site [chemical binding]; other site 400668009931 subunit interaction site [polypeptide binding]; other site 400668009932 PHB binding site; other site 400668009933 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 400668009934 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668009935 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 400668009936 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 400668009937 enoyl-CoA hydratase; Provisional; Region: PRK08140 400668009938 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 400668009939 substrate binding site [chemical binding]; other site 400668009940 oxyanion hole (OAH) forming residues; other site 400668009941 trimer interface [polypeptide binding]; other site 400668009942 enoyl-CoA hydratase-isomerase; Provisional; Region: PRK09674 400668009943 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 400668009944 substrate binding site [chemical binding]; other site 400668009945 oxyanion hole (OAH) forming residues; other site 400668009946 trimer interface [polypeptide binding]; other site 400668009947 phenylacetic acid degradation protein PaaY; Region: PaaY; TIGR02287 400668009948 paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to...; Region: LbH_paaY_like; cd04745 400668009949 putative trimer interface [polypeptide binding]; other site 400668009950 putative metal binding site [ion binding]; other site 400668009951 PaaX-like protein; Region: PaaX; pfam07848 400668009952 phenylacetic acid degradation operon negative regulatory protein PaaX; Region: PaaX_trns_reg; TIGR02277 400668009953 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 400668009954 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 400668009955 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668009956 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 400668009957 Walker A/P-loop; other site 400668009958 ATP binding site [chemical binding]; other site 400668009959 Q-loop/lid; other site 400668009960 ABC transporter signature motif; other site 400668009961 Walker B; other site 400668009962 D-loop; other site 400668009963 H-loop/switch region; other site 400668009964 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668009965 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668009966 DNA binding site [nucleotide binding] 400668009967 domain linker motif; other site 400668009968 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 400668009969 dimerization interface [polypeptide binding]; other site 400668009970 ligand binding site [chemical binding]; other site 400668009971 Tagatose 6 phosphate kinase; Region: Tagatose_6_P_K; cl09211 400668009972 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 400668009973 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 400668009974 substrate binding site [chemical binding]; other site 400668009975 ATP binding site [chemical binding]; other site 400668009976 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 400668009977 TM-ABC transporter signature motif; other site 400668009978 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 400668009979 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 400668009980 Walker A/P-loop; other site 400668009981 ATP binding site [chemical binding]; other site 400668009982 Q-loop/lid; other site 400668009983 ABC transporter signature motif; other site 400668009984 Walker B; other site 400668009985 D-loop; other site 400668009986 H-loop/switch region; other site 400668009987 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 400668009988 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_12; cd06322 400668009989 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 400668009990 putative ligand binding site [chemical binding]; other site 400668009991 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 400668009992 active site 400668009993 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 400668009994 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 400668009995 substrate binding site [chemical binding]; other site 400668009996 dimer interface [polypeptide binding]; other site 400668009997 catalytic triad [active] 400668009998 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 400668009999 Helix-turn-helix domains; Region: HTH; cl00088 400668010000 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 400668010001 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 400668010002 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668010003 DNA-binding site [nucleotide binding]; DNA binding site 400668010004 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 400668010005 DctM-like transporters; Region: DctM; pfam06808 400668010006 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668010007 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668010008 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668010009 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668010010 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010011 Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria; Region: RLP_NonPhot; cd08207 400668010012 Ribulose 1,5-bisphosphate carboxylase, large subunit [Carbohydrate transport and metabolism]; Region: RbcL; COG1850 400668010013 dimer interface [polypeptide binding]; other site 400668010014 active site 400668010015 catalytic residue [active] 400668010016 metal binding site [ion binding]; metal-binding site 400668010017 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 400668010018 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 400668010019 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 400668010020 E3 interaction surface; other site 400668010021 lipoyl attachment site [posttranslational modification]; other site 400668010022 e3 binding domain; Region: E3_binding; pfam02817 400668010023 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 400668010024 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 400668010025 tetramer interface [polypeptide binding]; other site 400668010026 TPP-binding site [chemical binding]; other site 400668010027 heterodimer interface [polypeptide binding]; other site 400668010028 phosphorylation loop region [posttranslational modification] 400668010029 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 400668010030 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 400668010031 alpha subunit interface [polypeptide binding]; other site 400668010032 TPP binding site [chemical binding]; other site 400668010033 heterodimer interface [polypeptide binding]; other site 400668010034 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 400668010035 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668010036 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 400668010037 putative DNA binding site [nucleotide binding]; other site 400668010038 putative Zn2+ binding site [ion binding]; other site 400668010039 Helix-turn-helix domains; Region: HTH; cl00088 400668010040 Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: MdoH; COG2943 400668010041 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 400668010042 Ligand binding site; other site 400668010043 DXD motif; other site 400668010044 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 400668010045 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 400668010046 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; cl01267 400668010047 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668010048 Helix-turn-helix domains; Region: HTH; cl00088 400668010049 phenol 2-monooxygenase; Provisional; Region: PRK08294 400668010050 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010051 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010052 FAD-dependent Phenol hydoxylase (PHOX) family, C-terminal TRX-fold domain; composed of proteins similar to PHOX from the aerobic topsoil yeast Trichosporon cutaneum. PHOX is a flavoprotein monooxygenase that catalyzes the hydroxylation of phenol and...; Region: PHOX_C; cd02979 400668010053 dimer interface [polypeptide binding]; other site 400668010054 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 400668010055 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668010056 Coenzyme A binding pocket [chemical binding]; other site 400668010057 Predicted amidohydrolase [General function prediction only]; Region: COG0388 400668010058 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 400668010059 putative active site [active] 400668010060 catalytic triad [active] 400668010061 putative dimer interface [polypeptide binding]; other site 400668010062 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 400668010063 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668010064 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668010065 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 400668010066 NAD(P) binding site [chemical binding]; other site 400668010067 catalytic residues [active] 400668010068 choline dehydrogenase; Validated; Region: PRK02106 400668010069 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010070 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 400668010071 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 400668010072 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010073 NAD(P) binding site [chemical binding]; other site 400668010074 active site 400668010075 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 400668010076 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668010077 Cupin domain; Region: Cupin_2; cl09118 400668010078 hypothetical protein; Provisional; Region: PRK06847 400668010079 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010080 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 400668010081 iron-sulfur cluster [ion binding]; other site 400668010082 [2Fe-2S] cluster binding site [ion binding]; other site 400668010083 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 400668010084 Protein export membrane protein; Region: SecD_SecF; cl14618 400668010085 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 400668010086 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 400668010087 C-terminal domain of Burkholderia sp. NF100 MhqB and similar proteins; MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion; Region: MhqB_like_C; cd08360 400668010088 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668010089 putative active site [active] 400668010090 putative metal binding site [ion binding]; other site 400668010091 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 400668010092 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 400668010093 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668010094 Helix-turn-helix domains; Region: HTH; cl00088 400668010095 The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold; Region: PBP2_NodD; cd08462 400668010096 putative substrate binding pocket [chemical binding]; other site 400668010097 putative dimerization interface [polypeptide binding]; other site 400668010098 Putative cyclase; Region: Cyclase; cl00814 400668010099 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668010100 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 400668010101 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 400668010102 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 400668010103 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 400668010104 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 400668010105 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668010106 DNA-binding site [nucleotide binding]; DNA binding site 400668010107 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 400668010108 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668010109 homodimer interface [polypeptide binding]; other site 400668010110 catalytic residue [active] 400668010111 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 400668010112 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 400668010113 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 400668010114 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 400668010115 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 400668010116 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 400668010117 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 400668010118 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 400668010119 Ligand binding site [chemical binding]; other site 400668010120 Electron transfer flavoprotein domain; Region: ETF; pfam01012 400668010121 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 400668010122 FAD binding domain; Region: FAD_binding_4; pfam01565 400668010123 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668010124 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668010125 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668010126 NMT1-like family; Region: NMT1_2; cl15260 400668010127 Domain of unknown function (DUF1338); Region: DUF1338; cl02226 400668010128 Domain of unknown function (DUF1338); Region: DUF1338; cl02226 400668010129 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 400668010130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010131 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_6; cd06154 400668010132 homotrimer interaction site [polypeptide binding]; other site 400668010133 putative active site [active] 400668010134 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010135 Ornithine cyclodeaminase/mu-crystallin family; Region: OCD_Mu_crystall; pfam02423 400668010136 The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate; Region: HPCD; cd07370 400668010137 putative active site [active] 400668010138 putative metal binding site [ion binding]; other site 400668010139 DctM-like transporters; Region: DctM; pfam06808 400668010140 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668010141 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668010142 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668010143 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668010144 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 400668010145 putative substrate binding pocket [chemical binding]; other site 400668010146 trimer interface [polypeptide binding]; other site 400668010147 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668010148 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 400668010149 NAD binding site [chemical binding]; other site 400668010150 catalytic residues [active] 400668010151 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 400668010152 DNA binding residues [nucleotide binding] 400668010153 dimerization interface [polypeptide binding]; other site 400668010154 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668010155 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 400668010156 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668010157 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668010158 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 400668010159 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 400668010160 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 400668010161 Cupin domain; Region: Cupin_2; cl09118 400668010162 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668010163 Domain of unknown function (DUF336); Region: DUF336; cl01249 400668010164 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 400668010165 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 400668010166 putative substrate translocation pore; other site 400668010167 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668010168 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 400668010169 Ligand Binding Site [chemical binding]; other site 400668010170 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668010171 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 400668010172 NAD(P) binding site [chemical binding]; other site 400668010173 catalytic residues [active] 400668010174 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668010175 NMT1-like family; Region: NMT1_2; cl15260 400668010176 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 400668010177 Naphthocyclinone hydroxylase; Region: NcnH; cd01159 400668010178 Flavin binding site [chemical binding]; other site 400668010179 Flavin Reductases; Region: FlaRed; cl00801 400668010180 Transcriptional regulators [Transcription]; Region: MarR; COG1846 400668010181 putative transporter; Provisional; Region: PRK11043 400668010182 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 400668010183 putative substrate translocation pore; other site 400668010184 Helix-turn-helix domains; Region: HTH; cl00088 400668010185 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 400668010186 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 400668010187 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668010188 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668010189 tetramerization interface [polypeptide binding]; other site 400668010190 NAD(P) binding site [chemical binding]; other site 400668010191 catalytic residues [active] 400668010192 transcriptional regulator EutR; Provisional; Region: PRK10130 400668010193 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 400668010194 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 400668010195 putative substrate translocation pore; other site 400668010196 amidase; Provisional; Region: PRK07869 400668010197 Amidase; Region: Amidase; cl11426 400668010198 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 400668010199 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 400668010200 HsdM N-terminal domain; Region: HsdM_N; pfam12161 400668010201 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 400668010202 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010203 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 400668010204 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 400668010205 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 400668010206 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 400668010207 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 400668010208 ATP binding site [chemical binding]; other site 400668010209 putative Mg++ binding site [ion binding]; other site 400668010210 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 400668010211 nucleotide binding region [chemical binding]; other site 400668010212 ATP-binding site [chemical binding]; other site 400668010213 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 400668010214 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 400668010215 Walker A motif; other site 400668010216 ATP binding site [chemical binding]; other site 400668010217 Walker B motif; other site 400668010218 arginine finger; other site 400668010219 Helix-turn-helix domains; Region: HTH; cl00088 400668010220 Domain of unknown function (DUF4095); Region: DUF4095; pfam13338 400668010221 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; cl00973 400668010222 putative amidase; Provisional; Region: PRK06169 400668010223 Amidase; Region: Amidase; cl11426 400668010224 allantoate amidohydrolase; Reviewed; Region: PRK12893 400668010225 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 400668010226 active site 400668010227 metal binding site [ion binding]; metal-binding site 400668010228 dimer interface [polypeptide binding]; other site 400668010229 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 400668010230 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 400668010231 Walker A/P-loop; other site 400668010232 ATP binding site [chemical binding]; other site 400668010233 Q-loop/lid; other site 400668010234 ABC transporter signature motif; other site 400668010235 Walker B; other site 400668010236 D-loop; other site 400668010237 H-loop/switch region; other site 400668010238 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 400668010239 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 400668010240 Walker A/P-loop; other site 400668010241 ATP binding site [chemical binding]; other site 400668010242 Q-loop/lid; other site 400668010243 ABC transporter signature motif; other site 400668010244 Walker B; other site 400668010245 D-loop; other site 400668010246 H-loop/switch region; other site 400668010247 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 400668010248 TM-ABC transporter signature motif; other site 400668010249 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 400668010250 TM-ABC transporter signature motif; other site 400668010251 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 400668010252 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 400668010253 putative ligand binding site [chemical binding]; other site 400668010254 Transcriptional regulators [Transcription]; Region: FadR; COG2186 400668010255 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668010256 DNA-binding site [nucleotide binding]; DNA binding site 400668010257 FCD domain; Region: FCD; cl11656 400668010258 Sporulation related domain; Region: SPOR; cl10051 400668010259 excinuclease ABC subunit B; Provisional; Region: PRK05298 400668010260 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 400668010261 ATP binding site [chemical binding]; other site 400668010262 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 400668010263 nucleotide binding region [chemical binding]; other site 400668010264 ATP-binding site [chemical binding]; other site 400668010265 Ultra-violet resistance protein B; Region: UvrB; pfam12344 400668010266 UvrB/uvrC motif; Region: UVR; pfam02151 400668010267 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668010268 high affinity sulphate transporter 1; Region: sulP; TIGR00815 400668010269 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668010270 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 400668010271 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 400668010272 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 400668010273 active site 400668010274 dimer interface [polypeptide binding]; other site 400668010275 tetratricopeptide repeat protein; Provisional; Region: PRK11788 400668010276 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 400668010277 binding surface 400668010278 TPR motif; other site 400668010279 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 400668010280 binding surface 400668010281 TPR motif; other site 400668010282 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 400668010283 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 400668010284 IHF dimer interface [polypeptide binding]; other site 400668010285 IHF - DNA interface [nucleotide binding]; other site 400668010286 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 400668010287 dimer interface [polypeptide binding]; other site 400668010288 substrate binding site [chemical binding]; other site 400668010289 metal binding sites [ion binding]; metal-binding site 400668010290 thioredoxin reductase; Provisional; Region: PRK10262 400668010291 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 400668010292 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 400668010293 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 400668010294 ATP binding site [chemical binding]; other site 400668010295 substrate interface [chemical binding]; other site 400668010296 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 400668010297 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 400668010298 substrate binding site [chemical binding]; other site 400668010299 ATP binding site [chemical binding]; other site 400668010300 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 400668010301 putative CheA interaction surface; other site 400668010302 Tim44-like domain; Region: Tim44; cl09208 400668010303 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 400668010304 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 400668010305 active site 400668010306 HIGH motif; other site 400668010307 dimer interface [polypeptide binding]; other site 400668010308 KMSKS motif; other site 400668010309 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 400668010310 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010311 Family description; Region: UvrD_C_2; cl15862 400668010312 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 400668010313 Family description; Region: UvrD_C_2; cl15862 400668010314 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 400668010315 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 400668010316 Exodeoxyribonuclease V, gamma subunit; Region: Exonuc_V_gamma; pfam04257 400668010317 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 400668010318 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 400668010319 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 400668010320 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 400668010321 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 400668010322 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 400668010323 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 400668010324 GIY-YIG motif/motif A; other site 400668010325 active site 400668010326 catalytic site [active] 400668010327 putative DNA binding site [nucleotide binding]; other site 400668010328 metal binding site [ion binding]; metal-binding site 400668010329 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 400668010330 response regulator; Provisional; Region: PRK09483 400668010331 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 400668010332 active site 400668010333 phosphorylation site [posttranslational modification] 400668010334 intermolecular recognition site; other site 400668010335 dimerization interface [polypeptide binding]; other site 400668010336 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 400668010337 DNA binding residues [nucleotide binding] 400668010338 dimerization interface [polypeptide binding]; other site 400668010339 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 400668010340 30S subunit binding site; other site 400668010341 YccA-like proteins; Region: YccA_like; cd10433 400668010342 DsrE/DsrF-like family; Region: DrsE; cl00672 400668010343 DsrE/DsrF-like family; Region: DrsE; cl00672 400668010344 DsrE/DsrF-like family; Region: DrsE; cl00672 400668010345 DsrC like protein; Region: DsrC; cl01101 400668010346 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 400668010347 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 400668010348 seryl-tRNA synthetase; Provisional; Region: PRK05431 400668010349 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 400668010350 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 400668010351 dimer interface [polypeptide binding]; other site 400668010352 active site 400668010353 motif 1; other site 400668010354 motif 2; other site 400668010355 motif 3; other site 400668010356 CrcB-like protein; Region: CRCB; cl09114 400668010357 recombination factor protein RarA; Reviewed; Region: PRK13342 400668010358 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 400668010359 Walker A motif; other site 400668010360 ATP binding site [chemical binding]; other site 400668010361 Walker B motif; other site 400668010362 arginine finger; other site 400668010363 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 400668010364 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 400668010365 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 400668010366 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 400668010367 DNA translocase FtsK; Provisional; Region: PRK10263 400668010368 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010369 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 400668010370 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668010371 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 400668010372 rRNA binding site [nucleotide binding]; other site 400668010373 predicted 30S ribosome binding site; other site 400668010374 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 400668010375 Clp amino terminal domain; Region: Clp_N; pfam02861 400668010376 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 400668010377 Walker A motif; other site 400668010378 ATP binding site [chemical binding]; other site 400668010379 Walker B motif; other site 400668010380 arginine finger; other site 400668010381 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 400668010382 Walker A motif; other site 400668010383 ATP binding site [chemical binding]; other site 400668010384 Walker B motif; other site 400668010385 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 400668010386 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 400668010387 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 400668010388 DNA-binding site [nucleotide binding]; DNA binding site 400668010389 RNA-binding motif; other site 400668010390 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 400668010391 nudix motif; other site 400668010392 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 400668010393 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 400668010394 Protein of unknown function (DUF489); Region: DUF489; cl01097 400668010395 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 400668010396 adenylosuccinate lyase; Provisional; Region: PRK09285 400668010397 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 400668010398 tetramer interface [polypeptide binding]; other site 400668010399 active site 400668010400 Cupin superfamily protein; Region: Cupin_4; pfam08007 400668010401 JmjC domain, hydroxylase; Region: JmjC; cl15814 400668010402 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 400668010403 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668010404 Coenzyme A binding pocket [chemical binding]; other site 400668010405 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668010406 Helix-turn-helix domains; Region: HTH; cl00088 400668010407 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 400668010408 dimerization interface [polypeptide binding]; other site 400668010409 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 400668010410 NAD(P) binding site [chemical binding]; other site 400668010411 catalytic residues [active] 400668010412 peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK11570 400668010413 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 400668010414 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668010415 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 400668010416 Ligand Binding Site [chemical binding]; other site 400668010417 DNA topoisomerase III; Provisional; Region: PRK07726 400668010418 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 400668010419 active site 400668010420 putative interdomain interaction site [polypeptide binding]; other site 400668010421 putative metal-binding site [ion binding]; other site 400668010422 putative nucleotide binding site [chemical binding]; other site 400668010423 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 400668010424 DNA binding groove [nucleotide binding] 400668010425 domain I; other site 400668010426 phosphate binding site [ion binding]; other site 400668010427 domain II; other site 400668010428 domain III; other site 400668010429 nucleotide binding site [chemical binding]; other site 400668010430 catalytic site [active] 400668010431 domain IV; other site 400668010432 LysE type translocator; Region: LysE; cl00565 400668010433 Phosphate transporter family; Region: PHO4; cl00396 400668010434 Phosphate transporter family; Region: PHO4; cl00396 400668010435 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 400668010436 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 400668010437 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 400668010438 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 400668010439 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668010440 NAD(P) binding site [chemical binding]; other site 400668010441 catalytic residues [active] 400668010442 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668010443 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668010444 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668010445 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 400668010446 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668010447 putative substrate translocation pore; other site 400668010448 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 400668010449 H+ Antiporter protein; Region: 2A0121; TIGR00900 400668010450 putative substrate translocation pore; other site 400668010451 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 400668010452 active site 400668010453 dihydromonapterin reductase; Provisional; Region: PRK06483 400668010454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010455 NAD(P) binding site [chemical binding]; other site 400668010456 active site 400668010457 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 400668010458 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 400668010459 Glycosyl transferase family 1; Region: Glyco_trans_1_3; pfam13528 400668010460 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 400668010461 active site 400668010462 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 400668010463 dimerization interface [polypeptide binding]; other site 400668010464 substrate binding site [chemical binding]; other site 400668010465 active site 400668010466 calcium binding site [ion binding]; other site 400668010467 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 400668010468 putative substrate binding pocket [chemical binding]; other site 400668010469 trimer interface [polypeptide binding]; other site 400668010470 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010471 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668010472 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_18; cd08357 400668010473 putative metal binding site [ion binding]; other site 400668010474 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668010475 dimer interface [polypeptide binding]; other site 400668010476 putative CheW interface [polypeptide binding]; other site 400668010477 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 400668010478 anti sigma factor interaction site; other site 400668010479 regulatory phosphorylation site [posttranslational modification]; other site 400668010480 Response regulator receiver domain; Region: Response_reg; pfam00072 400668010481 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 400668010482 active site 400668010483 phosphorylation site [posttranslational modification] 400668010484 intermolecular recognition site; other site 400668010485 dimerization interface [polypeptide binding]; other site 400668010486 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 400668010487 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 400668010488 Response regulator receiver domain; Region: Response_reg; pfam00072 400668010489 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 400668010490 active site 400668010491 phosphorylation site [posttranslational modification] 400668010492 intermolecular recognition site; other site 400668010493 dimerization interface [polypeptide binding]; other site 400668010494 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 400668010495 putative binding surface; other site 400668010496 active site 400668010497 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 400668010498 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 400668010499 ATP binding site [chemical binding]; other site 400668010500 Mg2+ binding site [ion binding]; other site 400668010501 G-X-G motif; other site 400668010502 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 400668010503 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 400668010504 putative CheA interaction surface; other site 400668010505 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 400668010506 PAS domain; Region: PAS_9; pfam13426 400668010507 putative active site [active] 400668010508 heme pocket [chemical binding]; other site 400668010509 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 400668010510 PAS domain; Region: PAS_9; pfam13426 400668010511 putative active site [active] 400668010512 heme pocket [chemical binding]; other site 400668010513 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668010514 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668010515 dimer interface [polypeptide binding]; other site 400668010516 putative CheW interface [polypeptide binding]; other site 400668010517 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 400668010518 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 400668010519 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010520 CheD chemotactic sensory transduction; Region: CheD; cl00810 400668010521 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 400668010522 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 400668010523 active site 400668010524 phosphorylation site [posttranslational modification] 400668010525 intermolecular recognition site; other site 400668010526 dimerization interface [polypeptide binding]; other site 400668010527 CheB methylesterase; Region: CheB_methylest; pfam01339 400668010528 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 400668010529 Integrase core domain; Region: rve; cl01316 400668010530 Integrase core domain; Region: rve_3; cl15866 400668010531 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 400668010532 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 400668010533 active site 400668010534 FMN binding site [chemical binding]; other site 400668010535 substrate binding site [chemical binding]; other site 400668010536 3Fe-4S cluster binding site [ion binding]; other site 400668010537 PAS domain S-box; Region: sensory_box; TIGR00229 400668010538 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 400668010539 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668010540 metal binding site [ion binding]; metal-binding site 400668010541 active site 400668010542 I-site; other site 400668010543 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 400668010544 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 400668010545 Protein of unknown function (DUF419); Region: DUF419; cl15265 400668010546 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 400668010547 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 400668010548 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 400668010549 ABC transporter; Region: ABC_tran_2; pfam12848 400668010550 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 400668010551 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 400668010552 Domain of unknown function DUF21; Region: DUF21; pfam01595 400668010553 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 400668010554 Transporter associated domain; Region: CorC_HlyC; cl08393 400668010555 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 400668010556 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 400668010557 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 400668010558 catalytic residues [active] 400668010559 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 400668010560 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668010561 Flagellin N-methylase; Region: FliB; cl00497 400668010562 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 400668010563 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 400668010564 dimerization interface [polypeptide binding]; other site 400668010565 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668010566 dimer interface [polypeptide binding]; other site 400668010567 putative CheW interface [polypeptide binding]; other site 400668010568 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 400668010569 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 400668010570 dimerization interface [polypeptide binding]; other site 400668010571 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668010572 dimer interface [polypeptide binding]; other site 400668010573 putative CheW interface [polypeptide binding]; other site 400668010574 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 400668010575 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 400668010576 non-specific DNA binding site [nucleotide binding]; other site 400668010577 salt bridge; other site 400668010578 sequence-specific DNA binding site [nucleotide binding]; other site 400668010579 Haemolysin-III related; Region: HlyIII; cl03831 400668010580 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 400668010581 Bacitracin resistance protein BacA; Region: BacA; cl00858 400668010582 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 400668010583 Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators; Region: HTH_HMRTR; cd04770 400668010584 DNA binding residues [nucleotide binding] 400668010585 dimer interface [polypeptide binding]; other site 400668010586 metal binding site [ion binding]; metal-binding site 400668010587 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 400668010588 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668010589 metal binding site [ion binding]; metal-binding site 400668010590 active site 400668010591 I-site; other site 400668010592 chaperone-modulator protein CbpM; Provisional; Region: PRK10265 400668010593 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 400668010594 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 400668010595 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 400668010596 HSP70 interaction site [polypeptide binding]; other site 400668010597 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 400668010598 substrate binding site [polypeptide binding]; other site 400668010599 dimer interface [polypeptide binding]; other site 400668010600 DNA-binding transcriptional regulator CsgD; Provisional; Region: PRK10100 400668010601 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 400668010602 DNA binding residues [nucleotide binding] 400668010603 dimerization interface [polypeptide binding]; other site 400668010604 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 400668010605 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 400668010606 Carbon starvation protein CstA; Region: CstA; pfam02554 400668010607 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 400668010608 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 400668010609 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 400668010610 active site 400668010611 phosphorylation site [posttranslational modification] 400668010612 intermolecular recognition site; other site 400668010613 dimerization interface [polypeptide binding]; other site 400668010614 LytTr DNA-binding domain; Region: LytTR; cl04498 400668010615 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 400668010616 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 400668010617 Histidine kinase; Region: His_kinase; pfam06580 400668010618 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 400668010619 TIGR03549 family protein; Region: TIGR03549 400668010620 OsmC-like protein; Region: OsmC; cl00767 400668010621 Uncharacterized conserved protein [Function unknown]; Region: COG1944; cl09146 400668010622 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 400668010623 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 400668010624 N-acetyl-D-glucosamine binding site [chemical binding]; other site 400668010625 catalytic residue [active] 400668010626 Cache domain; Region: Cache_2; cl07034 400668010627 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668010628 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 400668010629 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668010630 dimer interface [polypeptide binding]; other site 400668010631 putative CheW interface [polypeptide binding]; other site 400668010632 Citrate transporter; Region: CitMHS; pfam03600 400668010633 Na+-H+ antiporter family; Region: Na_H_antiport_2; cl15264 400668010634 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 400668010635 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH6; cd08194 400668010636 putative active site [active] 400668010637 metal binding site [ion binding]; metal-binding site 400668010638 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 400668010639 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668010640 tetrameric interface [polypeptide binding]; other site 400668010641 NAD binding site [chemical binding]; other site 400668010642 catalytic residues [active] 400668010643 Transcriptional regulator [Transcription]; Region: IclR; COG1414 400668010644 Helix-turn-helix domains; Region: HTH; cl00088 400668010645 Bacterial transcriptional regulator; Region: IclR; pfam01614 400668010646 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 400668010647 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 400668010648 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668010649 Helix-turn-helix domains; Region: HTH; cl00088 400668010650 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 400668010651 MafB19-like deaminase; Region: MafB19-deam; pfam14437 400668010652 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 400668010653 putative transposase OrfB; Reviewed; Region: PHA02517 400668010654 HTH-like domain; Region: HTH_21; pfam13276 400668010655 Integrase core domain; Region: rve; cl01316 400668010656 Integrase core domain; Region: rve_3; cl15866 400668010657 Helix-turn-helix domains; Region: HTH; cl00088 400668010658 Penicillin amidase; Region: Penicil_amidase; pfam01804 400668010659 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 400668010660 Sel1 repeat; Region: Sel1; cl02723 400668010661 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 400668010662 Sel1 repeat; Region: Sel1; cl02723 400668010663 Sel1 repeat; Region: Sel1; cl02723 400668010664 Sel1 repeat; Region: Sel1; cl02723 400668010665 Sel1 repeat; Region: Sel1; cl02723 400668010666 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 400668010667 Sel1 repeat; Region: Sel1; cl02723 400668010668 Sel1 repeat; Region: Sel1; cl02723 400668010669 Sel1 repeat; Region: Sel1; cl02723 400668010670 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 400668010671 Sel1 repeat; Region: Sel1; cl02723 400668010672 Sel1 repeat; Region: Sel1; cl02723 400668010673 Sel1 repeat; Region: Sel1; cl02723 400668010674 Sel1 repeat; Region: Sel1; cl02723 400668010675 Sel1 repeat; Region: Sel1; cl02723 400668010676 Sel1 repeat; Region: Sel1; cl02723 400668010677 Sel1 repeat; Region: Sel1; cl02723 400668010678 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 400668010679 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 400668010680 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 400668010681 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 400668010682 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 400668010683 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 400668010684 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 400668010685 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668010686 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 400668010687 Precorrin-8X methylmutase; Region: CbiC; pfam02570 400668010688 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 400668010689 Precorrin-6x reductase [Coenzyme metabolism]; Region: CobK; COG2099 400668010690 CbiD; Region: CbiD; cl00828 400668010691 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 400668010692 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010693 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 400668010694 catalytic triad [active] 400668010695 cobaltochelatase subunit; Region: Cob-chelat-sub; TIGR02442 400668010696 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 400668010697 Walker A motif; other site 400668010698 ATP binding site [chemical binding]; other site 400668010699 Walker B motif; other site 400668010700 arginine finger; other site 400668010701 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 400668010702 metal ion-dependent adhesion site (MIDAS); other site 400668010703 PAS fold; Region: PAS_4; pfam08448 400668010704 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 400668010705 putative active site [active] 400668010706 heme pocket [chemical binding]; other site 400668010707 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 400668010708 PAS domain; Region: PAS_9; pfam13426 400668010709 putative active site [active] 400668010710 heme pocket [chemical binding]; other site 400668010711 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 400668010712 dimer interface [polypeptide binding]; other site 400668010713 phosphorylation site [posttranslational modification] 400668010714 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 400668010715 ATP binding site [chemical binding]; other site 400668010716 Mg2+ binding site [ion binding]; other site 400668010717 G-X-G motif; other site 400668010718 Response regulator receiver domain; Region: Response_reg; pfam00072 400668010719 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 400668010720 active site 400668010721 phosphorylation site [posttranslational modification] 400668010722 intermolecular recognition site; other site 400668010723 dimerization interface [polypeptide binding]; other site 400668010724 Response regulator receiver domain; Region: Response_reg; pfam00072 400668010725 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 400668010726 active site 400668010727 phosphorylation site [posttranslational modification] 400668010728 intermolecular recognition site; other site 400668010729 dimerization interface [polypeptide binding]; other site 400668010730 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 400668010731 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668010732 metal binding site [ion binding]; metal-binding site 400668010733 active site 400668010734 I-site; other site 400668010735 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 400668010736 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 400668010737 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 400668010738 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 400668010739 Helix-turn-helix domains; Region: HTH; cl00088 400668010740 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 400668010741 putative dimerization interface [polypeptide binding]; other site 400668010742 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668010743 Helix-turn-helix domains; Region: HTH; cl00088 400668010744 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 400668010745 substrate binding pocket [chemical binding]; other site 400668010746 dimerization interface [polypeptide binding]; other site 400668010747 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668010748 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_1; cd08352 400668010749 putative metal binding site [ion binding]; other site 400668010750 peroxidase; Provisional; Region: PRK15000 400668010751 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 400668010752 dimer interface [polypeptide binding]; other site 400668010753 decamer (pentamer of dimers) interface [polypeptide binding]; other site 400668010754 catalytic triad [active] 400668010755 peroxidatic and resolving cysteines [active] 400668010756 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 400668010757 putative GSH binding site [chemical binding]; other site 400668010758 catalytic residues [active] 400668010759 ornithine carbamoyltransferase; Provisional; Region: PRK00779 400668010760 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 400668010761 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010762 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668010763 Helix-turn-helix domains; Region: HTH; cl00088 400668010764 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 400668010765 putative dimerization interface [polypeptide binding]; other site 400668010766 sensor protein RstB; Provisional; Region: PRK10604 400668010767 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 400668010768 dimer interface [polypeptide binding]; other site 400668010769 phosphorylation site [posttranslational modification] 400668010770 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 400668010771 ATP binding site [chemical binding]; other site 400668010772 Mg2+ binding site [ion binding]; other site 400668010773 G-X-G motif; other site 400668010774 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 400668010775 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 400668010776 active site 400668010777 phosphorylation site [posttranslational modification] 400668010778 intermolecular recognition site; other site 400668010779 dimerization interface [polypeptide binding]; other site 400668010780 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 400668010781 DNA binding site [nucleotide binding] 400668010782 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 400668010783 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 400668010784 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 400668010785 RNA binding surface [nucleotide binding]; other site 400668010786 PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to...; Region: PseudoU_synth_RluB; cd02556 400668010787 probable active site [active] 400668010788 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 400668010789 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 400668010790 Intracellular septation protein A; Region: IspA; cl01098 400668010791 YCII-related domain; Region: YCII; cl00999 400668010792 Rdx family; Region: Rdx; cl01407 400668010793 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 400668010794 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 400668010795 substrate binding site [chemical binding]; other site 400668010796 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668010797 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 400668010798 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668010799 serine acetyltransferase; Provisional; Region: cysE; PRK11132 400668010800 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 400668010801 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 400668010802 trimer interface [polypeptide binding]; other site 400668010803 active site 400668010804 substrate binding site [chemical binding]; other site 400668010805 CoA binding site [chemical binding]; other site 400668010806 Uncharacterized protein family (UPF0270); Region: UPF0270; cl01180 400668010807 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 400668010808 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 400668010809 nucleotide binding pocket [chemical binding]; other site 400668010810 K-X-D-G motif; other site 400668010811 catalytic site [active] 400668010812 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 400668010813 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 400668010814 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 400668010815 Dimer interface [polypeptide binding]; other site 400668010816 BRCT sequence motif; other site 400668010817 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 400668010818 FtsZ protein binding site [polypeptide binding]; other site 400668010819 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 400668010820 binding surface 400668010821 TPR repeat; Region: TPR_11; pfam13414 400668010822 TPR motif; other site 400668010823 Cytochrome C biogenesis protein; Region: CcmH; cl01179 400668010824 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 400668010825 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 400668010826 catalytic residues [active] 400668010827 central insert; other site 400668010828 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 400668010829 CcmE; Region: CcmE; cl00994 400668010830 Heme exporter protein D (CcmD); Region: CcmD; cl11475 400668010831 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 400668010832 CcmB protein; Region: CcmB; cl01016 400668010833 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 400668010834 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010835 Walker A/P-loop; other site 400668010836 ATP binding site [chemical binding]; other site 400668010837 Q-loop/lid; other site 400668010838 ABC transporter signature motif; other site 400668010839 Walker B; other site 400668010840 D-loop; other site 400668010841 H-loop/switch region; other site 400668010842 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 400668010843 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 400668010844 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 400668010845 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 400668010846 putative CheA interaction surface; other site 400668010847 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 400668010848 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 400668010849 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 400668010850 P-loop; other site 400668010851 Magnesium ion binding site [ion binding]; other site 400668010852 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 400668010853 Magnesium ion binding site [ion binding]; other site 400668010854 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 400668010855 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 400668010856 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 400668010857 ligand binding site [chemical binding]; other site 400668010858 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 400668010859 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 400668010860 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 400668010861 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 400668010862 active site 400668010863 phosphorylation site [posttranslational modification] 400668010864 intermolecular recognition site; other site 400668010865 dimerization interface [polypeptide binding]; other site 400668010866 CheB methylesterase; Region: CheB_methylest; pfam01339 400668010867 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 400668010868 putative binding surface; other site 400668010869 active site 400668010870 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 400668010871 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 400668010872 ATP binding site [chemical binding]; other site 400668010873 Mg2+ binding site [ion binding]; other site 400668010874 G-X-G motif; other site 400668010875 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 400668010876 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 400668010877 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 400668010878 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 400668010879 active site 400668010880 phosphorylation site [posttranslational modification] 400668010881 intermolecular recognition site; other site 400668010882 dimerization interface [polypeptide binding]; other site 400668010883 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 400668010884 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668010885 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 400668010886 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 400668010887 DNA binding residues [nucleotide binding] 400668010888 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 400668010889 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010890 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 400668010891 FHIPEP family; Region: FHIPEP; pfam00771 400668010892 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 400668010893 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 400668010894 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 400668010895 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 400668010896 FliP family; Region: FliP; cl00593 400668010897 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 400668010898 flagellar motor switch protein; Validated; Region: fliN; PRK05698 400668010899 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 400668010900 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 400668010901 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 400668010902 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 400668010903 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 400668010904 Response regulator receiver domain; Region: Response_reg; pfam00072 400668010905 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 400668010906 active site 400668010907 phosphorylation site [posttranslational modification] 400668010908 intermolecular recognition site; other site 400668010909 dimerization interface [polypeptide binding]; other site 400668010910 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 400668010911 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 400668010912 anti sigma factor interaction site; other site 400668010913 regulatory phosphorylation site [posttranslational modification]; other site 400668010914 flagellar biosynthesis chaperone; Validated; Region: fliJ; cl09161 400668010915 Flagellar FliJ protein; Region: FliJ; pfam02050 400668010916 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 400668010917 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 400668010918 Walker A motif/ATP binding site; other site 400668010919 Walker B motif; other site 400668010920 flagellar assembly protein H; Validated; Region: fliH; PRK05687 400668010921 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 400668010922 Flagellar assembly protein FliH; Region: FliH; pfam02108 400668010923 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 400668010924 MgtE intracellular N domain; Region: MgtE_N; cl15244 400668010925 FliG C-terminal domain; Region: FliG_C; pfam01706 400668010926 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 400668010927 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 400668010928 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 400668010929 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 400668010930 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668010931 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 400668010932 active site 400668010933 phosphorylation site [posttranslational modification] 400668010934 intermolecular recognition site; other site 400668010935 dimerization interface [polypeptide binding]; other site 400668010936 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 400668010937 Walker A motif; other site 400668010938 ATP binding site [chemical binding]; other site 400668010939 Walker B motif; other site 400668010940 arginine finger; other site 400668010941 Helix-turn-helix domains; Region: HTH; cl00088 400668010942 sensory histidine kinase AtoS; Provisional; Region: PRK11360 400668010943 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 400668010944 dimer interface [polypeptide binding]; other site 400668010945 phosphorylation site [posttranslational modification] 400668010946 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 400668010947 ATP binding site [chemical binding]; other site 400668010948 G-X-G motif; other site 400668010949 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 400668010950 Helix-turn-helix domains; Region: HTH; cl00088 400668010951 AAA domain; Region: AAA_26; pfam13500 400668010952 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010953 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668010954 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 400668010955 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 400668010956 S-adenosylmethionine binding site [chemical binding]; other site 400668010957 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 400668010958 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 400668010959 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 400668010960 substrate-cofactor binding pocket; other site 400668010961 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668010962 catalytic residue [active] 400668010963 biotin synthase; Provisional; Region: PRK15108 400668010964 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 400668010965 FeS/SAM binding site; other site 400668010966 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 400668010967 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 400668010968 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668010969 active site 400668010970 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 400668010971 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 400668010972 inhibitor-cofactor binding pocket; inhibition site 400668010973 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668010974 catalytic residue [active] 400668010975 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 400668010976 PAS fold; Region: PAS_3; pfam08447 400668010977 putative active site [active] 400668010978 heme pocket [chemical binding]; other site 400668010979 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668010980 dimer interface [polypeptide binding]; other site 400668010981 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 400668010982 putative CheW interface [polypeptide binding]; other site 400668010983 replicative DNA helicase; Provisional; Region: PRK05748 400668010984 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 400668010985 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 400668010986 Walker A motif; other site 400668010987 ATP binding site [chemical binding]; other site 400668010988 Walker B motif; other site 400668010989 DNA binding loops [nucleotide binding] 400668010990 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 400668010991 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 400668010992 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 400668010993 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 400668010994 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 400668010995 MltA-interacting protein MipA; Region: MipA; cl01504 400668010996 Predicted permeases [General function prediction only]; Region: RarD; COG2962 400668010997 EamA-like transporter family; Region: EamA; cl01037 400668010998 EamA-like transporter family; Region: EamA; cl01037 400668010999 EamA-like transporter family; Region: EamA; cl01037 400668011000 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 400668011001 EamA-like transporter family; Region: EamA; cl01037 400668011002 EamA-like transporter family; Region: EamA; cl01037 400668011003 ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]; Region: ThiQ; COG3840 400668011004 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011005 Walker A/P-loop; other site 400668011006 ATP binding site [chemical binding]; other site 400668011007 Q-loop/lid; other site 400668011008 ABC transporter signature motif; other site 400668011009 Walker B; other site 400668011010 D-loop; other site 400668011011 H-loop/switch region; other site 400668011012 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 400668011013 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 400668011014 dimer interface [polypeptide binding]; other site 400668011015 conserved gate region; other site 400668011016 putative PBP binding loops; other site 400668011017 ABC-ATPase subunit interface; other site 400668011018 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 400668011019 dimer interface [polypeptide binding]; other site 400668011020 conserved gate region; other site 400668011021 putative PBP binding loops; other site 400668011022 ABC-ATPase subunit interface; other site 400668011023 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 400668011024 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 400668011025 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 400668011026 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 400668011027 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 400668011028 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668011029 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 400668011030 Walker A/P-loop; other site 400668011031 ATP binding site [chemical binding]; other site 400668011032 Q-loop/lid; other site 400668011033 ABC transporter signature motif; other site 400668011034 Walker B; other site 400668011035 D-loop; other site 400668011036 H-loop/switch region; other site 400668011037 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 400668011038 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 400668011039 putative ribose interaction site [chemical binding]; other site 400668011040 putative ADP binding site [chemical binding]; other site 400668011041 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668011042 active site 400668011043 nucleotide binding site [chemical binding]; other site 400668011044 HIGH motif; other site 400668011045 KMSKS motif; other site 400668011046 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 400668011047 N-acyl-D-glucosamine 2-epimerase [Carbohydrate transport and metabolism]; Region: COG2942 400668011048 dimerization interface [polypeptide binding]; other site 400668011049 putative active cleft [active] 400668011050 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 400668011051 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 400668011052 NADP binding site [chemical binding]; other site 400668011053 homopentamer interface [polypeptide binding]; other site 400668011054 substrate binding site [chemical binding]; other site 400668011055 active site 400668011056 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 400668011057 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 400668011058 putative active site [active] 400668011059 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 400668011060 ADP-heptose:LPS heptosyltransferase II; Provisional; Region: PRK10916; cl15782 400668011061 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 400668011062 putative metal binding site; other site 400668011063 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 400668011064 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 400668011065 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]; Region: COG3083 400668011066 Sulfatase; Region: Sulfatase; cl10460 400668011067 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 400668011068 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011069 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 400668011070 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011071 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 400668011072 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 400668011073 active site residue [active] 400668011074 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 400668011075 active site residue [active] 400668011076 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 400668011077 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 400668011078 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668011079 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 400668011080 MatE; Region: MatE; cl10513 400668011081 MatE; Region: MatE; cl10513 400668011082 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 400668011083 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 400668011084 Walker A motif; other site 400668011085 ATP binding site [chemical binding]; other site 400668011086 Walker B motif; other site 400668011087 arginine finger; other site 400668011088 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 400668011089 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668011090 active site 400668011091 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 400668011092 Integrase core domain; Region: rve; cl01316 400668011093 Integrase core domain; Region: rve_3; cl15866 400668011094 LysE type translocator; Region: LysE; cl00565 400668011095 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 400668011096 Helix-turn-helix domains; Region: HTH; cl00088 400668011097 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 400668011098 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668011099 metal binding site [ion binding]; metal-binding site 400668011100 active site 400668011101 I-site; other site 400668011102 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 400668011103 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 400668011104 C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases; Region: GST_C_Omega_like; cd03190 400668011105 putative dimer interface [polypeptide binding]; other site 400668011106 N-terminal domain interface [polypeptide binding]; other site 400668011107 putative substrate binding pocket (H-site) [chemical binding]; other site 400668011108 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 400668011109 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 400668011110 'elongating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type I and II and polyketide synthases.They are characterized by the utlization of acyl carrier protein (ACP) thioesters as...; Region: elong_cond_enzymes; cd00828 400668011111 active site 400668011112 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668011113 Helix-turn-helix domains; Region: HTH; cl00088 400668011114 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 400668011115 putative effector binding pocket; other site 400668011116 dimerization interface [polypeptide binding]; other site 400668011117 YceI-like domain; Region: YceI; cl01001 400668011118 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011119 active site 400668011120 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 400668011121 active site 400668011122 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 400668011123 active site 400668011124 substrate-binding site [chemical binding]; other site 400668011125 metal-binding site [ion binding] 400668011126 ATP binding site [chemical binding]; other site 400668011127 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011128 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 400668011129 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 400668011130 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 400668011131 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 400668011132 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 400668011133 active site 400668011134 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668011135 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011136 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668011137 hypothetical protein; Provisional; Region: PRK11239 400668011138 Protein of unknown function, DUF480; Region: DUF480; cl01209 400668011139 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 400668011140 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; cl01132 400668011141 Protein of unknown function (DUF419); Region: DUF419; cl15265 400668011142 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 400668011143 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 400668011144 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011145 homodimer interface [polypeptide binding]; other site 400668011146 catalytic residue [active] 400668011147 transcriptional regulator BetI; Validated; Region: PRK00767 400668011148 Helix-turn-helix domains; Region: HTH; cl00088 400668011149 Bacterial transcriptional repressor; Region: TetR_C_6; cl07106 400668011150 NMT1-like family; Region: NMT1_2; cl15260 400668011151 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 400668011152 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 400668011153 dimer interface [polypeptide binding]; other site 400668011154 conserved gate region; other site 400668011155 putative PBP binding loops; other site 400668011156 ABC-ATPase subunit interface; other site 400668011157 choline ABC transporter, ATP-binding protein; Region: ABC_choXWV_ATP; TIGR03415 400668011158 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011159 Walker A/P-loop; other site 400668011160 ATP binding site [chemical binding]; other site 400668011161 Q-loop/lid; other site 400668011162 ABC transporter signature motif; other site 400668011163 Walker B; other site 400668011164 D-loop; other site 400668011165 H-loop/switch region; other site 400668011166 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 400668011167 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 400668011168 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 400668011169 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011170 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 400668011171 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 400668011172 catalytic triad [active] 400668011173 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668011174 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 400668011175 dimer interface [polypeptide binding]; other site 400668011176 conserved gate region; other site 400668011177 putative PBP binding loops; other site 400668011178 ABC-ATPase subunit interface; other site 400668011179 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668011180 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 400668011181 dimer interface [polypeptide binding]; other site 400668011182 conserved gate region; other site 400668011183 putative PBP binding loops; other site 400668011184 ABC-ATPase subunit interface; other site 400668011185 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 400668011186 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011187 Walker A/P-loop; other site 400668011188 ATP binding site [chemical binding]; other site 400668011189 Q-loop/lid; other site 400668011190 ABC transporter signature motif; other site 400668011191 Walker B; other site 400668011192 D-loop; other site 400668011193 H-loop/switch region; other site 400668011194 TOBE domain; Region: TOBE_2; cl01440 400668011195 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 400668011196 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 400668011197 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 400668011198 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 400668011199 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 400668011200 DNA binding residues [nucleotide binding] 400668011201 dimerization interface [polypeptide binding]; other site 400668011202 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011203 FAD dependent oxidoreductase; Region: DAO; pfam01266 400668011204 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 400668011205 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 400668011206 NAD(P) binding site [chemical binding]; other site 400668011207 catalytic residues [active] 400668011208 putative MFS family transporter protein; Provisional; Region: PRK03633 400668011209 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 400668011210 putative substrate translocation pore; other site 400668011211 LysE type translocator; Region: LysE; cl00565 400668011212 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 400668011213 Helix-turn-helix domains; Region: HTH; cl00088 400668011214 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 400668011215 dimerization interface [polypeptide binding]; other site 400668011216 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 400668011217 active site 400668011218 tetramer interface; other site 400668011219 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 400668011220 TM-ABC transporter signature motif; other site 400668011221 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 400668011222 TM-ABC transporter signature motif; other site 400668011223 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 400668011224 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 400668011225 Walker A/P-loop; other site 400668011226 ATP binding site [chemical binding]; other site 400668011227 Q-loop/lid; other site 400668011228 ABC transporter signature motif; other site 400668011229 Walker B; other site 400668011230 D-loop; other site 400668011231 H-loop/switch region; other site 400668011232 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 400668011233 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 400668011234 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 400668011235 putative ligand binding site [chemical binding]; other site 400668011236 Membrane transport protein; Region: Mem_trans; cl09117 400668011237 Helix-turn-helix domains; Region: HTH; cl00088 400668011238 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 400668011239 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 400668011240 putative dimerization interface [polypeptide binding]; other site 400668011241 Cupin domain; Region: Cupin_2; cl09118 400668011242 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 400668011243 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 400668011244 FAD binding pocket [chemical binding]; other site 400668011245 FAD binding motif [chemical binding]; other site 400668011246 phosphate binding motif [ion binding]; other site 400668011247 NAD binding pocket [chemical binding]; other site 400668011248 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I-E; cd09648 400668011249 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-E; cd09719 400668011250 KilA-N domain; Region: KilA-N; pfam04383 400668011251 CRISPR/Cas system-associated RAMP superfamily protein Cas6e; Region: Cas6_I-E; cd09727 400668011252 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 400668011253 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-E; cd09756 400668011254 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-E; cl09608 400668011255 CRISPR/Cas system-associated protein Cse2; Region: Cse2_I-E; cd09731 400668011256 CRISPR/Cas system-associated protein Cse1; Region: Cse1_I-E; cd09729 400668011257 helicase Cas3; Provisional; Region: PRK09694 400668011258 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 400668011259 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011260 Predicted transcriptional regulator [Transcription]; Region: COG2378 400668011261 WYL domain; Region: WYL; cl14852 400668011262 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011263 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 400668011264 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 400668011265 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011266 homodimer interface [polypeptide binding]; other site 400668011267 catalytic residue [active] 400668011268 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 400668011269 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 400668011270 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 400668011271 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 400668011272 anchoring element; other site 400668011273 dimer interface [polypeptide binding]; other site 400668011274 ATP binding site [chemical binding]; other site 400668011275 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 400668011276 active site 400668011277 metal binding site [ion binding]; metal-binding site 400668011278 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 400668011279 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 400668011280 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 400668011281 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 400668011282 putative acyl-acceptor binding pocket; other site 400668011283 ADP-ribose pyrophosphatase NudF; Provisional; Region: nudF; PRK10729 400668011284 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 400668011285 dimer interface [polypeptide binding]; other site 400668011286 ADP-ribose binding site [chemical binding]; other site 400668011287 active site 400668011288 nudix motif; other site 400668011289 metal binding site [ion binding]; metal-binding site 400668011290 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 400668011291 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 400668011292 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 400668011293 NAD(P) binding site [chemical binding]; other site 400668011294 homodimer interface [polypeptide binding]; other site 400668011295 substrate binding site [chemical binding]; other site 400668011296 active site 400668011297 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 400668011298 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 400668011299 inhibitor-cofactor binding pocket; inhibition site 400668011300 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011301 catalytic residue [active] 400668011302 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 400668011303 ligand binding site; other site 400668011304 tetramer interface; other site 400668011305 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 400668011306 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 400668011307 pseudaminic acid synthase; Region: PseI; TIGR03586 400668011308 NeuB family; Region: NeuB; cl00496 400668011309 SAF domain; Region: SAF; cl00555 400668011310 Thiamin pyrophosphokinase, catalytic domain; Region: TPK_catalytic; cl09135 400668011311 Flagellar protein FliS; Region: FliS; cl00654 400668011312 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 400668011313 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 400668011314 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 400668011315 FlaG protein; Region: FlaG; cl00591 400668011316 flagellin; Provisional; Region: PRK12802 400668011317 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 400668011318 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 400668011319 flagellin; Provisional; Region: PRK12802 400668011320 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 400668011321 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 400668011322 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 400668011323 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 400668011324 Zn2+ binding site [ion binding]; other site 400668011325 Mg2+ binding site [ion binding]; other site 400668011326 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 400668011327 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 400668011328 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 400668011329 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 400668011330 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 400668011331 Rod binding protein; Region: Rod-binding; cl01626 400668011332 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 400668011333 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 400668011334 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 400668011335 Flagellar L-ring protein; Region: FlgH; cl00905 400668011336 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 400668011337 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 400668011338 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 400668011339 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 400668011340 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 400668011341 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 400668011342 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 400668011343 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 400668011344 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 400668011345 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 400668011346 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 400668011347 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 400668011348 FlgD Ig-like domain; Region: FlgD_ig; cl15790 400668011349 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 400668011350 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 400668011351 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 400668011352 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 400668011353 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 400668011354 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 400668011355 catalytic residues [active] 400668011356 flavin mononucleotide phosphatase; Provisional; Region: PRK10748 400668011357 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 400668011358 motif II; other site 400668011359 GAF domain; Region: GAF; cl15785 400668011360 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 400668011361 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 400668011362 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 400668011363 diaminopimelate decarboxylase; Region: lysA; TIGR01048 400668011364 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 400668011365 active site 400668011366 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668011367 substrate binding site [chemical binding]; other site 400668011368 catalytic residues [active] 400668011369 dimer interface [polypeptide binding]; other site 400668011370 argininosuccinate lyase; Provisional; Region: PRK00855 400668011371 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 400668011372 active sites [active] 400668011373 tetramer interface [polypeptide binding]; other site 400668011374 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 400668011375 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 400668011376 domain interfaces; other site 400668011377 active site 400668011378 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 400668011379 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 400668011380 active site 400668011381 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 400668011382 HemX; Region: HemX; pfam04375 400668011383 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 400668011384 HemY protein N-terminus; Region: HemY_N; pfam07219 400668011385 PAS domain; Region: PAS_9; pfam13426 400668011386 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 400668011387 putative active site [active] 400668011388 heme pocket [chemical binding]; other site 400668011389 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668011390 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668011391 dimer interface [polypeptide binding]; other site 400668011392 putative CheW interface [polypeptide binding]; other site 400668011393 Protein of unknown function (DUF328); Region: DUF328; cl01143 400668011394 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 400668011395 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 400668011396 S-adenosylmethionine binding site [chemical binding]; other site 400668011397 peptide chain release factor 1; Validated; Region: prfA; PRK00591 400668011398 RF-1 domain; Region: RF-1; cl02875 400668011399 RF-1 domain; Region: RF-1; cl02875 400668011400 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 400668011401 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 400668011402 tRNA; other site 400668011403 putative tRNA binding site [nucleotide binding]; other site 400668011404 putative NADP binding site [chemical binding]; other site 400668011405 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 400668011406 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 400668011407 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 400668011408 binding surface 400668011409 TPR motif; other site 400668011410 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 400668011411 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 400668011412 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 400668011413 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 400668011414 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 400668011415 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 400668011416 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668011417 active site 400668011418 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 400668011419 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 400668011420 5S rRNA interface [nucleotide binding]; other site 400668011421 CTC domain interface [polypeptide binding]; other site 400668011422 L16 interface [polypeptide binding]; other site 400668011423 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 400668011424 putative active site [active] 400668011425 catalytic residue [active] 400668011426 GTP-binding protein YchF; Reviewed; Region: PRK09601 400668011427 YchF GTPase; Region: YchF; cd01900 400668011428 G1 box; other site 400668011429 GTP/Mg2+ binding site [chemical binding]; other site 400668011430 Switch I region; other site 400668011431 G2 box; other site 400668011432 Switch II region; other site 400668011433 G3 box; other site 400668011434 G4 box; other site 400668011435 G5 box; other site 400668011436 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 400668011437 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 400668011438 Clp amino terminal domain; Region: Clp_N; pfam02861 400668011439 Clp amino terminal domain; Region: Clp_N; pfam02861 400668011440 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 400668011441 Walker A motif; other site 400668011442 ATP binding site [chemical binding]; other site 400668011443 Walker B motif; other site 400668011444 arginine finger; other site 400668011445 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 400668011446 Walker A motif; other site 400668011447 ATP binding site [chemical binding]; other site 400668011448 Walker B motif; other site 400668011449 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 400668011450 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 400668011451 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 400668011452 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 400668011453 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 400668011454 RNA binding surface [nucleotide binding]; other site 400668011455 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 400668011456 active site 400668011457 Outer membrane lipoprotein; Region: YfiO; pfam13525 400668011458 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 400668011459 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 400668011460 putative N-terminal domain interface [polypeptide binding]; other site 400668011461 putative dimer interface [polypeptide binding]; other site 400668011462 putative substrate binding pocket (H-site) [chemical binding]; other site 400668011463 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 400668011464 DNA-binding site [nucleotide binding]; DNA binding site 400668011465 RNA-binding motif; other site 400668011466 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 400668011467 DTW domain; Region: DTW; cl01221 400668011468 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668011469 Cupin domain; Region: Cupin_2; cl09118 400668011470 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 400668011471 trimer interface [polypeptide binding]; other site 400668011472 eyelet of channel; other site 400668011473 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; cl01201 400668011474 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 400668011475 DNA-binding site [nucleotide binding]; DNA binding site 400668011476 RNA-binding motif; other site 400668011477 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 400668011478 oxaloacetate decarboxylase; Provisional; Region: PRK14040 400668011479 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 400668011480 active site 400668011481 catalytic residues [active] 400668011482 metal binding site [ion binding]; metal-binding site 400668011483 homodimer binding site [polypeptide binding]; other site 400668011484 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 400668011485 carboxyltransferase (CT) interaction site; other site 400668011486 biotinylation site [posttranslational modification]; other site 400668011487 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 400668011488 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 400668011489 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 400668011490 FMN binding site [chemical binding]; other site 400668011491 active site 400668011492 catalytic residues [active] 400668011493 substrate binding site [chemical binding]; other site 400668011494 Global regulator protein family; Region: CsrA; cl00670 400668011495 aspartate kinase; Reviewed; Region: PRK06635 400668011496 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 400668011497 putative nucleotide binding site [chemical binding]; other site 400668011498 putative catalytic residues [active] 400668011499 putative Mg ion binding site [ion binding]; other site 400668011500 putative aspartate binding site [chemical binding]; other site 400668011501 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 400668011502 putative allosteric regulatory site; other site 400668011503 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 400668011504 putative allosteric regulatory residue; other site 400668011505 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 400668011506 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 400668011507 motif 1; other site 400668011508 active site 400668011509 motif 2; other site 400668011510 motif 3; other site 400668011511 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 400668011512 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 400668011513 DHHA1 domain; Region: DHHA1; pfam02272 400668011514 alanine racemase; Reviewed; Region: alr; PRK00053 400668011515 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 400668011516 active site 400668011517 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 400668011518 substrate binding site [chemical binding]; other site 400668011519 catalytic residues [active] 400668011520 dimer interface [polypeptide binding]; other site 400668011521 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 400668011522 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011523 RecX family; Region: RecX; cl00936 400668011524 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; cl00250 400668011525 30S subunit binding site; other site 400668011526 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 400668011527 Helix-turn-helix domains; Region: HTH; cl00088 400668011528 The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold; Region: PBP2_NhaR; cd08429 400668011529 putative dimerization interface [polypeptide binding]; other site 400668011530 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 400668011531 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668011532 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 400668011533 Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins...; Region: FhuD; cd01146 400668011534 siderophore binding site; other site 400668011535 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 400668011536 ABC-ATPase subunit interface; other site 400668011537 dimer interface [polypeptide binding]; other site 400668011538 putative PBP binding regions; other site 400668011539 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 400668011540 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 400668011541 ABC-ATPase subunit interface; other site 400668011542 dimer interface [polypeptide binding]; other site 400668011543 putative PBP binding regions; other site 400668011544 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 400668011545 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 400668011546 Walker A/P-loop; other site 400668011547 ATP binding site [chemical binding]; other site 400668011548 Q-loop/lid; other site 400668011549 ABC transporter signature motif; other site 400668011550 Walker B; other site 400668011551 D-loop; other site 400668011552 H-loop/switch region; other site 400668011553 ferrichrome receptor precursor protein; Provisional; Region: PRK14050 400668011554 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 400668011555 N-terminal plug; other site 400668011556 ligand-binding site [chemical binding]; other site 400668011557 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 400668011558 active site 400668011559 putative metal dependent hydrolase; Provisional; Region: PRK11598 400668011560 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 400668011561 Sulfatase; Region: Sulfatase; cl10460 400668011562 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 400668011563 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 400668011564 Catalytic domain of Protein Kinases; Region: PKc; cd00180 400668011565 active site 400668011566 ATP binding site [chemical binding]; other site 400668011567 substrate binding site [chemical binding]; other site 400668011568 activation loop (A-loop); other site 400668011569 RNA polymerase sigma factor, TIGR02999 family; Region: Sig-70_X6 400668011570 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 400668011571 putative active site [active] 400668011572 putative NTP binding site [chemical binding]; other site 400668011573 putative nucleic acid binding site [nucleotide binding]; other site 400668011574 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011575 G4 box; other site 400668011576 G5 box; other site 400668011577 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 400668011578 Cytochrome c; Region: Cytochrom_C; cl11414 400668011579 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 400668011580 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011581 Family description; Region: UvrD_C_2; cl15862 400668011582 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 400668011583 Membrane transport protein; Region: Mem_trans; cl09117 400668011584 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 400668011585 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 400668011586 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011587 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 400668011588 Tryptophan-rich protein (DUF2389); Region: DUF2389; cl09726 400668011589 Membrane fusogenic activity; Region: BMFP; cl01115 400668011590 Nitrogen regulatory protein P-II; Region: P-II; cl00412 400668011591 Nitrogen regulatory protein P-II; Region: P-II; smart00938 400668011592 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 400668011593 Predicted amidohydrolase [General function prediction only]; Region: COG0388 400668011594 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 400668011595 putative active site [active] 400668011596 catalytic triad [active] 400668011597 putative dimer interface [polypeptide binding]; other site 400668011598 DNA repair protein RadA; Provisional; Region: PRK11823 400668011599 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 400668011600 Walker A motif/ATP binding site; other site 400668011601 ATP binding site [chemical binding]; other site 400668011602 Walker B motif; other site 400668011603 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 400668011604 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 400668011605 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 400668011606 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 400668011607 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668011608 tetrameric interface [polypeptide binding]; other site 400668011609 NAD binding site [chemical binding]; other site 400668011610 catalytic residues [active] 400668011611 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668011612 Helix-turn-helix domains; Region: HTH; cl00088 400668011613 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 400668011614 dimerization interface [polypeptide binding]; other site 400668011615 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 400668011616 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 400668011617 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 400668011618 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 400668011619 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668011620 Helix-turn-helix domains; Region: HTH; cl00088 400668011621 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 400668011622 substrate binding pocket [chemical binding]; other site 400668011623 dimerization interface [polypeptide binding]; other site 400668011624 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 400668011625 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 400668011626 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 400668011627 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668011628 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 400668011629 NAD(P) binding site [chemical binding]; other site 400668011630 catalytic residues [active] 400668011631 Succinylarginine dihydrolase; Region: AstB; cl01511 400668011632 Domain of unknown function (DUF1904); Region: DUF1904; pfam08921 400668011633 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 400668011634 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 400668011635 active site 400668011636 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 400668011637 homotrimer interface [polypeptide binding]; other site 400668011638 Walker A motif; other site 400668011639 GTP binding site [chemical binding]; other site 400668011640 Walker B motif; other site 400668011641 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 400668011642 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 400668011643 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011644 homodimer interface [polypeptide binding]; other site 400668011645 catalytic residue [active] 400668011646 CobD/Cbib protein; Region: CobD_Cbib; cl00561 400668011647 cobyric acid synthase; Provisional; Region: PRK00784 400668011648 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011649 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011650 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 400668011651 catalytic triad [active] 400668011652 Predicted esterase [General function prediction only]; Region: COG0627 400668011653 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 400668011654 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 400668011655 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 400668011656 substrate binding site [chemical binding]; other site 400668011657 catalytic Zn binding site [ion binding]; other site 400668011658 NAD binding site [chemical binding]; other site 400668011659 structural Zn binding site [ion binding]; other site 400668011660 dimer interface [polypeptide binding]; other site 400668011661 Helix-turn-helix domains; Region: HTH; cl00088 400668011662 LysR family transcriptional regulator; Provisional; Region: PRK14997 400668011663 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 400668011664 dimerization interface [polypeptide binding]; other site 400668011665 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 400668011666 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 400668011667 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668011668 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 400668011669 Coenzyme A binding pocket [chemical binding]; other site 400668011670 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 400668011671 aspartate racemase; Region: asp_race; TIGR00035 400668011672 aspartate ammonia-lyase; Provisional; Region: PRK13353 400668011673 Class II fumarases; Region: Fumarase_classII; cd01362 400668011674 active site 400668011675 tetramer interface [polypeptide binding]; other site 400668011676 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668011677 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 400668011678 Mechanosensitive ion channel; Region: MS_channel; pfam00924 400668011679 YebG protein; Region: YebG; cl01217 400668011680 Protein of unknown function (DUF2805); Region: DUF2805; cl11923 400668011681 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668011682 Helix-turn-helix domains; Region: HTH; cl00088 400668011683 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 400668011684 substrate binding pocket [chemical binding]; other site 400668011685 dimerization interface [polypeptide binding]; other site 400668011686 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668011687 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 400668011688 Walker A/P-loop; other site 400668011689 ATP binding site [chemical binding]; other site 400668011690 Q-loop/lid; other site 400668011691 ABC transporter signature motif; other site 400668011692 Walker B; other site 400668011693 D-loop; other site 400668011694 H-loop/switch region; other site 400668011695 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668011696 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 400668011697 dimer interface [polypeptide binding]; other site 400668011698 conserved gate region; other site 400668011699 putative PBP binding loops; other site 400668011700 ABC-ATPase subunit interface; other site 400668011701 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 400668011702 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668011703 substrate binding pocket [chemical binding]; other site 400668011704 membrane-bound complex binding site; other site 400668011705 hinge residues; other site 400668011706 cystathionine gamma-synthase; Provisional; Region: PRK08249 400668011707 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 400668011708 homodimer interface [polypeptide binding]; other site 400668011709 substrate-cofactor binding pocket; other site 400668011710 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011711 catalytic residue [active] 400668011712 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 400668011713 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011714 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 400668011715 Walker A/P-loop; other site 400668011716 ATP binding site [chemical binding]; other site 400668011717 Q-loop/lid; other site 400668011718 ABC transporter signature motif; other site 400668011719 Walker B; other site 400668011720 D-loop; other site 400668011721 H-loop/switch region; other site 400668011722 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 400668011723 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 400668011724 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 400668011725 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 400668011726 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; cl01353 400668011727 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4307 400668011728 Uncharacterized protein conserved in bacteria (DUF2248); Region: DUF2248; pfam10005 400668011729 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668011730 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668011731 DNA binding site [nucleotide binding] 400668011732 domain linker motif; other site 400668011733 Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Region: PBP1_RegR_EndR_KdgR_like; cd06283 400668011734 putative dimerization interface [polypeptide binding]; other site 400668011735 putative ligand binding site [chemical binding]; other site 400668011736 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668011737 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668011738 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668011739 DctM-like transporters; Region: DctM; pfam06808 400668011740 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668011741 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 400668011742 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 400668011743 substrate binding site [chemical binding]; other site 400668011744 ATP binding site [chemical binding]; other site 400668011745 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional; Region: PRK15409 400668011746 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011747 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 400668011748 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668011749 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668011750 dimer interface [polypeptide binding]; other site 400668011751 putative CheW interface [polypeptide binding]; other site 400668011752 TM2 domain; Region: TM2; cl00984 400668011753 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 400668011754 Catalytic site [active] 400668011755 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668011756 Helix-turn-helix domains; Region: HTH; cl00088 400668011757 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 400668011758 putative effector binding pocket; other site 400668011759 dimerization interface [polypeptide binding]; other site 400668011760 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 400668011761 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 400668011762 phosphate binding site [ion binding]; other site 400668011763 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 400668011764 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668011765 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668011766 Helix-turn-helix domains; Region: HTH; cl00088 400668011767 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 400668011768 dimerization interface [polypeptide binding]; other site 400668011769 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 400668011770 Helix-turn-helix domains; Region: HTH; cl00088 400668011771 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 400668011772 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 400668011773 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011774 Protein of unknown function (DUF1006); Region: DUF1006; cl15826 400668011775 L-asparaginase II; Region: Asparaginase_II; cl01842 400668011776 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 400668011777 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 400668011778 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 400668011779 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 400668011780 active site 400668011781 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 400668011782 Catalytic domain of Protein Kinases; Region: PKc; cd00180 400668011783 active site 400668011784 ATP binding site [chemical binding]; other site 400668011785 substrate binding site [chemical binding]; other site 400668011786 activation loop (A-loop); other site 400668011787 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 400668011788 cyanate hydratase; Validated; Region: PRK02866 400668011789 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 400668011790 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 400668011791 oligomer interface [polypeptide binding]; other site 400668011792 active site 400668011793 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 400668011794 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668011795 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668011796 dimer interface [polypeptide binding]; other site 400668011797 putative CheW interface [polypeptide binding]; other site 400668011798 recombinase A; Provisional; Region: recA; PRK09354 400668011799 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 400668011800 hexamer interface [polypeptide binding]; other site 400668011801 Walker A motif; other site 400668011802 ATP binding site [chemical binding]; other site 400668011803 Walker B motif; other site 400668011804 Competence-damaged protein; Region: CinA; cl00666 400668011805 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 400668011806 MutS domain I; Region: MutS_I; pfam01624 400668011807 MutS domain II; Region: MutS_II; pfam05188 400668011808 MutS family domain IV; Region: MutS_IV; pfam05190 400668011809 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 400668011810 Walker A/P-loop; other site 400668011811 ATP binding site [chemical binding]; other site 400668011812 Q-loop/lid; other site 400668011813 ABC transporter signature motif; other site 400668011814 Walker B; other site 400668011815 D-loop; other site 400668011816 H-loop/switch region; other site 400668011817 Ferredoxin [Energy production and conversion]; Region: COG1146 400668011818 4Fe-4S binding domain; Region: Fer4; cl02805 400668011819 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 400668011820 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 400668011821 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 400668011822 Dehydratase family; Region: ILVD_EDD; cl00340 400668011823 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 400668011824 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 400668011825 PAS fold; Region: PAS_3; pfam08447 400668011826 putative active site [active] 400668011827 heme pocket [chemical binding]; other site 400668011828 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668011829 metal binding site [ion binding]; metal-binding site 400668011830 active site 400668011831 I-site; other site 400668011832 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 400668011833 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 400668011834 folate binding site [chemical binding]; other site 400668011835 NADP+ binding site [chemical binding]; other site 400668011836 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 400668011837 dimerization interface [polypeptide binding]; other site 400668011838 active site 400668011839 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668011840 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 400668011841 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 400668011842 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 400668011843 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 400668011844 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional; Region: PRK11061 400668011845 GAF domain; Region: GAF; cl15785 400668011846 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 400668011847 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 400668011848 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 400668011849 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 400668011850 putative active site [active] 400668011851 Ap4A binding site [chemical binding]; other site 400668011852 nudix motif; other site 400668011853 putative metal binding site [ion binding]; other site 400668011854 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 400668011855 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668011856 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 400668011857 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 400668011858 S-adenosylmethionine binding site [chemical binding]; other site 400668011859 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 400668011860 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 400668011861 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011862 Walker A/P-loop; other site 400668011863 ATP binding site [chemical binding]; other site 400668011864 Q-loop/lid; other site 400668011865 ABC transporter signature motif; other site 400668011866 Walker B; other site 400668011867 D-loop; other site 400668011868 H-loop/switch region; other site 400668011869 TOBE domain; Region: TOBE_2; cl01440 400668011870 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 400668011871 dimer interface [polypeptide binding]; other site 400668011872 conserved gate region; other site 400668011873 putative PBP binding loops; other site 400668011874 ABC-ATPase subunit interface; other site 400668011875 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668011876 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668011877 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 400668011878 HDOD domain; Region: HDOD; pfam08668 400668011879 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011880 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 400668011881 proline aminopeptidase P II; Provisional; Region: PRK10879 400668011882 Aminopeptidase P, N-terminal domain; Region: AMP_N; cl08433 400668011883 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 400668011884 active site 400668011885 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 400668011886 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14192 400668011887 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 400668011888 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 400668011889 homodimer interface [polypeptide binding]; other site 400668011890 NADP binding site [chemical binding]; other site 400668011891 substrate binding site [chemical binding]; other site 400668011892 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 400668011893 DHH family; Region: DHH; pfam01368 400668011894 DHHA1 domain; Region: DHHA1; pfam02272 400668011895 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 400668011896 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 400668011897 putative substrate translocation pore; other site 400668011898 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668011899 metal binding site [ion binding]; metal-binding site 400668011900 active site 400668011901 I-site; other site 400668011902 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 400668011903 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 400668011904 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 400668011905 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 400668011906 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011907 catalytic residue [active] 400668011908 homoserine dehydrogenase; Provisional; Region: PRK06349 400668011909 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011910 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 400668011911 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 400668011912 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 400668011913 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 400668011914 dimerization domain [polypeptide binding]; other site 400668011915 dimer interface [polypeptide binding]; other site 400668011916 catalytic residues [active] 400668011917 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 400668011918 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 400668011919 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 400668011920 RimM N-terminal domain; Region: RimM; pfam01782 400668011921 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 400668011922 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 400668011923 signal recognition particle protein; Provisional; Region: PRK10867 400668011924 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 400668011925 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 400668011926 P loop; other site 400668011927 GTP binding site [chemical binding]; other site 400668011928 Signal peptide binding domain; Region: SRP_SPB; pfam02978 400668011929 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 400668011930 Domain of unknown function DUF21; Region: DUF21; pfam01595 400668011931 hypothetical protein; Provisional; Region: PRK11573 400668011932 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 400668011933 Transporter associated domain; Region: CorC_HlyC; cl08393 400668011934 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 400668011935 nudix motif; other site 400668011936 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 400668011937 Protein of unknown function DUF72; Region: DUF72; cl00777 400668011938 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 400668011939 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 400668011940 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 400668011941 Mechanosensitive ion channel; Region: MS_channel; pfam00924 400668011942 Protein of unknown function (DUF2489); Region: DUF2489; pfam10675 400668011943 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 400668011944 active site 400668011945 dimerization interface [polypeptide binding]; other site 400668011946 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 400668011947 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 400668011948 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668011949 active site 400668011950 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 400668011951 active site 400668011952 DNA polymerase IV; Validated; Region: PRK02406 400668011953 DNA binding site [nucleotide binding] 400668011954 LPP20 lipoprotein; Region: LPP20; cl15824 400668011955 Protein of unknown function (DUF904); Region: DUF904; cl11531 400668011956 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 400668011957 putative active site [active] 400668011958 putative metal binding site [ion binding]; other site 400668011959 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 400668011960 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 400668011961 substrate-cofactor binding pocket; other site 400668011962 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668011963 catalytic residue [active] 400668011964 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 400668011965 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011966 NAD(P) binding site [chemical binding]; other site 400668011967 NADH pyrophosphatase; Reviewed; Region: nudC; PRK00241 400668011968 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 400668011969 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 400668011970 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 400668011971 putative NADH binding site [chemical binding]; other site 400668011972 putative active site [active] 400668011973 nudix motif; other site 400668011974 putative metal binding site [ion binding]; other site 400668011975 Glutaminase; Region: Glutaminase; cl00907 400668011976 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 400668011977 Domain of unknown function (DUF3412); Region: DUF3412; pfam11892 400668011978 Predicted ATPase [General function prediction only]; Region: COG1485 400668011979 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668011980 Helix-turn-helix domains; Region: HTH; cl00088 400668011981 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 400668011982 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 400668011983 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 400668011984 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 400668011985 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 400668011986 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 400668011987 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 400668011988 active site 400668011989 catalytic residues [active] 400668011990 metal binding site [ion binding]; metal-binding site 400668011991 DmpG-like communication domain; Region: DmpG_comm; pfam07836 400668011992 acetaldehyde dehydrogenase; Validated; Region: PRK08300 400668011993 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668011994 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 400668011995 Dehydratase family; Region: ILVD_EDD; cl00340 400668011996 DctM-like transporters; Region: DctM; pfam06808 400668011997 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668011998 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668011999 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668012000 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668012001 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 400668012002 Helix-turn-helix domains; Region: HTH; cl00088 400668012003 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 400668012004 dimerization interface [polypeptide binding]; other site 400668012005 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668012006 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 400668012007 putative substrate translocation pore; other site 400668012008 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 400668012009 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 400668012010 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 400668012011 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 400668012012 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 400668012013 Secretin and TonB N terminus short domain; Region: STN; cl06624 400668012014 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 400668012015 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 400668012016 Protein of unknown function (DUF3374); Region: DUF3374; cl11904 400668012017 fec operon regulator FecR; Reviewed; Region: PRK09774 400668012018 FecR protein; Region: FecR; pfam04773 400668012019 RNA polymerase sigma factor; Provisional; Region: PRK12528 400668012020 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668012021 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 400668012022 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 400668012023 putative C-terminal domain interface [polypeptide binding]; other site 400668012024 putative GSH binding site (G-site) [chemical binding]; other site 400668012025 putative dimer interface [polypeptide binding]; other site 400668012026 C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases; Region: GST_C_GTT1_like; cd03189 400668012027 putative N-terminal domain interface [polypeptide binding]; other site 400668012028 putative dimer interface [polypeptide binding]; other site 400668012029 putative substrate binding pocket (H-site) [chemical binding]; other site 400668012030 Cupin domain; Region: Cupin_2; cl09118 400668012031 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668012032 enterobactin receptor protein; Provisional; Region: PRK13483 400668012033 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 400668012034 N-terminal plug; other site 400668012035 ligand-binding site [chemical binding]; other site 400668012036 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 400668012037 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 400668012038 metal binding site [ion binding]; metal-binding site 400668012039 dimer interface [polypeptide binding]; other site 400668012040 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_2; cd05679 400668012041 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 400668012042 metal binding site [ion binding]; metal-binding site 400668012043 putative dimer interface [polypeptide binding]; other site 400668012044 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 400668012045 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 400668012046 Walker A/P-loop; other site 400668012047 ATP binding site [chemical binding]; other site 400668012048 Q-loop/lid; other site 400668012049 ABC transporter signature motif; other site 400668012050 Walker B; other site 400668012051 D-loop; other site 400668012052 H-loop/switch region; other site 400668012053 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668012054 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 400668012055 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 400668012056 Walker A/P-loop; other site 400668012057 ATP binding site [chemical binding]; other site 400668012058 Q-loop/lid; other site 400668012059 ABC transporter signature motif; other site 400668012060 Walker B; other site 400668012061 D-loop; other site 400668012062 H-loop/switch region; other site 400668012063 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668012064 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 400668012065 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 400668012066 dimer interface [polypeptide binding]; other site 400668012067 conserved gate region; other site 400668012068 putative PBP binding loops; other site 400668012069 ABC-ATPase subunit interface; other site 400668012070 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 400668012071 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 400668012072 dimer interface [polypeptide binding]; other site 400668012073 conserved gate region; other site 400668012074 putative PBP binding loops; other site 400668012075 ABC-ATPase subunit interface; other site 400668012076 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_10; cd08515 400668012077 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 400668012078 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668012079 Helix-turn-helix domains; Region: HTH; cl00088 400668012080 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 400668012081 dimerization interface [polypeptide binding]; other site 400668012082 D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive...; Region: D-Ser-dehyd; cd06447 400668012083 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 400668012084 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668012085 catalytic residue [active] 400668012086 amidase; Provisional; Region: PRK07486 400668012087 Amidase; Region: Amidase; cl11426 400668012088 Thermostable hemolysin; Region: T_hemolysin; pfam12261 400668012089 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 400668012090 AMP-binding enzyme; Region: AMP-binding; cl15778 400668012091 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 400668012092 heme binding pocket [chemical binding]; other site 400668012093 heme ligand [chemical binding]; other site 400668012094 short chain dehydrogenase; Provisional; Region: PRK09072 400668012095 classical (c) SDRs; Region: SDR_c; cd05233 400668012096 NAD(P) binding site [chemical binding]; other site 400668012097 active site 400668012098 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 400668012099 TPR motif; other site 400668012100 binding surface 400668012101 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 400668012102 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 400668012103 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012104 malonyl-CoA synthase; Validated; Region: PRK07514 400668012105 AMP-binding enzyme; Region: AMP-binding; cl15778 400668012106 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 400668012107 DNA alkylation repair enzyme [DNA replication, recombination, and repair]; Region: COG4335 400668012108 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012109 metal binding site [ion binding]; metal-binding site 400668012110 active site 400668012111 I-site; other site 400668012112 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012113 metal binding site [ion binding]; metal-binding site 400668012114 active site 400668012115 I-site; other site 400668012116 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 400668012117 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 400668012118 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 400668012119 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012120 metal binding site [ion binding]; metal-binding site 400668012121 active site 400668012122 I-site; other site 400668012123 putative arabinose transporter; Provisional; Region: PRK03545 400668012124 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 400668012125 putative substrate translocation pore; other site 400668012126 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 400668012127 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 400668012128 dimerization interface [polypeptide binding]; other site 400668012129 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668012130 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012131 dimer interface [polypeptide binding]; other site 400668012132 putative CheW interface [polypeptide binding]; other site 400668012133 PAS fold; Region: PAS_4; pfam08448 400668012134 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 400668012135 putative active site [active] 400668012136 heme pocket [chemical binding]; other site 400668012137 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012138 metal binding site [ion binding]; metal-binding site 400668012139 active site 400668012140 I-site; other site 400668012141 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 400668012142 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 400668012143 Helix-turn-helix domains; Region: HTH; cl00088 400668012144 DNA-binding transcriptional regulator IlvY; Provisional; Region: PRK11716 400668012145 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 400668012146 putative dimerization interface [polypeptide binding]; other site 400668012147 ketol-acid reductoisomerase; Validated; Region: PRK05225 400668012148 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012149 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 400668012150 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 400668012151 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 400668012152 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012153 Walker A/P-loop; other site 400668012154 ATP binding site [chemical binding]; other site 400668012155 Q-loop/lid; other site 400668012156 ABC transporter signature motif; other site 400668012157 Walker B; other site 400668012158 D-loop; other site 400668012159 H-loop/switch region; other site 400668012160 ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]; Region: ModF; COG1119 400668012161 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012162 Walker A/P-loop; other site 400668012163 ATP binding site [chemical binding]; other site 400668012164 Q-loop/lid; other site 400668012165 ABC transporter signature motif; other site 400668012166 Walker B; other site 400668012167 D-loop; other site 400668012168 H-loop/switch region; other site 400668012169 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 400668012170 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668012171 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668012172 RloB-like protein; Region: RloB; pfam13707 400668012173 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012174 AAA domain; Region: AAA_21; pfam13304 400668012175 Walker A/P-loop; other site 400668012176 ATP binding site [chemical binding]; other site 400668012177 Q-loop/lid; other site 400668012178 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012179 Q-loop/lid; other site 400668012180 ABC transporter signature motif; other site 400668012181 Walker B; other site 400668012182 D-loop; other site 400668012183 H-loop/switch region; other site 400668012184 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 400668012185 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 400668012186 HIGH motif; other site 400668012187 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 400668012188 active site 400668012189 KMSKS motif; other site 400668012190 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 400668012191 tRNA binding surface [nucleotide binding]; other site 400668012192 anticodon binding site; other site 400668012193 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668012194 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668012195 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668012196 NMT1-like family; Region: NMT1_2; cl15260 400668012197 tricarballylate utilization protein B; Provisional; Region: PRK15033 400668012198 tricarballylate dehydrogenase; Validated; Region: PRK08274 400668012199 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668012200 Helix-turn-helix domains; Region: HTH; cl00088 400668012201 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 400668012202 putative dimerization interface [polypeptide binding]; other site 400668012203 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 400668012204 Protein of unknown function (DUF3184); Region: DUF3184; pfam11380 400668012205 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668012206 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 400668012207 substrate binding pocket [chemical binding]; other site 400668012208 membrane-bound complex binding site; other site 400668012209 hinge residues; other site 400668012210 biofilm formation regulator HmsP; Provisional; Region: PRK11829 400668012211 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012212 metal binding site [ion binding]; metal-binding site 400668012213 active site 400668012214 I-site; other site 400668012215 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012216 metal binding site [ion binding]; metal-binding site 400668012217 active site 400668012218 I-site; other site 400668012219 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 400668012220 GTPase RsgA; Reviewed; Region: PRK01889 400668012221 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 400668012222 GTPase/Zn-binding domain interface [polypeptide binding]; other site 400668012223 GTP/Mg2+ binding site [chemical binding]; other site 400668012224 G4 box; other site 400668012225 G5 box; other site 400668012226 G1 box; other site 400668012227 Switch I region; other site 400668012228 G2 box; other site 400668012229 G3 box; other site 400668012230 Switch II region; other site 400668012231 Short C-terminal domain; Region: SHOCT; cl01373 400668012232 putative S-transferase; Provisional; Region: PRK11752 400668012233 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 400668012234 C-terminal domain interface [polypeptide binding]; other site 400668012235 GSH binding site (G-site) [chemical binding]; other site 400668012236 dimer interface [polypeptide binding]; other site 400668012237 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 400668012238 dimer interface [polypeptide binding]; other site 400668012239 N-terminal domain interface [polypeptide binding]; other site 400668012240 active site 400668012241 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 400668012242 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 400668012243 FAD binding pocket [chemical binding]; other site 400668012244 FAD binding motif [chemical binding]; other site 400668012245 phosphate binding motif [ion binding]; other site 400668012246 beta-alpha-beta structure motif; other site 400668012247 NAD binding pocket [chemical binding]; other site 400668012248 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 400668012249 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 400668012250 phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex; Provisional; Region: PRK10251 400668012251 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 400668012252 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 400668012253 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 400668012254 putative acyl-acceptor binding pocket; other site 400668012255 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668012256 Phosphopantetheine attachment site; Region: PP-binding; cl09936 400668012257 Predicted membrane protein [Function unknown]; Region: COG4648 400668012258 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 400668012259 AMP-binding enzyme; Region: AMP-binding; cl15778 400668012260 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 400668012261 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 400668012262 active site 400668012263 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 400668012264 Predicted exporter [General function prediction only]; Region: COG4258 400668012265 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 400668012266 Protein of unknown function (DUF3261); Region: DUF3261; pfam11659 400668012267 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 400668012268 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 400668012269 dimer interface [polypeptide binding]; other site 400668012270 active site 400668012271 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 400668012272 putative active site 1 [active] 400668012273 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668012274 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 400668012275 NAD(P) binding site [chemical binding]; other site 400668012276 homotetramer interface [polypeptide binding]; other site 400668012277 homodimer interface [polypeptide binding]; other site 400668012278 active site 400668012279 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 400668012280 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 400668012281 dimer interface [polypeptide binding]; other site 400668012282 active site 400668012283 This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as...; Region: NfsA_FRP; cd02146 400668012284 dimer interface [polypeptide binding]; other site 400668012285 FMN binding site [chemical binding]; other site 400668012286 NADPH bind site [chemical binding]; other site 400668012287 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 400668012288 catalytic triad [active] 400668012289 dimer interface [polypeptide binding]; other site 400668012290 FAD dependent oxidoreductase; Region: DAO; pfam01266 400668012291 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012292 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 400668012293 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 400668012294 putative dimer interface [polypeptide binding]; other site 400668012295 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668012296 Helix-turn-helix domains; Region: HTH; cl00088 400668012297 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 400668012298 putative effector binding pocket; other site 400668012299 dimerization interface [polypeptide binding]; other site 400668012300 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 400668012301 dimer interface [polypeptide binding]; other site 400668012302 FMN binding site [chemical binding]; other site 400668012303 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012304 metal binding site [ion binding]; metal-binding site 400668012305 active site 400668012306 I-site; other site 400668012307 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 400668012308 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 400668012309 non-specific DNA binding site [nucleotide binding]; other site 400668012310 salt bridge; other site 400668012311 sequence-specific DNA binding site [nucleotide binding]; other site 400668012312 N-formylglutamate amidohydrolase; Region: FGase; cl01522 400668012313 imidazolonepropionase; Validated; Region: PRK09356 400668012314 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 400668012315 active site 400668012316 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 400668012317 active sites [active] 400668012318 tetramer interface [polypeptide binding]; other site 400668012319 urocanate hydratase; Provisional; Region: PRK05414 400668012320 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 400668012321 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_E; cd01313 400668012322 active site 400668012323 HutD; Region: HutD; cl01532 400668012324 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 400668012325 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668012326 DNA-binding site [nucleotide binding]; DNA binding site 400668012327 UTRA domain; Region: UTRA; cl01230 400668012328 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 400668012329 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 400668012330 hydrophobic ligand binding site; other site 400668012331 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 400668012332 proline dipeptidase; Provisional; Region: PRK13607 400668012333 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cl00279 400668012334 active site 400668012335 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668012336 NMT1-like family; Region: NMT1_2; cl15260 400668012337 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668012338 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668012339 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668012340 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 400668012341 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012342 dimer interface [polypeptide binding]; other site 400668012343 putative CheW interface [polypeptide binding]; other site 400668012344 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 400668012345 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cl12060 400668012346 Metal-binding active site; metal-binding site 400668012347 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 400668012348 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 400668012349 dimer interface [polypeptide binding]; other site 400668012350 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 400668012351 active site 400668012352 Fe binding site [ion binding]; other site 400668012353 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 400668012354 Helix-turn-helix domains; Region: HTH; cl00088 400668012355 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 400668012356 dimerization interface [polypeptide binding]; other site 400668012357 Membrane transport protein; Region: Mem_trans; cl09117 400668012358 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 400668012359 trimer interface [polypeptide binding]; other site 400668012360 active site 400668012361 dimer interface [polypeptide binding]; other site 400668012362 Membrane transport protein; Region: Mem_trans; cl09117 400668012363 Transcriptional regulators [Transcription]; Region: FadR; COG2186 400668012364 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668012365 DNA-binding site [nucleotide binding]; DNA binding site 400668012366 FCD domain; Region: FCD; cl11656 400668012367 shikimate 5-dehydrogenase; Reviewed; Region: PRK12549 400668012368 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 400668012369 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 400668012370 shikimate binding site; other site 400668012371 NAD(P) binding site [chemical binding]; other site 400668012372 Subunit B of Class III Extradiol ring-cleavage dioxygenases; Region: Extradiol_Dioxygenase_3B_like; cl00599 400668012373 active site 400668012374 metal binding site [ion binding]; metal-binding site 400668012375 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB); Region: LigA_like_1; cd07925 400668012376 putative dimer interface [polypeptide binding]; other site 400668012377 putative tetramer interface [polypeptide binding]; other site 400668012378 putative active site [active] 400668012379 Helix-turn-helix domains; Region: HTH; cl00088 400668012380 Helix-turn-helix domains; Region: HTH; cl00088 400668012381 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 400668012382 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 400668012383 dimerization interface [polypeptide binding]; other site 400668012384 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 400668012385 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012386 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 400668012387 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 400668012388 active site 400668012389 catalytic tetrad [active] 400668012390 pyruvate carboxylase subunit B; Validated; Region: PRK09282 400668012391 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 400668012392 active site 400668012393 catalytic residues [active] 400668012394 metal binding site [ion binding]; metal-binding site 400668012395 homodimer binding site [polypeptide binding]; other site 400668012396 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 400668012397 carboxyltransferase (CT) interaction site; other site 400668012398 biotinylation site [posttranslational modification]; other site 400668012399 pyruvate carboxylase subunit A; Validated; Region: PRK07178 400668012400 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 400668012401 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668012402 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 400668012403 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668012404 Helix-turn-helix domains; Region: HTH; cl00088 400668012405 The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold; Region: PBP2_CbbR_RubisCO_like; cd08419 400668012406 putative dimerization interface [polypeptide binding]; other site 400668012407 PAS domain; Region: PAS_9; pfam13426 400668012408 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 400668012409 putative active site [active] 400668012410 heme pocket [chemical binding]; other site 400668012411 PAS domain; Region: PAS_9; pfam13426 400668012412 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 400668012413 putative active site [active] 400668012414 heme pocket [chemical binding]; other site 400668012415 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012416 dimer interface [polypeptide binding]; other site 400668012417 putative CheW interface [polypeptide binding]; other site 400668012418 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 400668012419 PAS domain; Region: PAS_9; pfam13426 400668012420 putative active site [active] 400668012421 heme pocket [chemical binding]; other site 400668012422 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 400668012423 PAS domain; Region: PAS_9; pfam13426 400668012424 putative active site [active] 400668012425 heme pocket [chemical binding]; other site 400668012426 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012427 dimer interface [polypeptide binding]; other site 400668012428 putative CheW interface [polypeptide binding]; other site 400668012429 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668012430 Helix-turn-helix domains; Region: HTH; cl00088 400668012431 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 400668012432 dimerization interface [polypeptide binding]; other site 400668012433 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668012434 NMT1-like family; Region: NMT1_2; cl15260 400668012435 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668012436 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668012437 Cysteine dioxygenase type I; Region: CDO_I; cl15835 400668012438 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 400668012439 active site residue [active] 400668012440 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 400668012441 active site residue [active] 400668012442 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 400668012443 active site residue [active] 400668012444 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 400668012445 active site residue [active] 400668012446 cystathionine beta-lyase; Provisional; Region: PRK09028 400668012447 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 400668012448 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668012449 catalytic residue [active] 400668012450 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668012451 high affinity sulphate transporter 1; Region: sulP; TIGR00815 400668012452 Sulfate transporter family; Region: Sulfate_transp; cl15842 400668012453 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 400668012454 Subunit B of Class III Extradiol ring-cleavage dioxygenases; Region: Extradiol_Dioxygenase_3B_like; cl00599 400668012455 active site 400668012456 metal binding site [ion binding]; metal-binding site 400668012457 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB); Region: LigA_like_1; cd07925 400668012458 putative dimer interface [polypeptide binding]; other site 400668012459 putative tetramer interface [polypeptide binding]; other site 400668012460 putative active site [active] 400668012461 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 400668012462 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most...; Region: PDC_hydrolase; cd01311 400668012463 active site 400668012464 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 400668012465 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 400668012466 Demethylmenaquinone methyltransferase; Region: Methyltransf_6; cl00480 400668012467 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 400668012468 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 400668012469 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668012470 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668012471 DctM-like transporters; Region: DctM; pfam06808 400668012472 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668012473 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 400668012474 catalytic triad [active] 400668012475 dimer interface [polypeptide binding]; other site 400668012476 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 400668012477 dimerization interface [polypeptide binding]; other site 400668012478 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668012479 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012480 dimer interface [polypeptide binding]; other site 400668012481 putative CheW interface [polypeptide binding]; other site 400668012482 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 400668012483 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668012484 DNA-binding site [nucleotide binding]; DNA binding site 400668012485 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 400668012486 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668012487 homodimer interface [polypeptide binding]; other site 400668012488 catalytic residue [active] 400668012489 PilZ domain; Region: PilZ; cl01260 400668012490 Protein of unknown function (DUF501); Region: DUF501; cl00652 400668012491 glycerol kinase; Provisional; Region: glpK; PRK00047 400668012492 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 400668012493 N- and C-terminal domain interface [polypeptide binding]; other site 400668012494 active site 400668012495 MgATP binding site [chemical binding]; other site 400668012496 catalytic site [active] 400668012497 metal binding site [ion binding]; metal-binding site 400668012498 glycerol binding site [chemical binding]; other site 400668012499 homotetramer interface [polypeptide binding]; other site 400668012500 homodimer interface [polypeptide binding]; other site 400668012501 FBP binding site [chemical binding]; other site 400668012502 protein IIAGlc interface [polypeptide binding]; other site 400668012503 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 400668012504 Helix-turn-helix domains; Region: HTH; cl00088 400668012505 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 400668012506 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 400668012507 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668012508 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 400668012509 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668012510 Helix-turn-helix domains; Region: HTH; cl00088 400668012511 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 400668012512 dimerization interface [polypeptide binding]; other site 400668012513 substrate binding pocket [chemical binding]; other site 400668012514 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 400668012515 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012516 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 400668012517 Protein of unknown function (DUF3392); Region: DUF3392; pfam11872 400668012518 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 400668012519 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012520 active site 400668012521 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 400668012522 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 400668012523 [2Fe-2S] cluster binding site [ion binding]; other site 400668012524 C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_GbcA-like; cd08884 400668012525 putative alpha subunit interface [polypeptide binding]; other site 400668012526 putative active site [active] 400668012527 putative substrate binding site [chemical binding]; other site 400668012528 Fe binding site [ion binding]; other site 400668012529 chaperone protein DnaJ; Provisional; Region: PRK10767 400668012530 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 400668012531 HSP70 interaction site [polypeptide binding]; other site 400668012532 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 400668012533 substrate binding site [polypeptide binding]; other site 400668012534 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 400668012535 Zn binding sites [ion binding]; other site 400668012536 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 400668012537 dimer interface [polypeptide binding]; other site 400668012538 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 400668012539 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 400668012540 dimer interface [polypeptide binding]; other site 400668012541 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 400668012542 recombination and repair protein; Provisional; Region: PRK10869 400668012543 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 400668012544 Walker A/P-loop; other site 400668012545 ATP binding site [chemical binding]; other site 400668012546 Q-loop/lid; other site 400668012547 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 400668012548 ABC transporter signature motif; other site 400668012549 Walker B; other site 400668012550 D-loop; other site 400668012551 H-loop/switch region; other site 400668012552 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 400668012553 metal binding site 2 [ion binding]; metal-binding site 400668012554 putative DNA binding helix; other site 400668012555 metal binding site 1 [ion binding]; metal-binding site 400668012556 dimer interface [polypeptide binding]; other site 400668012557 structural Zn2+ binding site [ion binding]; other site 400668012558 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 400668012559 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 400668012560 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 400668012561 putative coenzyme Q binding site [chemical binding]; other site 400668012562 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 400668012563 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 400668012564 SmpB-tmRNA interface; other site 400668012565 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 400668012566 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 400668012567 Catalytic site [active] 400668012568 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 400668012569 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 400668012570 Yip1 domain; Region: Yip1; cl12048 400668012571 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012572 dimer interface [polypeptide binding]; other site 400668012573 putative CheW interface [polypeptide binding]; other site 400668012574 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 400668012575 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 400668012576 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 400668012577 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 400668012578 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 400668012579 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 400668012580 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 400668012581 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 400668012582 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 400668012583 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 400668012584 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 400668012585 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 400668012586 PAS domain S-box; Region: sensory_box; TIGR00229 400668012587 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 400668012588 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012589 metal binding site [ion binding]; metal-binding site 400668012590 active site 400668012591 I-site; other site 400668012592 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 400668012593 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 400668012594 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 400668012595 transcription termination factor Rho; Provisional; Region: rho; PRK09376 400668012596 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 400668012597 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 400668012598 RNA binding site [nucleotide binding]; other site 400668012599 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 400668012600 multimer interface [polypeptide binding]; other site 400668012601 Walker A motif; other site 400668012602 ATP binding site [chemical binding]; other site 400668012603 Walker B motif; other site 400668012604 FMN reductase; Validated; Region: fre; PRK08051 400668012605 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 400668012606 FAD binding pocket [chemical binding]; other site 400668012607 FAD binding motif [chemical binding]; other site 400668012608 phosphate binding motif [ion binding]; other site 400668012609 beta-alpha-beta structure motif; other site 400668012610 NAD binding pocket [chemical binding]; other site 400668012611 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012612 Predicted dehydrogenase [General function prediction only]; Region: COG0579 400668012613 FOG: CBS domain [General function prediction only]; Region: COG0517 400668012614 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 400668012615 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 400668012616 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 400668012617 dimerization interface [polypeptide binding]; other site 400668012618 domain crossover interface; other site 400668012619 redox-dependent activation switch; other site 400668012620 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 400668012621 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 400668012622 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 400668012623 ABC transporter; Region: ABC_tran_2; pfam12848 400668012624 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 400668012625 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 400668012626 dimer interface [polypeptide binding]; other site 400668012627 allosteric magnesium binding site [ion binding]; other site 400668012628 active site 400668012629 aspartate-rich active site metal binding site; other site 400668012630 Schiff base residues; other site 400668012631 polyphosphate kinase; Provisional; Region: PRK05443 400668012632 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 400668012633 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 400668012634 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 400668012635 putative domain interface [polypeptide binding]; other site 400668012636 putative active site [active] 400668012637 catalytic site [active] 400668012638 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 400668012639 putative domain interface [polypeptide binding]; other site 400668012640 putative active site [active] 400668012641 catalytic site [active] 400668012642 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668012643 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 400668012644 substrate binding pocket [chemical binding]; other site 400668012645 membrane-bound complex binding site; other site 400668012646 hinge residues; other site 400668012647 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 400668012648 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 400668012649 dimerization interface [polypeptide binding]; other site 400668012650 ATP binding site [chemical binding]; other site 400668012651 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 400668012652 dimerization interface [polypeptide binding]; other site 400668012653 ATP binding site [chemical binding]; other site 400668012654 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 400668012655 putative active site [active] 400668012656 catalytic triad [active] 400668012657 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 400668012658 nucleoside/Zn binding site; other site 400668012659 dimer interface [polypeptide binding]; other site 400668012660 catalytic motif [active] 400668012661 FOG: CBS domain [General function prediction only]; Region: COG0517 400668012662 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_15; cd04803 400668012663 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 400668012664 DNA-binding site [nucleotide binding]; DNA binding site 400668012665 RNA-binding motif; other site 400668012666 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 400668012667 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668012668 active site 400668012669 HIGH motif; other site 400668012670 nucleotide binding site [chemical binding]; other site 400668012671 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 400668012672 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 400668012673 active site 400668012674 KMSKS motif; other site 400668012675 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 400668012676 tRNA binding surface [nucleotide binding]; other site 400668012677 anticodon binding site; other site 400668012678 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 400668012679 multifunctional aminopeptidase A; Provisional; Region: PRK00913 400668012680 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 400668012681 interface (dimer of trimers) [polypeptide binding]; other site 400668012682 Substrate-binding/catalytic site; other site 400668012683 Zn-binding sites [ion binding]; other site 400668012684 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 400668012685 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 400668012686 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 400668012687 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 400668012688 aminotransferase; Validated; Region: PRK07337 400668012689 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 400668012690 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668012691 homodimer interface [polypeptide binding]; other site 400668012692 catalytic residue [active] 400668012693 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 400668012694 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668012695 active site 400668012696 HIGH motif; other site 400668012697 nucleotide binding site [chemical binding]; other site 400668012698 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668012699 active site 400668012700 KMSKS motif; other site 400668012701 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668012702 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 400668012703 active site 400668012704 phosphorylation site [posttranslational modification] 400668012705 dimerization interface [polypeptide binding]; other site 400668012706 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 400668012707 Walker A motif; other site 400668012708 ATP binding site [chemical binding]; other site 400668012709 Walker B motif; other site 400668012710 arginine finger; other site 400668012711 poly(A) polymerase; Region: pcnB; TIGR01942 400668012712 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 400668012713 active site 400668012714 NTP binding site [chemical binding]; other site 400668012715 metal binding triad [ion binding]; metal-binding site 400668012716 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 400668012717 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 400668012718 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 400668012719 catalytic center binding site [active] 400668012720 ATP binding site [chemical binding]; other site 400668012721 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 400668012722 oligomerization interface [polypeptide binding]; other site 400668012723 active site 400668012724 metal binding site [ion binding]; metal-binding site 400668012725 pantoate--beta-alanine ligase; Region: panC; TIGR00018 400668012726 Pantoate-beta-alanine ligase; Region: PanC; cd00560 400668012727 active site 400668012728 ATP-binding site [chemical binding]; other site 400668012729 pantoate-binding site; other site 400668012730 HXXH motif; other site 400668012731 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 400668012732 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 400668012733 active site 400668012734 dimer interface [polypeptide binding]; other site 400668012735 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 400668012736 dimer interface [polypeptide binding]; other site 400668012737 active site 400668012738 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 400668012739 Putative addiction module component; Region: Unstab_antitox; cl09921 400668012740 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668012741 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 400668012742 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668012743 Fic family protein [Function unknown]; Region: COG3177 400668012744 Protein of unknown function (DUF1349); Region: DUF1349; cl01397 400668012745 Cupin domain; Region: Cupin_2; cl09118 400668012746 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668012747 Helix-turn-helix domain; Region: HTH_18; pfam12833 400668012748 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668012749 lipoate-protein ligase A; Provisional; Region: lplA; PRK03822 400668012750 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 400668012751 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 400668012752 Cache domain; Region: Cache_1; pfam02743 400668012753 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 400668012754 dimerization interface [polypeptide binding]; other site 400668012755 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668012756 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012757 dimer interface [polypeptide binding]; other site 400668012758 putative CheW interface [polypeptide binding]; other site 400668012759 choline dehydrogenase; Validated; Region: PRK02106 400668012760 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 400668012761 Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like; Region: ALDH_PADH_NahF; cd07113 400668012762 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668012763 NAD(P) binding site [chemical binding]; other site 400668012764 catalytic residues [active] 400668012765 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 400668012766 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668012767 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 400668012768 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 400668012769 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 400668012770 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 400668012771 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 400668012772 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668012773 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 400668012774 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 400668012775 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668012776 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 400668012777 IMP binding site; other site 400668012778 dimer interface [polypeptide binding]; other site 400668012779 interdomain contacts; other site 400668012780 partial ornithine binding site; other site 400668012781 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 400668012782 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 400668012783 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 400668012784 catalytic site [active] 400668012785 subunit interface [polypeptide binding]; other site 400668012786 DJ-1 family protein; Region: not_thiJ; TIGR01383 400668012787 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 400668012788 conserved cys residue [active] 400668012789 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 400668012790 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668012791 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 400668012792 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 400668012793 substrate binding pocket [chemical binding]; other site 400668012794 membrane-bound complex binding site; other site 400668012795 hinge residues; other site 400668012796 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668012797 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 400668012798 dimer interface [polypeptide binding]; other site 400668012799 conserved gate region; other site 400668012800 putative PBP binding loops; other site 400668012801 ABC-ATPase subunit interface; other site 400668012802 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 400668012803 CoA-transferase family III; Region: CoA_transf_3; pfam02515 400668012804 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 400668012805 CoA-transferase family III; Region: CoA_transf_3; pfam02515 400668012806 BCCT family transporter; Region: BCCT; cl00569 400668012807 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 400668012808 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH6; cd08194 400668012809 putative active site [active] 400668012810 metal binding site [ion binding]; metal-binding site 400668012811 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 400668012812 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668012813 tetrameric interface [polypeptide binding]; other site 400668012814 NAD binding site [chemical binding]; other site 400668012815 catalytic residues [active] 400668012816 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 400668012817 Helix-turn-helix domains; Region: HTH; cl00088 400668012818 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 400668012819 dimerization interface [polypeptide binding]; other site 400668012820 substrate binding pocket [chemical binding]; other site 400668012821 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 400668012822 tetramer interfaces [polypeptide binding]; other site 400668012823 binuclear metal-binding site [ion binding]; other site 400668012824 thiamine monophosphate kinase; Provisional; Region: PRK05731 400668012825 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 400668012826 ATP binding site [chemical binding]; other site 400668012827 dimerization interface [polypeptide binding]; other site 400668012828 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 400668012829 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 400668012830 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 400668012831 catalytic motif [active] 400668012832 Zn binding site [ion binding]; other site 400668012833 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 400668012834 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 400668012835 ATP cone domain; Region: ATP-cone; pfam03477 400668012836 EamA-like transporter family; Region: EamA; cl01037 400668012837 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 400668012838 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012839 Walker A/P-loop; other site 400668012840 ATP binding site [chemical binding]; other site 400668012841 Q-loop/lid; other site 400668012842 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 400668012843 ABC transporter signature motif; other site 400668012844 Walker B; other site 400668012845 D-loop; other site 400668012846 ABC transporter; Region: ABC_tran_2; pfam12848 400668012847 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 400668012848 Abi-like protein; Region: Abi_2; cl01988 400668012849 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 400668012850 Helix-turn-helix domains; Region: HTH; cl00088 400668012851 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 400668012852 dimerization interface [polypeptide binding]; other site 400668012853 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668012854 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668012855 dimer interface [polypeptide binding]; other site 400668012856 putative CheW interface [polypeptide binding]; other site 400668012857 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 400668012858 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668012859 G1 box; other site 400668012860 GTP/Mg2+ binding site [chemical binding]; other site 400668012861 G2 box; other site 400668012862 Switch I region; other site 400668012863 G3 box; other site 400668012864 Switch II region; other site 400668012865 G4 box; other site 400668012866 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 400668012867 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 400668012868 putative acyl-acceptor binding pocket; other site 400668012869 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 400668012870 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668012871 metal binding site [ion binding]; metal-binding site 400668012872 active site 400668012873 I-site; other site 400668012874 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 400668012875 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668012876 Protein of unknown function (DUF890); Region: Methyltransf_10; pfam05971 400668012877 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668012878 Helix-turn-helix domains; Region: HTH; cl00088 400668012879 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 400668012880 substrate binding pocket [chemical binding]; other site 400668012881 dimerization interface [polypeptide binding]; other site 400668012882 EamA-like transporter family; Region: EamA; cl01037 400668012883 CSS motif domain associated with EAL; Region: CSS-motif; pfam12792 400668012884 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 400668012885 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 400668012886 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 400668012887 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 400668012888 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 400668012889 S-adenosylmethionine binding site [chemical binding]; other site 400668012890 Uncharacterized conserved protein [Function unknown]; Region: COG3496 400668012891 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 400668012892 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 400668012893 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012894 short chain dehydrogenase; Provisional; Region: PRK06101 400668012895 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012896 NAD(P) binding site [chemical binding]; other site 400668012897 active site 400668012898 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 400668012899 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 400668012900 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668012901 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 400668012902 DNA binding residues [nucleotide binding] 400668012903 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 400668012904 Cupin domain; Region: Cupin_2; cl09118 400668012905 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668012906 putative acyl-acceptor binding pocket; other site 400668012907 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668012908 N-terminal Early set domain associated with the catalytic domain of isoamylase-like (also called glycogen 6-glucanohydrolase) proteins; Region: E_set_Isoamylase_like_N; cd07184 400668012909 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668012910 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 400668012911 tetrameric interface [polypeptide binding]; other site 400668012912 NAD binding site [chemical binding]; other site 400668012913 catalytic residues [active] 400668012914 choline dehydrogenase; Validated; Region: PRK02106 400668012915 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668012916 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 400668012917 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 400668012918 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 400668012919 active site 400668012920 metal binding site [ion binding]; metal-binding site 400668012921 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 400668012922 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; cl01049 400668012923 DNA-J related protein; Region: DNAJ_related; pfam12339 400668012924 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 400668012925 HSP70 interaction site [polypeptide binding]; other site 400668012926 MltA specific insert domain; Region: MltA; cl08398 400668012927 3D domain; Region: 3D; cl01439 400668012928 Gram-negative bacterial tonB protein; Region: TonB; cl10048 400668012929 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 400668012930 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 400668012931 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 400668012932 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 400668012933 magnesium Mg(2+) and cobalt Co(2+) transport protein (corA); Region: corA; TIGR00383 400668012934 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668012935 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 400668012936 Walker A/P-loop; other site 400668012937 ATP binding site [chemical binding]; other site 400668012938 Q-loop/lid; other site 400668012939 ABC transporter signature motif; other site 400668012940 Walker B; other site 400668012941 D-loop; other site 400668012942 H-loop/switch region; other site 400668012943 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 400668012944 dimer interface [polypeptide binding]; other site 400668012945 conserved gate region; other site 400668012946 putative PBP binding loops; other site 400668012947 ABC-ATPase subunit interface; other site 400668012948 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 400668012949 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668012950 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 400668012951 dimer interface [polypeptide binding]; other site 400668012952 conserved gate region; other site 400668012953 putative PBP binding loops; other site 400668012954 ABC-ATPase subunit interface; other site 400668012955 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 400668012956 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 400668012957 substrate binding pocket [chemical binding]; other site 400668012958 membrane-bound complex binding site; other site 400668012959 hinge residues; other site 400668012960 Transcriptional regulators [Transcription]; Region: GntR; COG1802 400668012961 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668012962 DNA-binding site [nucleotide binding]; DNA binding site 400668012963 FCD domain; Region: FCD; cl11656 400668012964 isoaspartyl dipeptidase; Provisional; Region: PRK10657 400668012965 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 400668012966 active site 400668012967 LysE type translocator; Region: LysE; cl00565 400668012968 Cupin domain; Region: Cupin_2; cl09118 400668012969 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668012970 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668012971 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668012972 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 400668012973 MatE; Region: MatE; cl10513 400668012974 MatE; Region: MatE; cl10513 400668012975 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 400668012976 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668012977 putative substrate translocation pore; other site 400668012978 amidohydrolase; Provisional; Region: PRK12393 400668012979 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 400668012980 active site 400668012981 putative substrate binding pocket [chemical binding]; other site 400668012982 NMT1-like family; Region: NMT1_2; cl15260 400668012983 NMT1/THI5 like; Region: NMT1; pfam09084 400668012984 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 400668012985 Helix-turn-helix domains; Region: HTH; cl00088 400668012986 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 400668012987 dimerization interface [polypeptide binding]; other site 400668012988 aldehyde dehydrogenase; Provisional; Region: PRK11903 400668012989 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 400668012990 dimer interface [polypeptide binding]; other site 400668012991 NADP binding site [chemical binding]; other site 400668012992 catalytic residues [active] 400668012993 Dehydratase family; Region: ILVD_EDD; cl00340 400668012994 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668012995 classical (c) SDRs; Region: SDR_c; cd05233 400668012996 NAD(P) binding site [chemical binding]; other site 400668012997 active site 400668012998 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 400668012999 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 400668013000 TM-ABC transporter signature motif; other site 400668013001 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 400668013002 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 400668013003 Walker A/P-loop; other site 400668013004 ATP binding site [chemical binding]; other site 400668013005 Q-loop/lid; other site 400668013006 ABC transporter signature motif; other site 400668013007 Walker B; other site 400668013008 D-loop; other site 400668013009 H-loop/switch region; other site 400668013010 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 400668013011 ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: XylF; COG4213 400668013012 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 400668013013 putative ligand binding site [chemical binding]; other site 400668013014 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 400668013015 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 400668013016 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013017 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 400668013018 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013019 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 400668013020 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 400668013021 active site 400668013022 dimer interface [polypeptide binding]; other site 400668013023 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 400668013024 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 400668013025 active site 400668013026 FMN binding site [chemical binding]; other site 400668013027 substrate binding site [chemical binding]; other site 400668013028 3Fe-4S cluster binding site [ion binding]; other site 400668013029 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 400668013030 domain interface; other site 400668013031 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668013032 AAA domain; Region: AAA_22; pfam13401 400668013033 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 400668013034 Sporulation related domain; Region: SPOR; cl10051 400668013035 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 400668013036 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 400668013037 active site 400668013038 dimer interface [polypeptide binding]; other site 400668013039 metal binding site [ion binding]; metal-binding site 400668013040 shikimate kinase; Reviewed; Region: aroK; PRK00131 400668013041 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 400668013042 ADP binding site [chemical binding]; other site 400668013043 magnesium binding site [ion binding]; other site 400668013044 putative shikimate binding site; other site 400668013045 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 400668013046 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 400668013047 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 400668013048 Transglycosylase; Region: Transgly; cl07896 400668013049 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 400668013050 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 400668013051 Malic enzyme, N-terminal domain; Region: malic; pfam00390 400668013052 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 400668013053 putative NAD(P) binding site [chemical binding]; other site 400668013054 Staphylococcal nuclease homologues; Region: SNc; smart00318 400668013055 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 400668013056 Catalytic site; other site 400668013057 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 400668013058 primosome assembly protein PriA; Validated; Region: PRK05580 400668013059 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 400668013060 ATP binding site [chemical binding]; other site 400668013061 putative Mg++ binding site [ion binding]; other site 400668013062 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 400668013063 nucleotide binding region [chemical binding]; other site 400668013064 ATP-binding site [chemical binding]; other site 400668013065 Sporulation related domain; Region: SPOR; cl10051 400668013066 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 400668013067 active site 400668013068 HslU subunit interaction site [polypeptide binding]; other site 400668013069 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 400668013070 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 400668013071 Walker A motif; other site 400668013072 ATP binding site [chemical binding]; other site 400668013073 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668013074 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 400668013075 Protein of unknown function (DUF971); Region: DUF971; cl01414 400668013076 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 400668013077 SCP-2 sterol transfer family; Region: SCP2; cl01225 400668013078 EamA-like transporter family; Region: EamA; cl01037 400668013079 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 400668013080 active site 400668013081 homodimer interface [polypeptide binding]; other site 400668013082 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 400668013083 arginine-tRNA ligase; Region: PLN02286 400668013084 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 400668013085 active site 400668013086 HIGH motif; other site 400668013087 KMSK motif region; other site 400668013088 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 400668013089 tRNA binding surface [nucleotide binding]; other site 400668013090 anticodon binding site; other site 400668013091 threonine dehydratase; Reviewed; Region: PRK09224 400668013092 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 400668013093 tetramer interface [polypeptide binding]; other site 400668013094 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668013095 catalytic residue [active] 400668013096 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 400668013097 putative Ile/Val binding site [chemical binding]; other site 400668013098 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 400668013099 putative Ile/Val binding site [chemical binding]; other site 400668013100 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 400668013101 tetramer (dimer of dimers) interface [polypeptide binding]; other site 400668013102 active site 400668013103 dimer interface [polypeptide binding]; other site 400668013104 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 400668013105 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 400668013106 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 400668013107 AMP binding site [chemical binding]; other site 400668013108 metal binding site [ion binding]; metal-binding site 400668013109 active site 400668013110 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 400668013111 Sugar fermentation stimulation protein; Region: SfsA; cl00647 400668013112 Cupin domain; Region: Cupin_2; cl09118 400668013113 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668013114 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668013115 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668013116 LysE type translocator; Region: LysE; cl00565 400668013117 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668013118 Helix-turn-helix domains; Region: HTH; cl00088 400668013119 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 400668013120 substrate binding pocket [chemical binding]; other site 400668013121 dimerization interface [polypeptide binding]; other site 400668013122 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 400668013123 putative substrate translocation pore; other site 400668013124 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 400668013125 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 400668013126 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 400668013127 Walker A motif; other site 400668013128 ATP binding site [chemical binding]; other site 400668013129 Walker B motif; other site 400668013130 arginine finger; other site 400668013131 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 400668013132 active site 400668013133 catalytic triad [active] 400668013134 GMP synthase; Reviewed; Region: guaA; PRK00074 400668013135 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 400668013136 AMP/PPi binding site [chemical binding]; other site 400668013137 candidate oxyanion hole; other site 400668013138 catalytic triad [active] 400668013139 potential glutamine specificity residues [chemical binding]; other site 400668013140 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 400668013141 ATP Binding subdomain [chemical binding]; other site 400668013142 Ligand Binding sites [chemical binding]; other site 400668013143 Dimerization subdomain; other site 400668013144 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 400668013145 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 400668013146 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 400668013147 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 400668013148 active site 400668013149 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 400668013150 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 400668013151 generic binding surface II; other site 400668013152 generic binding surface I; other site 400668013153 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 400668013154 metabolite-proton symporter; Region: 2A0106; TIGR00883 400668013155 putative substrate translocation pore; other site 400668013156 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 400668013157 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_2; cd05679 400668013158 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 400668013159 metal binding site [ion binding]; metal-binding site 400668013160 putative dimer interface [polypeptide binding]; other site 400668013161 Transcriptional regulator [Transcription]; Region: LysR; COG0583 400668013162 Helix-turn-helix domains; Region: HTH; cl00088 400668013163 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 400668013164 dimerization interface [polypeptide binding]; other site 400668013165 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668013166 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 400668013167 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668013168 dimer interface [polypeptide binding]; other site 400668013169 putative CheW interface [polypeptide binding]; other site 400668013170 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668013171 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 400668013172 active site 400668013173 phosphorylation site [posttranslational modification] 400668013174 intermolecular recognition site; other site 400668013175 dimerization interface [polypeptide binding]; other site 400668013176 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 400668013177 Walker A motif; other site 400668013178 ATP binding site [chemical binding]; other site 400668013179 Walker B motif; other site 400668013180 arginine finger; other site 400668013181 Helix-turn-helix domains; Region: HTH; cl00088 400668013182 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 400668013183 dimer interface [polypeptide binding]; other site 400668013184 phosphorylation site [posttranslational modification] 400668013185 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 400668013186 ATP binding site [chemical binding]; other site 400668013187 Mg2+ binding site [ion binding]; other site 400668013188 G-X-G motif; other site 400668013189 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 400668013190 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 400668013191 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 400668013192 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668013193 NMT1-like family; Region: NMT1_2; cl15260 400668013194 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 400668013195 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 400668013196 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 400668013197 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 400668013198 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 400668013199 dimer interface [polypeptide binding]; other site 400668013200 phosphorylation site [posttranslational modification] 400668013201 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 400668013202 ATP binding site [chemical binding]; other site 400668013203 Mg2+ binding site [ion binding]; other site 400668013204 G-X-G motif; other site 400668013205 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668013206 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 400668013207 active site 400668013208 phosphorylation site [posttranslational modification] 400668013209 intermolecular recognition site; other site 400668013210 dimerization interface [polypeptide binding]; other site 400668013211 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 400668013212 DNA binding site [nucleotide binding] 400668013213 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 400668013214 EamA-like transporter family; Region: EamA; cl01037 400668013215 EamA-like transporter family; Region: EamA; cl01037 400668013216 Ion transport protein; Region: Ion_trans; pfam00520 400668013217 Polycystin cation channel; Region: PKD_channel; pfam08016 400668013218 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 400668013219 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668013220 NAD binding site [chemical binding]; other site 400668013221 catalytic residues [active] 400668013222 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 400668013223 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013224 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668013225 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013226 NAD(P) binding site [chemical binding]; other site 400668013227 active site 400668013228 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 400668013229 substrate binding site [chemical binding]; other site 400668013230 ATP binding site [chemical binding]; other site 400668013231 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 400668013232 TM-ABC transporter signature motif; other site 400668013233 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 400668013234 TM-ABC transporter signature motif; other site 400668013235 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 400668013236 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 400668013237 Walker A/P-loop; other site 400668013238 ATP binding site [chemical binding]; other site 400668013239 Q-loop/lid; other site 400668013240 ABC transporter signature motif; other site 400668013241 Walker B; other site 400668013242 D-loop; other site 400668013243 H-loop/switch region; other site 400668013244 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 400668013245 Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_methylthioribose_binding_like; cd06305 400668013246 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 400668013247 putative ligand binding site [chemical binding]; other site 400668013248 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 400668013249 intersubunit interface [polypeptide binding]; other site 400668013250 active site 400668013251 Zn2+ binding site [ion binding]; other site 400668013252 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013253 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 400668013254 NAD(P) binding site [chemical binding]; other site 400668013255 active site 400668013256 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 400668013257 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668013258 DNA-binding site [nucleotide binding]; DNA binding site 400668013259 UTRA domain; Region: UTRA; cl01230 400668013260 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 400668013261 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668013262 putative substrate translocation pore; other site 400668013263 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 400668013264 dimer interaction site [polypeptide binding]; other site 400668013265 substrate-binding tunnel; other site 400668013266 active site 400668013267 catalytic site [active] 400668013268 substrate binding site [chemical binding]; other site 400668013269 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 400668013270 DUF35 OB-fold domain; Region: DUF35; pfam01796 400668013271 thiolase; Provisional; Region: PRK06158 400668013272 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 400668013273 active site 400668013274 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 400668013275 AMP-binding enzyme; Region: AMP-binding; cl15778 400668013276 putative acyltransferase; Provisional; Region: PRK05790 400668013277 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 400668013278 dimer interface [polypeptide binding]; other site 400668013279 active site 400668013280 Mechanosensitive ion channel; Region: MS_channel; pfam00924 400668013281 Membrane transport protein; Region: Mem_trans; cl09117 400668013282 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 400668013283 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_11; cd06321 400668013284 putative ligand binding site [chemical binding]; other site 400668013285 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 400668013286 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668013287 Walker A/P-loop; other site 400668013288 ATP binding site [chemical binding]; other site 400668013289 Q-loop/lid; other site 400668013290 ABC transporter signature motif; other site 400668013291 Walker B; other site 400668013292 D-loop; other site 400668013293 H-loop/switch region; other site 400668013294 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 400668013295 TM-ABC transporter signature motif; other site 400668013296 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 400668013297 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 400668013298 ligand binding site [chemical binding]; other site 400668013299 TMAO reductase sytem sensor TorS; Region: TMAO_torS; TIGR02956 400668013300 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 400668013301 PAS fold; Region: PAS_7; pfam12860 400668013302 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 400668013303 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 400668013304 dimer interface [polypeptide binding]; other site 400668013305 phosphorylation site [posttranslational modification] 400668013306 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 400668013307 ATP binding site [chemical binding]; other site 400668013308 G-X-G motif; other site 400668013309 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 400668013310 Response regulator receiver domain; Region: Response_reg; pfam00072 400668013311 active site 400668013312 phosphorylation site [posttranslational modification] 400668013313 intermolecular recognition site; other site 400668013314 dimerization interface [polypeptide binding]; other site 400668013315 osmolarity response regulator; Provisional; Region: ompR; PRK09468 400668013316 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 400668013317 active site 400668013318 phosphorylation site [posttranslational modification] 400668013319 intermolecular recognition site; other site 400668013320 dimerization interface [polypeptide binding]; other site 400668013321 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 400668013322 DNA binding site [nucleotide binding] 400668013323 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 400668013324 catalytic loop [active] 400668013325 iron binding site [ion binding]; other site 400668013326 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 400668013327 ATP binding site [chemical binding]; other site 400668013328 putative Mg++ binding site [ion binding]; other site 400668013329 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 400668013330 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 400668013331 ATP binding site [chemical binding]; other site 400668013332 putative Mg++ binding site [ion binding]; other site 400668013333 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 400668013334 nucleotide binding region [chemical binding]; other site 400668013335 ATP-binding site [chemical binding]; other site 400668013336 Helicase associated domain (HA2); Region: HA2; cl04503 400668013337 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 400668013338 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 400668013339 WYL domain; Region: WYL; cl14852 400668013340 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 400668013341 active site 400668013342 NTP binding site [chemical binding]; other site 400668013343 metal binding triad [ion binding]; metal-binding site 400668013344 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 400668013345 Walker A motif; other site 400668013346 ATP binding site [chemical binding]; other site 400668013347 Walker B motif; other site 400668013348 arginine finger; other site 400668013349 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 400668013350 active site 400668013351 substrate binding site [chemical binding]; other site 400668013352 catalytic site [active] 400668013353 Protein of unknown function (DUF4231); Region: DUF4231; pfam14015 400668013354 Transposase domain (DUF772); Region: DUF772; cl15789 400668013355 Transposase domain (DUF772); Region: DUF772; cl15789 400668013356 Transposase domain (DUF772); Region: DUF772; cl15789 400668013357 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 400668013358 active site 400668013359 catalytic residues [active] 400668013360 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 400668013361 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 400668013362 Protein of unknown function DUF262; Region: DUF262; cl14890 400668013363 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 400668013364 non-specific DNA binding site [nucleotide binding]; other site 400668013365 salt bridge; other site 400668013366 sequence-specific DNA binding site [nucleotide binding]; other site 400668013367 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 400668013368 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 400668013369 ATP binding site [chemical binding]; other site 400668013370 putative Mg++ binding site [ion binding]; other site 400668013371 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 400668013372 DNA binding site [nucleotide binding] 400668013373 Int/Topo IB signature motif; other site 400668013374 active site 400668013375 catalytic residues [active] 400668013376 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 400668013377 DNA binding site [nucleotide binding] 400668013378 Int/Topo IB signature motif; other site 400668013379 active site 400668013380 catalytic residues [active] 400668013381 ATP-dependent RNA helicase HrpB; Provisional; Region: PRK11664 400668013382 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 400668013383 nucleotide binding region [chemical binding]; other site 400668013384 ATP-binding site [chemical binding]; other site 400668013385 Helicase associated domain (HA2); Region: HA2; cl04503 400668013386 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 400668013387 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 400668013388 LytB protein; Region: LYTB; cl00507 400668013389 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 400668013390 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 400668013391 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 400668013392 lipoprotein signal peptidase; Provisional; Region: PRK14787 400668013393 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 400668013394 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 400668013395 active site 400668013396 HIGH motif; other site 400668013397 nucleotide binding site [chemical binding]; other site 400668013398 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 400668013399 active site 400668013400 KMSKS motif; other site 400668013401 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 400668013402 tRNA binding surface [nucleotide binding]; other site 400668013403 anticodon binding site; other site 400668013404 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 400668013405 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 400668013406 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 400668013407 active site 400668013408 Riboflavin kinase; Region: Flavokinase; cl03312 400668013409 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 400668013410 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 400668013411 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 400668013412 gamma-glutamyl kinase; Provisional; Region: PRK05429 400668013413 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 400668013414 nucleotide binding site [chemical binding]; other site 400668013415 homotetrameric interface [polypeptide binding]; other site 400668013416 putative phosphate binding site [ion binding]; other site 400668013417 putative allosteric binding site; other site 400668013418 PUA domain; Region: PUA; cl00607 400668013419 GTPase CgtA; Reviewed; Region: obgE; PRK12298 400668013420 GTP1/OBG; Region: GTP1_OBG; pfam01018 400668013421 Obg GTPase; Region: Obg; cd01898 400668013422 G1 box; other site 400668013423 GTP/Mg2+ binding site [chemical binding]; other site 400668013424 Switch I region; other site 400668013425 G2 box; other site 400668013426 G3 box; other site 400668013427 Switch II region; other site 400668013428 G4 box; other site 400668013429 G5 box; other site 400668013430 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 400668013431 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 400668013432 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 400668013433 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 400668013434 substrate binding pocket [chemical binding]; other site 400668013435 chain length determination region; other site 400668013436 substrate-Mg2+ binding site; other site 400668013437 catalytic residues [active] 400668013438 aspartate-rich region 1; other site 400668013439 active site lid residues [active] 400668013440 aspartate-rich region 2; other site 400668013441 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 400668013442 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 400668013443 active site 1 [active] 400668013444 dimer interface [polypeptide binding]; other site 400668013445 active site 2 [active] 400668013446 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 400668013447 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 400668013448 dimer interface [polypeptide binding]; other site 400668013449 active site 400668013450 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 400668013451 putative acyl-acceptor binding pocket; other site 400668013452 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668013453 putative acyl-acceptor binding pocket; other site 400668013454 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]; Region: COG1026 400668013455 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 400668013456 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 400668013457 Peptidase M16C associated; Region: M16C_assoc; pfam08367 400668013458 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 400668013459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 400668013460 Smr domain; Region: Smr; cl02619 400668013461 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 400668013462 dimer interface [polypeptide binding]; other site 400668013463 ssDNA binding site [nucleotide binding]; other site 400668013464 tetramer (dimer of dimers) interface [polypeptide binding]; other site 400668013465 Major Facilitator Superfamily; Region: MFS_1; pfam07690 400668013466 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 400668013467 putative substrate translocation pore; other site 400668013468 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 400668013469 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 400668013470 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 400668013471 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 400668013472 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 400668013473 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 400668013474 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 400668013475 alphaNTD homodimer interface [polypeptide binding]; other site 400668013476 alphaNTD - beta interaction site [polypeptide binding]; other site 400668013477 alphaNTD - beta' interaction site [polypeptide binding]; other site 400668013478 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 400668013479 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 400668013480 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 400668013481 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 400668013482 RNA binding surface [nucleotide binding]; other site 400668013483 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 400668013484 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 400668013485 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 400668013486 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 400668013487 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 400668013488 SecY translocase; Region: SecY; pfam00344 400668013489 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 400668013490 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 400668013491 23S rRNA binding site [nucleotide binding]; other site 400668013492 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 400668013493 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 400668013494 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 400668013495 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 400668013496 5S rRNA interface [nucleotide binding]; other site 400668013497 23S rRNA interface [nucleotide binding]; other site 400668013498 L5 interface [polypeptide binding]; other site 400668013499 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 400668013500 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 400668013501 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 400668013502 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 400668013503 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 400668013504 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 400668013505 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 400668013506 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 400668013507 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 400668013508 KOW motif; Region: KOW; cl00354 400668013509 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 400668013510 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 400668013511 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 400668013512 23S rRNA interface [nucleotide binding]; other site 400668013513 putative translocon interaction site; other site 400668013514 signal recognition particle (SRP54) interaction site; other site 400668013515 L23 interface [polypeptide binding]; other site 400668013516 trigger factor interaction site; other site 400668013517 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 400668013518 23S rRNA interface [nucleotide binding]; other site 400668013519 5S rRNA interface [nucleotide binding]; other site 400668013520 putative antibiotic binding site [chemical binding]; other site 400668013521 L25 interface [polypeptide binding]; other site 400668013522 L27 interface [polypeptide binding]; other site 400668013523 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 400668013524 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 400668013525 G-X-X-G motif; other site 400668013526 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 400668013527 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 400668013528 putative translocon binding site; other site 400668013529 protein-rRNA interface [nucleotide binding]; other site 400668013530 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 400668013531 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 400668013532 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 400668013533 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 400668013534 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 400668013535 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 400668013536 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 400668013537 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 400668013538 elongation factor Tu; Reviewed; Region: PRK00049 400668013539 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 400668013540 G1 box; other site 400668013541 GEF interaction site [polypeptide binding]; other site 400668013542 GTP/Mg2+ binding site [chemical binding]; other site 400668013543 Switch I region; other site 400668013544 G2 box; other site 400668013545 G3 box; other site 400668013546 Switch II region; other site 400668013547 G4 box; other site 400668013548 G5 box; other site 400668013549 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 400668013550 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 400668013551 Antibiotic Binding Site [chemical binding]; other site 400668013552 elongation factor G; Reviewed; Region: PRK00007 400668013553 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 400668013554 G1 box; other site 400668013555 putative GEF interaction site [polypeptide binding]; other site 400668013556 GTP/Mg2+ binding site [chemical binding]; other site 400668013557 Switch I region; other site 400668013558 G2 box; other site 400668013559 G3 box; other site 400668013560 Switch II region; other site 400668013561 G4 box; other site 400668013562 G5 box; other site 400668013563 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 400668013564 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 400668013565 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 400668013566 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 400668013567 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 400668013568 S17 interaction site [polypeptide binding]; other site 400668013569 S8 interaction site; other site 400668013570 16S rRNA interaction site [nucleotide binding]; other site 400668013571 streptomycin interaction site [chemical binding]; other site 400668013572 23S rRNA interaction site [nucleotide binding]; other site 400668013573 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 400668013574 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 400668013575 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 400668013576 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 400668013577 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 400668013578 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 400668013579 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 400668013580 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 400668013581 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 400668013582 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 400668013583 DNA binding site [nucleotide binding] 400668013584 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 400668013585 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 400668013586 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 400668013587 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 400668013588 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 400668013589 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 400668013590 RPB11 interaction site [polypeptide binding]; other site 400668013591 RPB12 interaction site [polypeptide binding]; other site 400668013592 Domain of unknown function (DUF4407); Region: DUF4407; pfam14362 400668013593 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 400668013594 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 400668013595 RPB1 interaction site [polypeptide binding]; other site 400668013596 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 400668013597 core dimer interface [polypeptide binding]; other site 400668013598 peripheral dimer interface [polypeptide binding]; other site 400668013599 L10 interface [polypeptide binding]; other site 400668013600 L11 interface [polypeptide binding]; other site 400668013601 putative EF-Tu interaction site [polypeptide binding]; other site 400668013602 putative EF-G interaction site [polypeptide binding]; other site 400668013603 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 400668013604 23S rRNA interface [nucleotide binding]; other site 400668013605 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 400668013606 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 400668013607 mRNA/rRNA interface [nucleotide binding]; other site 400668013608 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 400668013609 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 400668013610 23S rRNA interface [nucleotide binding]; other site 400668013611 L7/L12 interface [polypeptide binding]; other site 400668013612 putative thiostrepton binding site; other site 400668013613 L25 interface [polypeptide binding]; other site 400668013614 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 400668013615 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 400668013616 putative homodimer interface [polypeptide binding]; other site 400668013617 KOW motif; Region: KOW; cl00354 400668013618 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 400668013619 Sporulation related domain; Region: SPOR; cl10051 400668013620 Type III pantothenate kinase; Region: Pan_kinase; cl09130 400668013621 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 400668013622 Helix-turn-helix domains; Region: HTH; cl00088 400668013623 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 400668013624 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 400668013625 Esterase/lipase [General function prediction only]; Region: COG1647 400668013626 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 400668013627 Glycosyl hydrolase family 1; Region: Glyco_hydro_1; cl01046 400668013628 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 400668013629 Periplasmic glucan biosynthesis protein, MdoG; Region: MdoG; cl15433 400668013630 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 400668013631 PAS fold; Region: PAS; pfam00989 400668013632 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 400668013633 PAS fold; Region: PAS_3; pfam08447 400668013634 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668013635 metal binding site [ion binding]; metal-binding site 400668013636 active site 400668013637 I-site; other site 400668013638 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 400668013639 pyrimidine utilization transport protein G; Region: RutG; TIGR03616 400668013640 uracil-xanthine permease; Region: ncs2; TIGR00801 400668013641 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 400668013642 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668013643 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 400668013644 DNA binding residues [nucleotide binding] 400668013645 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 400668013646 FecR protein; Region: FecR; pfam04773 400668013647 Secretin and TonB N terminus short domain; Region: STN; cl06624 400668013648 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 400668013649 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 400668013650 Tetratricopeptide repeat; Region: TPR_16; pfam13432 400668013651 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 400668013652 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668013653 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668013654 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668013655 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668013656 Tetratricopeptide repeat; Region: TPR_12; pfam13424 400668013657 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 400668013658 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 400668013659 dimer interface [polypeptide binding]; other site 400668013660 conserved gate region; other site 400668013661 putative PBP binding loops; other site 400668013662 ABC-ATPase subunit interface; other site 400668013663 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 400668013664 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 400668013665 dimer interface [polypeptide binding]; other site 400668013666 putative PBP binding loops; other site 400668013667 ABC-ATPase subunit interface; other site 400668013668 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 400668013669 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668013670 Walker A/P-loop; other site 400668013671 ATP binding site [chemical binding]; other site 400668013672 Q-loop/lid; other site 400668013673 ABC transporter signature motif; other site 400668013674 Walker B; other site 400668013675 D-loop; other site 400668013676 H-loop/switch region; other site 400668013677 TOBE domain; Region: TOBE_2; cl01440 400668013678 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 400668013679 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 400668013680 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 400668013681 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668013682 dimer interface [polypeptide binding]; other site 400668013683 putative CheW interface [polypeptide binding]; other site 400668013684 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 400668013685 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013686 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 400668013687 L-serine binding site [chemical binding]; other site 400668013688 ACT domain interface; other site 400668013689 tRNA (uracil-5-)-methyltransferase; Region: trmA_only; TIGR02143 400668013690 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 400668013691 S-adenosylmethionine binding site [chemical binding]; other site 400668013692 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 400668013693 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 400668013694 hypothetical protein; Provisional; Region: PRK08185 400668013695 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 400668013696 intersubunit interface [polypeptide binding]; other site 400668013697 active site 400668013698 zinc binding site [ion binding]; other site 400668013699 Na+ binding site [ion binding]; other site 400668013700 Phosphoglycerate kinase; Region: PGK; pfam00162 400668013701 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 400668013702 substrate binding site [chemical binding]; other site 400668013703 hinge regions; other site 400668013704 ADP binding site [chemical binding]; other site 400668013705 catalytic site [active] 400668013706 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 400668013707 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668013708 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 400668013709 transketolase; Reviewed; Region: PRK12753 400668013710 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 400668013711 TPP-binding site [chemical binding]; other site 400668013712 dimer interface [polypeptide binding]; other site 400668013713 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 400668013714 PYR/PP interface [polypeptide binding]; other site 400668013715 dimer interface [polypeptide binding]; other site 400668013716 TPP binding site [chemical binding]; other site 400668013717 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 400668013718 S-adenosylmethionine synthetase; Validated; Region: PRK05250 400668013719 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 400668013720 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 400668013721 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 400668013722 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 400668013723 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 400668013724 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 400668013725 glutathione synthetase; Provisional; Region: PRK05246 400668013726 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 400668013727 ATP-grasp domain; Region: ATP-grasp_4; cl03087 400668013728 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 400668013729 Gram-negative bacterial tonB protein; Region: TonB; cl10048 400668013730 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 400668013731 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 400668013732 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 400668013733 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 400668013734 DNA binding residues [nucleotide binding] 400668013735 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 400668013736 FtsX-like permease family; Region: FtsX; cl15850 400668013737 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 400668013738 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668013739 Walker A/P-loop; other site 400668013740 ATP binding site [chemical binding]; other site 400668013741 Q-loop/lid; other site 400668013742 ABC transporter signature motif; other site 400668013743 Walker B; other site 400668013744 D-loop; other site 400668013745 H-loop/switch region; other site 400668013746 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 400668013747 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 400668013748 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 400668013749 P loop; other site 400668013750 GTP binding site [chemical binding]; other site 400668013751 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 400668013752 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 400668013753 S-adenosylmethionine binding site [chemical binding]; other site 400668013754 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 400668013755 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 400668013756 dimer interface [polypeptide binding]; other site 400668013757 putative CheW interface [polypeptide binding]; other site 400668013758 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 400668013759 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 400668013760 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 400668013761 S-adenosylmethionine binding site [chemical binding]; other site 400668013762 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 400668013763 active site 400668013764 dimerization interface [polypeptide binding]; other site 400668013765 HemN family oxidoreductase; Provisional; Region: PRK05660 400668013766 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 400668013767 FeS/SAM binding site; other site 400668013768 HemN C-terminal domain; Region: HemN_C; pfam06969 400668013769 BCCT family transporter; Region: BCCT; cl00569 400668013770 Predicted membrane protein [Function unknown]; Region: COG2119 400668013771 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 400668013772 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 400668013773 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 400668013774 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 400668013775 ligand binding site [chemical binding]; other site 400668013776 flexible hinge region; other site 400668013777 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 400668013778 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 400668013779 metal binding triad; other site 400668013780 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 400668013781 active site 400668013782 substrate binding site [chemical binding]; other site 400668013783 catalytic site [active] 400668013784 Transcriptional regulators [Transcription]; Region: PurR; COG1609 400668013785 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 400668013786 DNA binding site [nucleotide binding] 400668013787 domain linker motif; other site 400668013788 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_3; cd06279 400668013789 putative dimerization interface [polypeptide binding]; other site 400668013790 putative ligand binding site [chemical binding]; other site 400668013791 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 400668013792 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 400668013793 active site 400668013794 catalytic site [active] 400668013795 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668013796 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668013797 Walker A/P-loop; other site 400668013798 ATP binding site [chemical binding]; other site 400668013799 Q-loop/lid; other site 400668013800 ABC transporter signature motif; other site 400668013801 Walker B; other site 400668013802 D-loop; other site 400668013803 H-loop/switch region; other site 400668013804 TOBE domain; Region: TOBE_2; cl01440 400668013805 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 400668013806 dimer interface [polypeptide binding]; other site 400668013807 conserved gate region; other site 400668013808 putative PBP binding loops; other site 400668013809 ABC-ATPase subunit interface; other site 400668013810 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 400668013811 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 400668013812 conserved gate region; other site 400668013813 putative PBP binding loops; other site 400668013814 ABC-ATPase subunit interface; other site 400668013815 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668013816 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 400668013817 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 400668013818 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 400668013819 putative substrate binding site [chemical binding]; other site 400668013820 putative ATP binding site [chemical binding]; other site 400668013821 osmolarity response regulator; Provisional; Region: ompR; PRK09468 400668013822 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 400668013823 active site 400668013824 phosphorylation site [posttranslational modification] 400668013825 intermolecular recognition site; other site 400668013826 dimerization interface [polypeptide binding]; other site 400668013827 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 400668013828 DNA binding site [nucleotide binding] 400668013829 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 400668013830 dimerization interface [polypeptide binding]; other site 400668013831 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 400668013832 dimer interface [polypeptide binding]; other site 400668013833 phosphorylation site [posttranslational modification] 400668013834 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 400668013835 ATP binding site [chemical binding]; other site 400668013836 Mg2+ binding site [ion binding]; other site 400668013837 G-X-G motif; other site 400668013838 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 400668013839 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 400668013840 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 400668013841 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 400668013842 dimer interface [polypeptide binding]; other site 400668013843 conserved gate region; other site 400668013844 putative PBP binding loops; other site 400668013845 ABC-ATPase subunit interface; other site 400668013846 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 400668013847 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 400668013848 dimer interface [polypeptide binding]; other site 400668013849 conserved gate region; other site 400668013850 putative PBP binding loops; other site 400668013851 ABC-ATPase subunit interface; other site 400668013852 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 400668013853 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 400668013854 Walker A/P-loop; other site 400668013855 ATP binding site [chemical binding]; other site 400668013856 Q-loop/lid; other site 400668013857 ABC transporter signature motif; other site 400668013858 Walker B; other site 400668013859 D-loop; other site 400668013860 H-loop/switch region; other site 400668013861 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 400668013862 Uncharacterized conserved protein (DUF2235); Region: DUF2235; cl01480 400668013863 bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed; Region: ushA; PRK09558 400668013864 Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain; Region: MPP_UshA_N; cd07405 400668013865 active site 400668013866 metal binding site [ion binding]; metal-binding site 400668013867 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 400668013868 biofilm formation regulator HmsP; Provisional; Region: PRK11829 400668013869 PAS domain S-box; Region: sensory_box; TIGR00229 400668013870 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 400668013871 putative active site [active] 400668013872 heme pocket [chemical binding]; other site 400668013873 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668013874 metal binding site [ion binding]; metal-binding site 400668013875 active site 400668013876 I-site; other site 400668013877 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 400668013878 ectoine/hydroxyectoine ABC transporter solute-binding protein; Region: ectoine_ehuB; TIGR02995 400668013879 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 400668013880 substrate binding pocket [chemical binding]; other site 400668013881 membrane-bound complex binding site; other site 400668013882 hinge residues; other site 400668013883 ribonuclease PH; Reviewed; Region: rph; PRK00173 400668013884 Ribonuclease PH; Region: RNase_PH_bact; cd11362 400668013885 hexamer interface [polypeptide binding]; other site 400668013886 active site 400668013887 hypothetical protein; Provisional; Region: PRK11820 400668013888 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 400668013889 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 400668013890 HipA N-terminal domain; Region: Couple_hipA; cl11853 400668013891 HipA-like N-terminal domain; Region: HipA_N; pfam07805 400668013892 HipA-like C-terminal domain; Region: HipA_C; pfam07804 400668013893 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 400668013894 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 400668013895 active site 400668013896 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 400668013897 Predicted transcriptional regulator [Transcription]; Region: COG2932 400668013898 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 400668013899 Catalytic site [active] 400668013900 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 400668013901 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 400668013902 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 400668013903 metal binding site [ion binding]; metal-binding site 400668013904 active site 400668013905 I-site; other site 400668013906 Ion transport protein; Region: Ion_trans; pfam00520 400668013907 Virulence protein [General function prediction only]; Region: COG3943 400668013908 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 400668013909 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 400668013910 Protein of unknown function (DUF524); Region: DUF524; pfam04411 400668013911 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 400668013912 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 400668013913 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 400668013914 cofactor binding site; other site 400668013915 DNA binding site [nucleotide binding] 400668013916 substrate interaction site [chemical binding]; other site 400668013917 HipA N-terminal domain; Region: Couple_hipA; cl11853 400668013918 HipA-like N-terminal domain; Region: HipA_N; pfam07805 400668013919 HipA-like C-terminal domain; Region: HipA_C; pfam07804 400668013920 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 400668013921 Cupin domain; Region: Cupin_2; cl09118 400668013922 Helix-turn-helix domain; Region: HTH_18; pfam12833 400668013923 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668013924 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 400668013925 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 400668013926 putative substrate translocation pore; other site 400668013927 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668013928 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668013929 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 400668013930 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 400668013931 dimer interface [polypeptide binding]; other site 400668013932 phosphorylation site [posttranslational modification] 400668013933 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 400668013934 ATP binding site [chemical binding]; other site 400668013935 Mg2+ binding site [ion binding]; other site 400668013936 G-X-G motif; other site 400668013937 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 400668013938 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 400668013939 Domain of unknown function (DUF3369); Region: DUF3369; pfam11849 400668013940 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 400668013941 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 400668013942 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 400668013943 catalytic site [active] 400668013944 G-X2-G-X-G-K; other site 400668013945 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 400668013946 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 400668013947 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 400668013948 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 400668013949 synthetase active site [active] 400668013950 NTP binding site [chemical binding]; other site 400668013951 metal binding site [ion binding]; metal-binding site 400668013952 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 400668013953 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 400668013954 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 400668013955 homotrimer interaction site [polypeptide binding]; other site 400668013956 putative active site [active] 400668013957 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 400668013958 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 400668013959 putative NAD(P) binding site [chemical binding]; other site 400668013960 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 400668013961 Helix-turn-helix domains; Region: HTH; cl00088 400668013962 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 400668013963 dimerization interface [polypeptide binding]; other site 400668013964 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 400668013965 Y-family of DNA polymerases; Region: PolY; cl12025 400668013966 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 400668013967 generic binding surface II; other site 400668013968 ssDNA binding site; other site 400668013969 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 400668013970 ATP binding site [chemical binding]; other site 400668013971 putative Mg++ binding site [ion binding]; other site 400668013972 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 400668013973 nucleotide binding region [chemical binding]; other site 400668013974 ATP-binding site [chemical binding]; other site 400668013975 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 400668013976 Helix-turn-helix domains; Region: HTH; cl00088 400668013977 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 400668013978 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 400668013979 substrate binding pocket [chemical binding]; other site 400668013980 membrane-bound complex binding site; other site 400668013981 hinge residues; other site 400668013982 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 400668013983 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 400668013984 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 400668013985 dimer interface [polypeptide binding]; other site 400668013986 conserved gate region; other site 400668013987 putative PBP binding loops; other site 400668013988 ABC-ATPase subunit interface; other site 400668013989 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 400668013990 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 400668013991 dimer interface [polypeptide binding]; other site 400668013992 conserved gate region; other site 400668013993 putative PBP binding loops; other site 400668013994 ABC-ATPase subunit interface; other site 400668013995 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 400668013996 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 400668013997 Walker A/P-loop; other site 400668013998 ATP binding site [chemical binding]; other site 400668013999 Q-loop/lid; other site 400668014000 ABC transporter signature motif; other site 400668014001 Walker B; other site 400668014002 D-loop; other site 400668014003 H-loop/switch region; other site 400668014004 HDOD domain; Region: HDOD; pfam08668 400668014005 UTRA domain; Region: UTRA; cl01230 400668014006 UbiA prenyltransferase family; Region: UbiA; cl00337 400668014007 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 400668014008 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 400668014009 active site 400668014010 phosphorylation site [posttranslational modification] 400668014011 intermolecular recognition site; other site 400668014012 dimerization interface [polypeptide binding]; other site 400668014013 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 400668014014 DNA binding site [nucleotide binding] 400668014015 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 400668014016 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 400668014017 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 400668014018 dimer interface [polypeptide binding]; other site 400668014019 phosphorylation site [posttranslational modification] 400668014020 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 400668014021 ATP binding site [chemical binding]; other site 400668014022 Mg2+ binding site [ion binding]; other site 400668014023 G-X-G motif; other site 400668014024 Response regulator receiver domain; Region: Response_reg; pfam00072 400668014025 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 400668014026 active site 400668014027 phosphorylation site [posttranslational modification] 400668014028 intermolecular recognition site; other site 400668014029 dimerization interface [polypeptide binding]; other site 400668014030 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 400668014031 oligopeptide ABC transporter substrate-binding protein OppA; Provisional; Region: PRK15104 400668014032 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 400668014033 peptide binding site [polypeptide binding]; other site 400668014034 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 400668014035 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 400668014036 dimer interface [polypeptide binding]; other site 400668014037 conserved gate region; other site 400668014038 putative PBP binding loops; other site 400668014039 ABC-ATPase subunit interface; other site 400668014040 oligopeptide ABC transporter permease OppC; Provisional; Region: PRK15406 400668014041 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 400668014042 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 400668014043 dimer interface [polypeptide binding]; other site 400668014044 conserved gate region; other site 400668014045 putative PBP binding loops; other site 400668014046 ABC-ATPase subunit interface; other site 400668014047 oligopeptide transporter ATP-binding component; Provisional; Region: oppD; PRK09473 400668014048 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 400668014049 Walker A/P-loop; other site 400668014050 ATP binding site [chemical binding]; other site 400668014051 Q-loop/lid; other site 400668014052 ABC transporter signature motif; other site 400668014053 Walker B; other site 400668014054 D-loop; other site 400668014055 H-loop/switch region; other site 400668014056 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668014057 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 400668014058 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 400668014059 Walker A/P-loop; other site 400668014060 ATP binding site [chemical binding]; other site 400668014061 Q-loop/lid; other site 400668014062 ABC transporter signature motif; other site 400668014063 Walker B; other site 400668014064 D-loop; other site 400668014065 H-loop/switch region; other site 400668014066 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668014067 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 400668014068 hybrid sensory histidine kinase BarA; Provisional; Region: PRK11107 400668014069 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 400668014070 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 400668014071 ATP binding site [chemical binding]; other site 400668014072 Mg2+ binding site [ion binding]; other site 400668014073 G-X-G motif; other site 400668014074 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 400668014075 GAF domain; Region: GAF; cl15785 400668014076 transcriptional regulator PhoU; Provisional; Region: PRK11115 400668014077 PhoU domain; Region: PhoU; pfam01895 400668014078 PhoU domain; Region: PhoU; pfam01895 400668014079 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 400668014080 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 400668014081 Walker A/P-loop; other site 400668014082 ATP binding site [chemical binding]; other site 400668014083 Q-loop/lid; other site 400668014084 ABC transporter signature motif; other site 400668014085 Walker B; other site 400668014086 D-loop; other site 400668014087 H-loop/switch region; other site 400668014088 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]; Region: COG4985 400668014089 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 400668014090 dimer interface [polypeptide binding]; other site 400668014091 conserved gate region; other site 400668014092 putative PBP binding loops; other site 400668014093 ABC-ATPase subunit interface; other site 400668014094 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 400668014095 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 400668014096 dimer interface [polypeptide binding]; other site 400668014097 conserved gate region; other site 400668014098 putative PBP binding loops; other site 400668014099 ABC-ATPase subunit interface; other site 400668014100 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 400668014101 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 400668014102 dimerization interface [polypeptide binding]; other site 400668014103 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 400668014104 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 400668014105 ATP binding site [chemical binding]; other site 400668014106 Mg2+ binding site [ion binding]; other site 400668014107 G-X-G motif; other site 400668014108 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 400668014109 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 400668014110 active site 400668014111 phosphorylation site [posttranslational modification] 400668014112 intermolecular recognition site; other site 400668014113 dimerization interface [polypeptide binding]; other site 400668014114 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 400668014115 Walker A motif; other site 400668014116 ATP binding site [chemical binding]; other site 400668014117 Walker B motif; other site 400668014118 arginine finger; other site 400668014119 Helix-turn-helix domains; Region: HTH; cl00088 400668014120 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 400668014121 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_Arsenic_SBP_like; cd06330 400668014122 putative ligand binding site [chemical binding]; other site 400668014123 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 400668014124 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 400668014125 tetramerization interface [polypeptide binding]; other site 400668014126 NAD(P) binding site [chemical binding]; other site 400668014127 catalytic residues [active] 400668014128 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 400668014129 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 400668014130 putative active site [active] 400668014131 metal binding site [ion binding]; metal-binding site 400668014132 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 400668014133 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 400668014134 DctM-like transporters; Region: DctM; pfam06808 400668014135 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 400668014136 Zeta-crystallin with NADP-dependent quinone reductase activity (QOR); Region: zeta_crystallin; cd08253 400668014137 NAD(P) binding site [chemical binding]; other site 400668014138 Cupin domain; Region: Cupin_2; cl09118 400668014139 DNA-binding transcriptional regulator ChbR; Provisional; Region: PRK10296 400668014140 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668014141 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668014142 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668014143 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 400668014144 Proline dehydrogenase; Region: Pro_dh; cl03282 400668014145 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 400668014146 Glutamate binding site [chemical binding]; other site 400668014147 NAD binding site [chemical binding]; other site 400668014148 catalytic residues [active] 400668014149 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 400668014150 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 400668014151 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 400668014152 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 400668014153 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 400668014154 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 400668014155 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 400668014156 dimer interface [polypeptide binding]; other site 400668014157 phosphorylation site [posttranslational modification] 400668014158 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 400668014159 ATP binding site [chemical binding]; other site 400668014160 Mg2+ binding site [ion binding]; other site 400668014161 G-X-G motif; other site 400668014162 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668014163 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 400668014164 active site 400668014165 phosphorylation site [posttranslational modification] 400668014166 intermolecular recognition site; other site 400668014167 dimerization interface [polypeptide binding]; other site 400668014168 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 400668014169 DNA binding site [nucleotide binding] 400668014170 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 400668014171 NMT1-like family; Region: NMT1_2; cl15260 400668014172 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 400668014173 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 400668014174 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668014175 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 400668014176 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668014177 DNA-binding site [nucleotide binding]; DNA binding site 400668014178 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 400668014179 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668014180 homodimer interface [polypeptide binding]; other site 400668014181 catalytic residue [active] 400668014182 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 400668014183 intersubunit interface [polypeptide binding]; other site 400668014184 active site 400668014185 Zn2+ binding site [ion binding]; other site 400668014186 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 400668014187 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 400668014188 inhibitor site; inhibition site 400668014189 active site 400668014190 dimer interface [polypeptide binding]; other site 400668014191 catalytic residue [active] 400668014192 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 400668014193 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668014194 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 400668014195 putative oxidoreductase; Provisional; Region: PRK11579 400668014196 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668014197 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 400668014198 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 400668014199 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 400668014200 Family description; Region: UvrD_C_2; cl15862 400668014201 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 400668014202 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 400668014203 pyridoxal 5'-phosphate binding site [chemical binding]; other site 400668014204 homodimer interface [polypeptide binding]; other site 400668014205 catalytic residue [active] 400668014206 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 400668014207 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 400668014208 catalytic residues [active] 400668014209 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 400668014210 active site 400668014211 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 400668014212 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 400668014213 Sulfatase; Region: Sulfatase; cl10460 400668014214 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 400668014215 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 400668014216 DNA-binding site [nucleotide binding]; DNA binding site 400668014217 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 400668014218 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668014219 catalytic residue [active] 400668014220 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 400668014221 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 400668014222 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 400668014223 catalytic residue [active] 400668014224 Fe-S metabolism associated domain; Region: SufE; cl00951 400668014225 LysE type translocator; Region: LysE; cl00565 400668014226 Helix-turn-helix domains; Region: HTH; cl00088 400668014227 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 400668014228 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 400668014229 dimerization interface [polypeptide binding]; other site 400668014230 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 400668014231 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 400668014232 Walker A/P-loop; other site 400668014233 ATP binding site [chemical binding]; other site 400668014234 Q-loop/lid; other site 400668014235 ABC transporter signature motif; other site 400668014236 Walker B; other site 400668014237 D-loop; other site 400668014238 H-loop/switch region; other site 400668014239 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668014240 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 400668014241 Walker A/P-loop; other site 400668014242 ATP binding site [chemical binding]; other site 400668014243 Q-loop/lid; other site 400668014244 ABC transporter signature motif; other site 400668014245 Walker B; other site 400668014246 D-loop; other site 400668014247 H-loop/switch region; other site 400668014248 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 400668014249 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 400668014250 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 400668014251 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 400668014252 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 400668014253 dimer interface [polypeptide binding]; other site 400668014254 conserved gate region; other site 400668014255 putative PBP binding loops; other site 400668014256 ABC-ATPase subunit interface; other site 400668014257 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 400668014258 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 400668014259 dimer interface [polypeptide binding]; other site 400668014260 conserved gate region; other site 400668014261 putative PBP binding loops; other site 400668014262 ABC-ATPase subunit interface; other site 400668014263 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_5; cd06232 400668014264 putative active site [active] 400668014265 Zn binding site [ion binding]; other site 400668014266 sulfur acceptor protein CsdL; Provisional; Region: PRK15116 400668014267 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 400668014268 putative ATP binding site [chemical binding]; other site 400668014269 putative substrate interface [chemical binding]; other site 400668014270 Predicted transcriptional regulators [Transcription]; Region: COG1378 400668014271 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 400668014272 dimerization interface [polypeptide binding]; other site 400668014273 putative Zn2+ binding site [ion binding]; other site 400668014274 putative DNA binding site [nucleotide binding]; other site 400668014275 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 400668014276 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 400668014277 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 400668014278 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 400668014279 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 400668014280 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 400668014281 alpha subunit interaction interface [polypeptide binding]; other site 400668014282 Walker A motif; other site 400668014283 ATP binding site [chemical binding]; other site 400668014284 Walker B motif; other site 400668014285 inhibitor binding site; inhibition site 400668014286 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 400668014287 ATP synthase; Region: ATP-synt; cl00365 400668014288 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 400668014289 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 400668014290 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 400668014291 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 400668014292 beta subunit interaction interface [polypeptide binding]; other site 400668014293 Walker A motif; other site 400668014294 ATP binding site [chemical binding]; other site 400668014295 Walker B motif; other site 400668014296 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 400668014297 Plant ATP synthase F0; Region: YMF19; cl07975 400668014298 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 400668014299 Plant ATP synthase F0; Region: YMF19; cl07975 400668014300 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 400668014301 ATP synthase subunit C; Region: ATP-synt_C; cl00466 400668014302 ATP synthase A chain; Region: ATP-synt_A; cl00413 400668014303 ATP synthase I chain; Region: ATP_synt_I; cl09170 400668014304 ParB-like partition proteins; Region: parB_part; TIGR00180 400668014305 ParB-like nuclease domain; Region: ParBc; cl02129 400668014306 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 400668014307 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 400668014308 P-loop; other site 400668014309 Magnesium ion binding site [ion binding]; other site 400668014310 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 400668014311 Magnesium ion binding site [ion binding]; other site 400668014312 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl15754 400668014313 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 400668014314 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668014315 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 400668014316 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 400668014317 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 400668014318 putative NAD(P) binding site [chemical binding]; other site 400668014319 putative substrate binding site [chemical binding]; other site 400668014320 catalytic Zn binding site [ion binding]; other site 400668014321 structural Zn binding site [ion binding]; other site 400668014322 dimer interface [polypeptide binding]; other site 400668014323 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 400668014324 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668014325 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 400668014326 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668014327 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 400668014328 Helix-turn-helix domains; Region: HTH; cl00088 400668014329 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 400668014330 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 400668014331 NADP binding site [chemical binding]; other site 400668014332 dimer interface [polypeptide binding]; other site 400668014333 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 400668014334 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 400668014335 dimer interface [polypeptide binding]; other site 400668014336 phosphorylation site [posttranslational modification] 400668014337 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 400668014338 ATP binding site [chemical binding]; other site 400668014339 Mg2+ binding site [ion binding]; other site 400668014340 G-X-G motif; other site 400668014341 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 400668014342 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 400668014343 active site 400668014344 phosphorylation site [posttranslational modification] 400668014345 intermolecular recognition site; other site 400668014346 dimerization interface [polypeptide binding]; other site 400668014347 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 400668014348 DNA binding site [nucleotide binding] 400668014349 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 400668014350 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668014351 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 400668014352 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 400668014353 Cation transport protein; Region: TrkH; cl10514 400668014354 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 400668014355 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 400668014356 NAD(P) binding site [chemical binding]; other site 400668014357 active site 400668014358 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 400668014359 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 400668014360 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 400668014361 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 400668014362 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 400668014363 trmE is a tRNA modification GTPase; Region: trmE; cd04164 400668014364 G1 box; other site 400668014365 GTP/Mg2+ binding site [chemical binding]; other site 400668014366 Switch I region; other site 400668014367 G2 box; other site 400668014368 Switch II region; other site 400668014369 G3 box; other site 400668014370 G4 box; other site 400668014371 G5 box; other site 400668014372 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 400668014373 membrane protein insertase; Provisional; Region: PRK01318 400668014374 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 400668014375 Ribonuclease P; Region: Ribonuclease_P; cl00457 400668014376 Ribosomal protein L34; Region: Ribosomal_L34; cl00370