-- dump date 20111121_013240 -- class Genbank::misc_feature -- table misc_feature_note -- id note 887061000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 887061000002 hypothetical protein; Validated; Region: PRK06672 887061000003 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...; Region: AAA; cd00009 887061000004 Walker A motif; other site 887061000005 ATP binding site [chemical binding]; other site 887061000006 Walker B motif; other site 887061000007 arginine finger; other site 887061000008 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 887061000009 DnaA box-binding interface [nucleotide binding]; other site 887061000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 887061000011 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...; Region: beta_clamp; cd00140 887061000012 putative DNA binding surface [nucleotide binding]; other site 887061000013 dimer interface [polypeptide binding]; other site 887061000014 beta-clamp/clamp loader binding surface; other site 887061000015 beta-clamp/translesion DNA polymerase binding surface; other site 887061000016 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 887061000017 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 887061000018 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 887061000019 anchoring element; other site 887061000020 dimer interface [polypeptide binding]; other site 887061000021 ATP binding site [chemical binding]; other site 887061000022 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...; Region: TOPRIM_TopoIIA_GyrB; cd03366 887061000023 active site 887061000024 putative metal-binding site [ion binding]; other site 887061000025 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 887061000026 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 887061000027 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 887061000028 G1 box; other site 887061000029 GTP/Mg2+ binding site [chemical binding]; other site 887061000030 Switch I region; other site 887061000031 G2 box; other site 887061000032 G3 box; other site 887061000033 Switch II region; other site 887061000034 G4 box; other site 887061000035 G5 box; other site 887061000036 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 887061000037 ATP binding site [chemical binding]; other site 887061000038 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 887061000039 CrcB-like protein; Region: CRCB; cl09114 887061000040 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 887061000041 Predicted dehydrogenase [General function prediction only]; Region: COG0579 887061000042 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 887061000043 domain; Region: Glyco_hydro_2; pfam00703 887061000044 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; cl14895 887061000045 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 887061000046 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 887061000047 putative substrate translocation pore; other site 887061000048 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061000049 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 887061000050 putative active site [active] 887061000051 heme pocket [chemical binding]; other site 887061000052 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 887061000053 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061000054 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 887061000055 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 887061000056 PAS fold; Region: PAS_4; pfam08448 887061000057 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 887061000058 GAF domain; Region: GAF; cl00853 887061000059 PAS fold; Region: PAS_4; pfam08448 887061000060 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 887061000061 putative active site [active] 887061000062 heme pocket [chemical binding]; other site 887061000063 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061000064 metal binding site [ion binding]; metal-binding site 887061000065 active site 887061000066 I-site; other site 887061000067 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 887061000068 Cytochrome c; Region: Cytochrom_C; cl11414 887061000069 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061000070 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061000071 Trp docking motif; other site 887061000072 'Velcro' closure; other site 887061000073 active site 887061000074 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 887061000075 GAF domain; Region: GAF; cl00853 887061000076 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...; Region: AAA; cd00009 887061000077 Walker A motif; other site 887061000078 ATP binding site [chemical binding]; other site 887061000079 Walker B motif; other site 887061000080 arginine finger; other site 887061000081 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061000082 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 887061000083 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061000084 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 887061000085 dimerization interface [polypeptide binding]; other site 887061000086 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061000087 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 887061000088 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 887061000089 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 887061000090 S-adenosylmethionine binding site [chemical binding]; other site 887061000091 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 887061000092 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061000093 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061000094 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 887061000095 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 887061000096 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 887061000097 carboxyltransferase (CT) interaction site; other site 887061000098 biotinylation site [posttranslational modification]; other site 887061000099 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 887061000100 trimer interface [polypeptide binding]; other site 887061000101 active site 887061000102 dimer interface [polypeptide binding]; other site 887061000103 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...; Region: TlpA_like_family; cd02966 887061000104 catalytic residues [active] 887061000105 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 887061000106 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 887061000107 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 887061000108 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 887061000109 DsbD alpha interface [polypeptide binding]; other site 887061000110 catalytic residues [active] 887061000111 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 887061000112 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 887061000113 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 887061000114 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 887061000115 catalytic loop [active] 887061000116 iron binding site [ion binding]; other site 887061000117 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...; Region: flavin_oxioreductase; cd06189 887061000118 FAD binding pocket [chemical binding]; other site 887061000119 FAD binding motif [chemical binding]; other site 887061000120 phosphate binding motif [ion binding]; other site 887061000121 beta-alpha-beta structure motif; other site 887061000122 NAD binding pocket [chemical binding]; other site 887061000123 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 887061000124 HemY protein N-terminus; Region: HemY_N; pfam07219 887061000125 HemX; Region: HemX; cl14667 887061000126 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 887061000127 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...; Region: HemD; cd06578 887061000128 active site 887061000129 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 887061000130 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 887061000131 domain interfaces; other site 887061000132 active site 887061000133 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 887061000134 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 887061000135 active site 887061000136 phosphorylation site [posttranslational modification] 887061000137 intermolecular recognition site; other site 887061000138 dimerization interface [polypeptide binding]; other site 887061000139 LytTr DNA-binding domain; Region: LytTR; cl04498 887061000140 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 887061000141 Histidine kinase; Region: His_kinase; pfam06580 887061000142 argininosuccinate lyase; Provisional; Region: PRK00855 887061000143 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 887061000144 active sites [active] 887061000145 tetramer interface [polypeptide binding]; other site 887061000146 Chlorophyllase enzyme; Region: Chlorophyllase2; cl14889 887061000147 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 887061000148 cellulose synthase catalytic subunit (UDP-forming); Region: CelA; TIGR03030 887061000149 CESA_CelA_like are involved in the elongation of the glucan chain of cellulose; Region: CESA_CelA_like; cd06421 887061000150 DXD motif; other site 887061000151 PilZ domain; Region: PilZ; cl01260 887061000152 Bacterial cellulose synthase subunit; Region: BcsB; pfam03170 887061000153 cellulose synthase regulator protein; Provisional; Region: PRK11114 887061000154 cyclase homology domain; Region: CHD; cd07302 887061000155 metal binding site [ion binding]; metal-binding site 887061000156 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 887061000157 Cellulose synthase operon protein C C-terminus (BCSC_C); Region: BCSC_C; pfam05420 887061000158 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 887061000159 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 887061000160 FeS/SAM binding site; other site 887061000161 HemN C-terminal region; Region: HemN_C; pfam06969 887061000162 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 Ham1-...; Region: HAM1; cd00515 887061000163 active site 887061000164 dimerization interface [polypeptide binding]; other site 887061000165 ribonuclease PH; Reviewed; Region: rph; PRK00173 887061000166 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 887061000167 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 887061000168 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 887061000169 Active site [active] 887061000170 Protein kinase domain; Region: Pkinase; pfam00069 887061000171 Catalytic domain of Protein Kinases; Region: PKc; cd00180 887061000172 active site 887061000173 ATP binding site [chemical binding]; other site 887061000174 substrate binding site [chemical binding]; other site 887061000175 activation loop (A-loop); other site 887061000176 hypothetical protein; Provisional; Region: PRK11820 887061000177 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 887061000178 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 887061000179 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...; Region: GMPK; cd00071 887061000180 catalytic site [active] 887061000181 G-X2-G-X-G-K; other site 887061000182 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 887061000183 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 887061000184 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061000185 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 887061000186 synthetase active site [active] 887061000187 NTP binding site [chemical binding]; other site 887061000188 metal binding site [ion binding]; metal-binding site 887061000189 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...; Region: TGS_RelA_SpoT; cd01668 887061000190 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 887061000191 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 887061000192 homotrimer interaction site [polypeptide binding]; other site 887061000193 putative active site [active] 887061000194 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 887061000195 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 four-...; Region: RecG_wedge_OBF; cd04488 887061000196 generic binding surface II; other site 887061000197 ssDNA binding site; other site 887061000198 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 887061000199 ATP binding site [chemical binding]; other site 887061000200 putative Mg++ binding site [ion binding]; other site 887061000201 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 887061000202 nucleotide binding region [chemical binding]; other site 887061000203 ATP-binding site [chemical binding]; other site 887061000204 Chorismate lyase; Region: Chor_lyase; cl01230 887061000205 UbiA prenyltransferase family; Region: UbiA; cl00337 887061000206 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 887061000207 23S rRNA interface [nucleotide binding]; other site 887061000208 L3 interface [polypeptide binding]; other site 887061000209 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 887061000210 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 887061000211 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061000212 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 887061000213 Polymer-forming cytoskeletal; Region: Bactofilin; cl09137 887061000214 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 887061000215 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 887061000216 dimer interface [polypeptide binding]; other site 887061000217 Citrate synthase; Region: Citrate_synt; pfam00285 887061000218 active site 887061000219 citrylCoA binding site [chemical binding]; other site 887061000220 NADH binding [chemical binding]; other site 887061000221 cationic pore residues; other site 887061000222 oxalacetate/citrate binding site [chemical binding]; other site 887061000223 coenzyme A binding site [chemical binding]; other site 887061000224 catalytic triad [active] 887061000225 Uncharacterised protein family (UPF0075); Region: UPF0075; cl04217 887061000226 putative peptidase; Provisional; Region: PRK11649 887061000227 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061000228 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 887061000229 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 887061000230 active site 887061000231 HIGH motif; other site 887061000232 dimer interface [polypeptide binding]; other site 887061000233 KMSKS motif; other site 887061000234 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 887061000235 ribosome maturation protein RimP; Reviewed; Region: PRK00092 887061000236 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 887061000237 Sm1 motif; other site 887061000238 predicted subunit interaction site [polypeptide binding]; other site 887061000239 RNA binding pocket [nucleotide binding]; other site 887061000240 Sm2 motif; other site 887061000241 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 887061000242 NusA N-terminal domain; Region: NusA_N; pfam08529 887061000243 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...; Region: S1_NusA; cd04455 887061000244 RNA binding site [nucleotide binding]; other site 887061000245 homodimer interface [polypeptide binding]; other site 887061000246 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 887061000247 G-X-X-G motif; other site 887061000248 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 887061000249 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 887061000250 translation initiation factor IF-2; Validated; Region: infB; PRK05306 887061000251 translation initiation factor IF-2; Region: IF-2; TIGR00487 887061000252 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 887061000253 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 887061000254 G1 box; other site 887061000255 putative GEF interaction site [polypeptide binding]; other site 887061000256 GTP/Mg2+ binding site [chemical binding]; other site 887061000257 Switch I region; other site 887061000258 G2 box; other site 887061000259 G3 box; other site 887061000260 Switch II region; other site 887061000261 G4 box; other site 887061000262 G5 box; other site 887061000263 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...; Region: IF2_mtIF2_II; cd03702 887061000264 Translation-initiation factor 2; Region: IF-2; pfam11987 887061000265 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...; Region: mtIF2_IVc; cd03692 887061000266 Ribosome-binding factor A; Region: RBFA; cl00542 887061000267 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 887061000268 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...; Region: PseudoU_synth_EcTruB; cd02573 887061000269 RNA binding site [nucleotide binding]; other site 887061000270 active site 887061000271 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...; Region: Ribosomal_S15p_S13e; cd00353 887061000272 16S/18S rRNA binding site [nucleotide binding]; other site 887061000273 25S rRNA binding site [nucleotide binding]; other site 887061000274 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 887061000275 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 887061000276 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 887061000277 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 887061000278 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 887061000279 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 887061000280 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 887061000281 putative nucleic acid binding region [nucleotide binding]; other site 887061000282 G-X-X-G motif; other site 887061000283 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 887061000284 RNA binding site [nucleotide binding]; other site 887061000285 domain interface; other site 887061000286 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 887061000287 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 887061000288 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 887061000289 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 887061000290 homodimer interface [polypeptide binding]; other site 887061000291 NADP binding site [chemical binding]; other site 887061000292 substrate binding site [chemical binding]; other site 887061000293 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061000294 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 887061000295 active site 887061000296 phosphorylation site [posttranslational modification] 887061000297 intermolecular recognition site; other site 887061000298 dimerization interface [polypeptide binding]; other site 887061000299 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...; Region: AAA; cd00009 887061000300 Walker A motif; other site 887061000301 ATP binding site [chemical binding]; other site 887061000302 Walker B motif; other site 887061000303 arginine finger; other site 887061000304 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061000305 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061000306 Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]; Region: ExeA; COG3267 887061000307 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 887061000308 Sporulation related domain; Region: SPOR; cl10051 887061000309 Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulD; COG1450 887061000310 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 887061000311 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 887061000312 TPR motif; other site 887061000313 binding surface 887061000314 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 887061000315 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 887061000316 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 887061000317 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 887061000318 Walker A motif; other site 887061000319 ATP binding site [chemical binding]; other site 887061000320 Walker B motif; other site 887061000321 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061000322 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061000323 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061000324 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 887061000325 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...; Region: ThiF_MoeB_HesA_family; cd00757 887061000326 ATP binding site [chemical binding]; other site 887061000327 substrate interface [chemical binding]; other site 887061000328 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 887061000329 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 887061000330 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 887061000331 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 887061000332 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 887061000333 HIGH motif; other site 887061000334 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 887061000335 active site 887061000336 KMSKS motif; other site 887061000337 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 887061000338 tRNA binding surface [nucleotide binding]; other site 887061000339 anticodon binding site; other site 887061000340 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 887061000341 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 two-...; Region: SirA_YedF_YeeD; cd00291 887061000342 CPxP motif; other site 887061000343 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 887061000344 active site residue [active] 887061000345 Bacterial sugar transferase; Region: Bac_transf; cl00939 887061000346 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 887061000347 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 887061000348 putative NAD(P) binding site [chemical binding]; other site 887061000349 active site 887061000350 putative substrate binding site [chemical binding]; other site 887061000351 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 887061000352 active site 887061000353 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 887061000354 Rhamnan synthesis protein F; Region: RgpF; cl01529 887061000355 Hypothetical methyltransferase; Region: Methyltransf_13; pfam08421 887061000356 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 887061000357 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 887061000358 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 887061000359 NADP-binding site; other site 887061000360 homotetramer interface [polypeptide binding]; other site 887061000361 substrate binding site [chemical binding]; other site 887061000362 homodimer interface [polypeptide binding]; other site 887061000363 active site 887061000364 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061000365 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 887061000366 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 887061000367 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 887061000368 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 887061000369 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 887061000370 NADP-binding site; other site 887061000371 homotetramer interface [polypeptide binding]; other site 887061000372 substrate binding site [chemical binding]; other site 887061000373 homodimer interface [polypeptide binding]; other site 887061000374 active site 887061000375 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 887061000376 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...; Region: AAA; cd00009 887061000377 Walker A motif; other site 887061000378 ATP binding site [chemical binding]; other site 887061000379 Walker B motif; other site 887061000380 arginine finger; other site 887061000381 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061000382 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 887061000383 active site 887061000384 intersubunit interface [polypeptide binding]; other site 887061000385 Zn2+ binding site [ion binding]; other site 887061000386 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000387 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 887061000388 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...; Region: PBPb; cd00134 887061000389 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000390 substrate binding pocket [chemical binding]; other site 887061000391 membrane-bound complex binding site; other site 887061000392 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061000393 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 887061000394 Walker A/P-loop; other site 887061000395 ATP binding site [chemical binding]; other site 887061000396 Q-loop/lid; other site 887061000397 ABC transporter signature motif; other site 887061000398 Walker B; other site 887061000399 D-loop; other site 887061000400 H-loop/switch region; other site 887061000401 Gram-negative bacterial tonB protein; Region: TonB; cl10048 887061000402 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061000403 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061000404 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 887061000405 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061000406 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...; Region: TM_PBP2; cl00427 887061000407 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...; Region: TM_PBP2; cd06261 887061000408 dimer interface [polypeptide binding]; other site 887061000409 conserved gate region; other site 887061000410 putative PBP binding loops; other site 887061000411 ABC-ATPase subunit interface; other site 887061000412 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 887061000413 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061000414 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 887061000415 N-terminal plug; other site 887061000416 ligand-binding site [chemical binding]; other site 887061000417 choline dehydrogenase; Validated; Region: PRK02106 887061000418 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061000419 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 887061000420 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 887061000421 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 887061000422 NAD(P) binding site [chemical binding]; other site 887061000423 catalytic residues [active] 887061000424 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 887061000425 putative substrate translocation pore; other site 887061000426 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 887061000427 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 887061000428 dimer interface [polypeptide binding]; other site 887061000429 decamer (pentamer of dimers) interface [polypeptide binding]; other site 887061000430 catalytic triad [active] 887061000431 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000432 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 887061000433 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 887061000434 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 887061000435 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 887061000436 Walker A/P-loop; other site 887061000437 ATP binding site [chemical binding]; other site 887061000438 Q-loop/lid; other site 887061000439 ABC transporter signature motif; other site 887061000440 Walker B; other site 887061000441 D-loop; other site 887061000442 H-loop/switch region; other site 887061000443 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 887061000444 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 887061000445 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061000446 Walker A/P-loop; other site 887061000447 ATP binding site [chemical binding]; other site 887061000448 Q-loop/lid; other site 887061000449 ABC transporter signature motif; other site 887061000450 Walker B; other site 887061000451 D-loop; other site 887061000452 H-loop/switch region; other site 887061000453 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061000454 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 887061000455 N-terminal plug; other site 887061000456 ligand-binding site [chemical binding]; other site 887061000457 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 887061000458 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 887061000459 putative FMN binding site [chemical binding]; other site 887061000460 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 887061000461 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 887061000462 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 887061000463 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 887061000464 dimer interface [polypeptide binding]; other site 887061000465 active site 887061000466 non-prolyl cis peptide bond; other site 887061000467 insertion regions; other site 887061000468 PAS domain S-box; Region: sensory_box; TIGR00229 887061000469 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 887061000470 putative active site [active] 887061000471 heme pocket [chemical binding]; other site 887061000472 GAF domain; Region: GAF; cl00853 887061000473 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061000474 metal binding site [ion binding]; metal-binding site 887061000475 active site 887061000476 I-site; other site 887061000477 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 887061000478 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 887061000479 active site pocket [active] 887061000480 putative dimer interface [polypeptide binding]; other site 887061000481 putative cataytic base [active] 887061000482 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 887061000483 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 887061000484 catalytic core [active] 887061000485 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 887061000486 TPR motif; other site 887061000487 binding surface 887061000488 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 887061000489 binding surface 887061000490 TPR motif; other site 887061000491 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 887061000492 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 887061000493 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 887061000494 TPR motif; other site 887061000495 binding surface 887061000496 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 887061000497 TPR motif; other site 887061000498 binding surface 887061000499 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 887061000500 binding surface 887061000501 TPR motif; other site 887061000502 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 887061000503 binding surface 887061000504 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 887061000505 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 887061000506 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 887061000507 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061000508 homodimer interface [polypeptide binding]; other site 887061000509 catalytic residue [active] 887061000510 CobD/Cbib protein; Region: CobD_Cbib; cl00561 887061000511 cobyric acid synthase; Provisional; Region: PRK00784 887061000512 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061000513 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 887061000514 catalytic triad [active] 887061000515 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 887061000516 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is...; Region: CobU; cd00544 887061000517 homotrimer interface [polypeptide binding]; other site 887061000518 Walker A motif; other site 887061000519 GTP binding site [chemical binding]; other site 887061000520 Walker B motif; other site 887061000521 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...; Region: BtuF; cd01144 887061000522 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 887061000523 cobalamin binding residues [chemical binding]; other site 887061000524 putative BtuC binding residues; other site 887061000525 dimer interface [polypeptide binding]; other site 887061000526 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(; Region: BluB; cd02145 887061000527 putative FMN binding site [chemical binding]; other site 887061000528 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 887061000529 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 887061000530 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 887061000531 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061000532 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 887061000533 catalytic triad [active] 887061000534 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 887061000535 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 887061000536 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...; Region: CobA_CobO_BtuR; cd00561 887061000537 homodimer interface [polypeptide binding]; other site 887061000538 Walker A motif; other site 887061000539 ATP binding site [chemical binding]; other site 887061000540 hydroxycobalamin binding site [chemical binding]; other site 887061000541 Walker B motif; other site 887061000542 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 887061000543 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 887061000544 N-terminal plug; other site 887061000545 ligand-binding site [chemical binding]; other site 887061000546 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 887061000547 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 887061000548 N-terminal plug; other site 887061000549 ligand-binding site [chemical binding]; other site 887061000550 Cell division protein ZapA; Region: ZapA; cl01146 887061000551 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; cl01467 887061000552 EVE domain; Region: EVE; cl00728 887061000553 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061000554 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 887061000555 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...; Region: WD40; cl02567 887061000556 structural tetrad; other site 887061000557 threonine dehydratase; Reviewed; Region: PRK09224 887061000558 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 887061000559 tetramer interface [polypeptide binding]; other site 887061000560 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061000561 catalytic residue [active] 887061000562 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 887061000563 putative Ile/Val binding site [chemical binding]; other site 887061000564 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 887061000565 putative Ile/Val binding site [chemical binding]; other site 887061000566 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 887061000567 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061000568 active site 887061000569 dimer interface [polypeptide binding]; other site 887061000570 transcriptional regulator PhoU; Provisional; Region: PRK11115 887061000571 PhoU domain; Region: PhoU; pfam01895 887061000572 PhoU domain; Region: PhoU; pfam01895 887061000573 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 887061000574 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 887061000575 polyphosphate kinase; Provisional; Region: PRK05443 887061000576 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 887061000577 putative domain interface [polypeptide binding]; other site 887061000578 putative active site [active] 887061000579 catalytic site [active] 887061000580 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 887061000581 putative domain interface [polypeptide binding]; other site 887061000582 putative active site [active] 887061000583 catalytic site [active] 887061000584 Bacterial Fe(2+) trafficking; Region: Iron_traffic; cl01104 887061000585 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 887061000586 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 887061000587 N-terminal plug; other site 887061000588 ligand-binding site [chemical binding]; other site 887061000589 superoxide dismutase; Provisional; Region: PRK10543 887061000590 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 887061000591 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 887061000592 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 887061000593 N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 887061000594 Int/Topo IB signature motif; other site 887061000595 active site 887061000596 Protein of unknown function, DUF484; Region: DUF484; cl01228 887061000597 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 887061000598 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 887061000599 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 887061000600 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 887061000601 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 887061000602 putative acyl-acceptor binding pocket; other site 887061000603 S-adenosylmethionine synthetase; Validated; Region: PRK05250 887061000604 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 887061000605 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 887061000606 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 887061000607 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 887061000608 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061000609 Zn2+ binding site [ion binding]; other site 887061000610 Mg2+ binding site [ion binding]; other site 887061000611 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 887061000612 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; Region: AdoHcyase; cd00401 887061000613 oligomerization interface [polypeptide binding]; other site 887061000614 active site 887061000615 NAD+ binding site [chemical binding]; other site 887061000616 Membrane protein of unknown function; Region: DUF360; cl00850 887061000617 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 887061000618 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...; Region: MTHFR; cd00537 887061000619 FAD binding site [chemical binding]; other site 887061000620 Protein of unknown function (DUF494); Region: DUF494; cl01103 887061000621 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 887061000622 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 887061000623 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 887061000624 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(...; Region: Pep_deformylase; cd00487 887061000625 active site 887061000626 catalytic residues [active] 887061000627 metal binding site [ion binding]; metal-binding site 887061000628 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 887061000629 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 887061000630 putative active site [active] 887061000631 substrate binding site [chemical binding]; other site 887061000632 putative cosubstrate binding site; other site 887061000633 catalytic site [active] 887061000634 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 887061000635 substrate binding site [chemical binding]; other site 887061000636 Peptidase family M48; Region: Peptidase_M48; cl12018 887061000637 16S rRNA methyltransferase B; Provisional; Region: PRK10901 887061000638 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 rRNA-...; Region: NusB_Sun; cl00223 887061000639 putative RNA binding site [nucleotide binding]; other site 887061000640 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 887061000641 S-adenosylmethionine binding site [chemical binding]; other site 887061000642 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 887061000643 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 connected by an extended linker. The...; Region: HAMP; cd06225 887061000644 dimerization interface [polypeptide binding]; other site 887061000645 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 trans-...; Region: HisKA; cd00082 887061000646 dimer interface [polypeptide binding]; other site 887061000647 phosphorylation site [posttranslational modification] 887061000648 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 887061000649 ATP binding site [chemical binding]; other site 887061000650 Mg2+ binding site [ion binding]; other site 887061000651 G-X-G motif; other site 887061000652 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061000653 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 887061000654 active site 887061000655 phosphorylation site [posttranslational modification] 887061000656 intermolecular recognition site; other site 887061000657 dimerization interface [polypeptide binding]; other site 887061000658 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061000659 TfoX N-terminal domain; Region: TfoX_N; cl01167 887061000660 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 887061000661 putative phosphate binding site [ion binding]; other site 887061000662 putative catalytic site [active] 887061000663 active site 887061000664 metal binding site A [ion binding]; metal-binding site 887061000665 DNA binding site [nucleotide binding] 887061000666 putative AP binding site [nucleotide binding]; other site 887061000667 putative metal binding site B [ion binding]; other site 887061000668 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide...; Region: NrdH; cd02976 887061000669 catalytic residues [active] 887061000670 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 887061000671 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 887061000672 active site 887061000673 Zn binding site [ion binding]; other site 887061000674 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3296 887061000675 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 887061000676 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 887061000677 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 887061000678 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 887061000679 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 887061000680 dimerization domain swap beta strand [polypeptide binding]; other site 887061000681 regulatory protein interface [polypeptide binding]; other site 887061000682 active site 887061000683 regulatory phosphorylation site [posttranslational modification]; other site 887061000684 PTS_IIA, PTS system, mannose/sorbose 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_man; cd00006 887061000685 active pocket/dimerization site; other site 887061000686 active site 887061000687 phosphorylation site [posttranslational modification] 887061000688 P-loop ATPase protein family; Region: ATP_bind_2; cl10035 887061000689 HPr kinase/phosphorylase; Provisional; Region: PRK05428 887061000690 DRTGG domain; Region: DRTGG; cl12147 887061000691 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-...; Region: HprK_C; cd01918 887061000692 Hpr binding site; other site 887061000693 active site 887061000694 homohexamer subunit interaction site [polypeptide binding]; other site 887061000695 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 887061000696 30S subunit binding site; other site 887061000697 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 887061000698 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 887061000699 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 887061000700 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 887061000701 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 887061000702 Walker A/P-loop; other site 887061000703 ATP binding site [chemical binding]; other site 887061000704 Q-loop/lid; other site 887061000705 ABC transporter signature motif; other site 887061000706 Walker B; other site 887061000707 D-loop; other site 887061000708 H-loop/switch region; other site 887061000709 OstA-like protein; Region: OstA; cl00844 887061000710 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 887061000711 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 887061000712 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; cl11391 887061000713 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 887061000714 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 5-...; Region: SIS_Kpsf; cd05014 887061000715 putative active site [active] 887061000716 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 887061000717 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 887061000718 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 887061000719 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061000720 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 887061000721 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 887061000722 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 887061000723 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 887061000724 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...; Region: MoaC_PE; cd01420 887061000725 trimer interface [polypeptide binding]; other site 887061000726 dimer interface [polypeptide binding]; other site 887061000727 putative active site [active] 887061000728 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 887061000729 Peptidase family M48; Region: Peptidase_M48; cl12018 887061000730 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 887061000731 TPR motif; other site 887061000732 binding surface 887061000733 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 887061000734 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 887061000735 peroxiredoxin; Region: AhpC; TIGR03137 887061000736 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...; Region: PRX_Typ2cys; cd03015 887061000737 dimer interface [polypeptide binding]; other site 887061000738 decamer (pentamer of dimers) interface [polypeptide binding]; other site 887061000739 catalytic triad [active] 887061000740 peroxidatic and resolving cysteines [active] 887061000741 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 887061000742 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...; Region: AhpF_NTD_N; cd02974 887061000743 catalytic residue [active] 887061000744 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 887061000745 catalytic residues [active] 887061000746 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061000747 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061000748 Domain of unknown function DUF20; Region: UPF0118; cl00465 887061000749 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 887061000750 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...; Region: PurM; cd02196 887061000751 dimerization interface [polypeptide binding]; other site 887061000752 putative ATP binding site [chemical binding]; other site 887061000753 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 887061000754 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 887061000755 16S rRNA methyltransferase B; Provisional; Region: PRK14902 887061000756 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; cl12011 887061000757 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 887061000758 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 887061000759 EamA-like transporter family; Region: EamA; cl01037 887061000760 EamA-like transporter family; Region: EamA; cl01037 887061000761 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 887061000762 amidase catalytic site [active] 887061000763 Zn binding residues [ion binding]; other site 887061000764 substrate binding site [chemical binding]; other site 887061000765 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 887061000766 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 887061000767 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061000768 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 887061000769 active site 887061000770 phosphorylation site [posttranslational modification] 887061000771 intermolecular recognition site; other site 887061000772 dimerization interface [polypeptide binding]; other site 887061000773 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...; Region: AAA; cd00009 887061000774 Walker A motif; other site 887061000775 ATP binding site [chemical binding]; other site 887061000776 Walker B motif; other site 887061000777 arginine finger; other site 887061000778 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061000779 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061000780 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 trans-...; Region: HisKA; cd00082 887061000781 dimer interface [polypeptide binding]; other site 887061000782 phosphorylation site [posttranslational modification] 887061000783 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 887061000784 ATP binding site [chemical binding]; other site 887061000785 Mg2+ binding site [ion binding]; other site 887061000786 G-X-G motif; other site 887061000787 RNA polymerase factor sigma-70; Validated; Region: PRK09047 887061000788 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...; Region: Sigma70_r4; cd06171 887061000789 DNA binding residues [nucleotide binding] 887061000790 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 887061000791 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 887061000792 RDD family; Region: RDD; cl00746 887061000793 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 887061000794 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 887061000795 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 887061000796 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 887061000797 multifunctional aminopeptidase A; Provisional; Region: PRK00913 887061000798 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...; Region: Peptidase_M17; cd00433 887061000799 interface (dimer of trimers) [polypeptide binding]; other site 887061000800 Substrate-binding/catalytic site; other site 887061000801 Zn-binding sites [ion binding]; other site 887061000802 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 887061000803 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 L-...; Region: GCS_H; cd06848 887061000804 lipoyl attachment site [posttranslational modification]; other site 887061000805 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 887061000806 Beta-lactamase; Region: Beta-lactamase; cl01009 887061000807 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 887061000808 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...; Region: TOPRIM_TopoIA_TopoI; cd03363 887061000809 active site 887061000810 interdomain interaction site; other site 887061000811 putative metal-binding site [ion binding]; other site 887061000812 nucleotide binding site [chemical binding]; other site 887061000813 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...; Region: TOP1Ac; cd00186 887061000814 domain I; other site 887061000815 DNA binding groove [nucleotide binding] 887061000816 phosphate binding site [ion binding]; other site 887061000817 domain II; other site 887061000818 domain III; other site 887061000819 nucleotide binding site [chemical binding]; other site 887061000820 catalytic site [active] 887061000821 domain IV; other site 887061000822 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 887061000823 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 887061000824 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...; Region: Alpha_ANH_like_II; cd01993 887061000825 Ligand Binding Site [chemical binding]; other site 887061000826 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 887061000827 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 887061000828 NADP binding site [chemical binding]; other site 887061000829 substrate binding pocket [chemical binding]; other site 887061000830 active site 887061000831 Uncharacterized conserved protein [Function unknown]; Region: COG1565 887061000832 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 887061000833 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; cl12011 887061000834 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 887061000835 G1 box; other site 887061000836 GTP/Mg2+ binding site [chemical binding]; other site 887061000837 Switch I region; other site 887061000838 G2 box; other site 887061000839 G3 box; other site 887061000840 Switch II region; other site 887061000841 G4 box; other site 887061000842 G5 box; other site 887061000843 Cytochrome c; Region: Cytochrom_C; cl11414 887061000844 Cytochrome c; Region: Cytochrom_C; cl11414 887061000845 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 887061000846 ResB-like family; Region: ResB; pfam05140 887061000847 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 887061000848 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061000849 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 887061000850 ATP binding site [chemical binding]; other site 887061000851 Mg2+ binding site [ion binding]; other site 887061000852 G-X-G motif; other site 887061000853 putative ABC transporter ATP-binding protein YrbF; Provisional; Region: PRK11831 887061000854 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 887061000855 Walker A/P-loop; other site 887061000856 ATP binding site [chemical binding]; other site 887061000857 Q-loop/lid; other site 887061000858 ABC transporter signature motif; other site 887061000859 Walker B; other site 887061000860 D-loop; other site 887061000861 H-loop/switch region; other site 887061000862 Domain of unknown function DUF140; Region: DUF140; cl00510 887061000863 mce related protein; Region: MCE; cl03606 887061000864 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 887061000865 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 887061000866 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 887061000867 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 887061000868 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency...; Region: ABC_subfamily_A; cd03263 887061000869 Walker A/P-loop; other site 887061000870 ATP binding site [chemical binding]; other site 887061000871 Q-loop/lid; other site 887061000872 ABC transporter signature motif; other site 887061000873 Walker B; other site 887061000874 D-loop; other site 887061000875 H-loop/switch region; other site 887061000876 ABC-2 type transporter; Region: ABC2_membrane; cl11417 887061000877 BolA-like protein; Region: BolA; cl00386 887061000878 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 887061000879 putative GSH binding site [chemical binding]; other site 887061000880 catalytic residues [active] 887061000881 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated; Region: PRK09369 887061000882 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 887061000883 hinge; other site 887061000884 active site 887061000885 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 887061000886 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 887061000887 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 oxidation of L-histidinol to L-...; Region: Histidinol_dh; cd06572 887061000888 NAD binding site [chemical binding]; other site 887061000889 dimerization interface [polypeptide binding]; other site 887061000890 product binding site; other site 887061000891 substrate binding site [chemical binding]; other site 887061000892 zinc binding site [ion binding]; other site 887061000893 catalytic residues [active] 887061000894 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 887061000895 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 887061000896 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061000897 homodimer interface [polypeptide binding]; other site 887061000898 catalytic residue [active] 887061000899 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 887061000900 active site 887061000901 dimer interface [polypeptide binding]; other site 887061000902 magnesium binding site [ion binding]; other site 887061000903 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 887061000904 putative active site pocket [active] 887061000905 4-fold oligomerization interface [polypeptide binding]; other site 887061000906 metal binding residues [ion binding]; metal-binding site 887061000907 3-fold/trimer interface [polypeptide binding]; other site 887061000908 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 887061000909 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 887061000910 putative active site [active] 887061000911 oxyanion strand; other site 887061000912 catalytic triad [active] 887061000913 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 887061000914 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-...; Region: HisA; cd04732 887061000915 catalytic residues [active] 887061000916 Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]; Region: HisF; COG0107 887061000917 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)-formimino-5-; Region: HisF; cd04731 887061000918 substrate binding site [chemical binding]; other site 887061000919 glutamase interaction surface [polypeptide binding]; other site 887061000920 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 887061000921 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 887061000922 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 887061000923 nucleotide binding site/active site [active] 887061000924 HIT family signature motif; other site 887061000925 catalytic residue [active] 887061000926 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 887061000927 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 887061000928 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 887061000929 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...; Region: Tryp_SPc; cl00149 887061000930 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 C-...; Region: PDZ_serine_protease; cd00987 887061000931 protein binding site [polypeptide binding]; other site 887061000932 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl01309 887061000933 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 887061000934 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 887061000935 [2Fe-2S] cluster binding site [ion binding]; other site 887061000936 cytochrome b; Provisional; Region: CYTB; MTH00145 887061000937 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cd00284 887061000938 Qi binding site; other site 887061000939 intrachain domain interface; other site 887061000940 interchain domain interface [polypeptide binding]; other site 887061000941 heme bH binding site [chemical binding]; other site 887061000942 heme bL binding site [chemical binding]; other site 887061000943 Qo binding site; other site 887061000944 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: cytochrome_b_C; cd00290 887061000945 interchain domain interface [polypeptide binding]; other site 887061000946 intrachain domain interface; other site 887061000947 Qi binding site; other site 887061000948 Qo binding site; other site 887061000949 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 887061000950 stringent starvation protein A; Provisional; Region: sspA; PRK09481 887061000951 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 887061000952 C-terminal domain interface [polypeptide binding]; other site 887061000953 putative GSH binding site (G-site) [chemical binding]; other site 887061000954 dimer interface [polypeptide binding]; other site 887061000955 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_C_SspA; cd03186 887061000956 dimer interface [polypeptide binding]; other site 887061000957 N-terminal domain interface [polypeptide binding]; other site 887061000958 Stringent starvation protein B; Region: SspB; cl01120 887061000959 elongation factor Tu; Reviewed; Region: PRK00049 887061000960 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 887061000961 G1 box; other site 887061000962 GEF interaction site [polypeptide binding]; other site 887061000963 GTP/Mg2+ binding site [chemical binding]; other site 887061000964 Switch I region; other site 887061000965 G2 box; other site 887061000966 G3 box; other site 887061000967 Switch II region; other site 887061000968 G4 box; other site 887061000969 G5 box; other site 887061000970 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 887061000971 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 887061000972 Antibiotic Binding Site [chemical binding]; other site 887061000973 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 887061000974 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 887061000975 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 887061000976 putative homodimer interface [polypeptide binding]; other site 887061000977 KOW (Kyprides, Ouzounis, Woese) motif; Region: KOW; smart00739 887061000978 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 887061000979 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 887061000980 23S rRNA interface [nucleotide binding]; other site 887061000981 L7/L12 interface [polypeptide binding]; other site 887061000982 putative thiostrepton binding site; other site 887061000983 L25 interface [polypeptide binding]; other site 887061000984 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...; Region: Ribosomal_L1; cd00403 887061000985 mRNA/rRNA interface [nucleotide binding]; other site 887061000986 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...; Region: Ribosomal_L10; cd05797 887061000987 23S rRNA interface [nucleotide binding]; other site 887061000988 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 887061000989 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 887061000990 core dimer interface [polypeptide binding]; other site 887061000991 peripheral dimer interface [polypeptide binding]; other site 887061000992 L10 interface [polypeptide binding]; other site 887061000993 L11 interface [polypeptide binding]; other site 887061000994 putative EF-Tu interaction site [polypeptide binding]; other site 887061000995 putative EF-G interaction site [polypeptide binding]; other site 887061000996 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 887061000997 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 887061000998 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 887061000999 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 887061001000 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 887061001001 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 887061001002 RPB11 interaction site [polypeptide binding]; other site 887061001003 RPB12 interaction site [polypeptide binding]; other site 887061001004 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 887061001005 RPB3 interaction site [polypeptide binding]; other site 887061001006 RPB1 interaction site [polypeptide binding]; other site 887061001007 RPB11 interaction site [polypeptide binding]; other site 887061001008 RPB10 interaction site [polypeptide binding]; other site 887061001009 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 887061001010 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 887061001011 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 887061001012 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 887061001013 DNA-directed RNA polymerase, beta'' subunit; Region: rpoC2_cyan; TIGR02388 887061001014 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 887061001015 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 887061001016 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 887061001017 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 887061001018 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 887061001019 DNA binding site [nucleotide binding] 887061001020 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 887061001021 Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the...; Region: Ribosomal_S12_like; cl00312 887061001022 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 887061001023 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 887061001024 elongation factor G; Reviewed; Region: PRK00007 887061001025 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 887061001026 G1 box; other site 887061001027 putative GEF interaction site [polypeptide binding]; other site 887061001028 GTP/Mg2+ binding site [chemical binding]; other site 887061001029 Switch I region; other site 887061001030 G2 box; other site 887061001031 G3 box; other site 887061001032 Switch II region; other site 887061001033 G4 box; other site 887061001034 G5 box; other site 887061001035 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...; Region: EFG_mtEFG_II; cd04088 887061001036 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...; Region: EFG_mtEFG1_IV; cd01434 887061001037 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...; Region: EFG_mtEFG_C; cd03713 887061001038 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 887061001039 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 887061001040 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 887061001041 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 887061001042 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 887061001043 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 887061001044 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 887061001045 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 887061001046 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 887061001047 protein-rRNA interface [nucleotide binding]; other site 887061001048 putative translocon binding site; other site 887061001049 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 887061001050 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...; Region: 30S_S3_KH; cd02412 887061001051 G-X-X-G motif; other site 887061001052 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 887061001053 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 887061001054 23S rRNA interface [nucleotide binding]; other site 887061001055 5S rRNA interface [nucleotide binding]; other site 887061001056 putative antibiotic binding site [chemical binding]; other site 887061001057 L25 interface [polypeptide binding]; other site 887061001058 L27 interface [polypeptide binding]; other site 887061001059 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...; Region: Ribosomal_L29_HIP; cd00427 887061001060 23S rRNA interface [nucleotide binding]; other site 887061001061 putative translocon interaction site; other site 887061001062 signal recognition particle (SRP54) interaction site; other site 887061001063 L23 interface [polypeptide binding]; other site 887061001064 trigger factor interaction site; other site 887061001065 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 887061001066 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 887061001067 KOW motif; Region: KOW; cl00354 887061001068 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 887061001069 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 887061001070 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 887061001071 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 887061001072 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 887061001073 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 887061001074 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 887061001075 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 887061001076 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 887061001077 5S rRNA interface [nucleotide binding]; other site 887061001078 L27 interface [polypeptide binding]; other site 887061001079 23S rRNA interface [nucleotide binding]; other site 887061001080 L5 interface [polypeptide binding]; other site 887061001081 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 887061001082 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 887061001083 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 887061001084 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...; Region: Ribosomal_L30; cd01658 887061001085 23S rRNA binding site [nucleotide binding]; other site 887061001086 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 887061001087 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 887061001088 SecY translocase; Region: SecY; pfam00344 887061001089 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 887061001090 rRNA binding site [nucleotide binding]; other site 887061001091 predicted 30S ribosome binding site; other site 887061001092 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 887061001093 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 887061001094 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 887061001095 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 887061001096 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 887061001097 RNA binding surface [nucleotide binding]; other site 887061001098 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 887061001099 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 887061001100 alphaNTD homodimer interface [polypeptide binding]; other site 887061001101 alphaNTD - beta interaction site [polypeptide binding]; other site 887061001102 alphaNTD - beta' interaction site [polypeptide binding]; other site 887061001103 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 887061001104 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 887061001105 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061001106 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 887061001107 MgtE intracellular N domain; Region: MgtE_N; cl15244 887061001108 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 887061001109 Divalent cation transporter; Region: MgtE; cl00786 887061001110 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 887061001111 Mechanosensitive ion channel; Region: MS_channel; pfam00924 887061001112 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 887061001113 Di-iron ligands [ion binding]; other site 887061001114 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 887061001115 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 887061001116 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 887061001117 trimer interface [polypeptide binding]; other site 887061001118 active site 887061001119 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 887061001120 Flavoprotein; Region: Flavoprotein; cl08021 887061001121 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 887061001122 hypothetical protein; Reviewed; Region: PRK00024 887061001123 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 887061001124 MPN+ (JAMM) motif; other site 887061001125 Zinc-binding site [ion binding]; other site 887061001126 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061001127 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 887061001128 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061001129 Uncharacterized conserved protein [Function unknown]; Region: COG2308 887061001130 Domain of unknown function (DUF404); Region: DUF404; pfam04169 887061001131 Domain of unknown function (DUF407); Region: DUF407; pfam04174 887061001132 Bacterial domain of unknown function (DUF403); Region: DUF403; cl00980 887061001133 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 887061001134 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061001135 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 887061001136 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 887061001137 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 oxidation via a membrane-anchored...; Region: MopB_Nitrate-R-NapA-like; cd02754 887061001138 [4Fe-4S] binding site [ion binding]; other site 887061001139 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 887061001140 molybdopterin cofactor binding site; other site 887061001141 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 oxidation via a membrane-anchored...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 887061001142 molybdopterin cofactor binding site; other site 887061001143 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 887061001144 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 887061001145 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 887061001146 [2Fe-2S] cluster binding site [ion binding]; other site 887061001147 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 887061001148 Active site [active] 887061001149 Catalytic domain of Protein Kinases; Region: PKc; cd00180 887061001150 active site 887061001151 ATP binding site [chemical binding]; other site 887061001152 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 887061001153 substrate binding site [chemical binding]; other site 887061001154 activation loop (A-loop); other site 887061001155 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 887061001156 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 887061001157 putative substrate translocation pore; other site 887061001158 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 887061001159 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061001160 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 887061001161 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 887061001162 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 887061001163 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061001164 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 887061001165 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 887061001166 Walker A/P-loop; other site 887061001167 ATP binding site [chemical binding]; other site 887061001168 Q-loop/lid; other site 887061001169 ABC transporter signature motif; other site 887061001170 Walker B; other site 887061001171 D-loop; other site 887061001172 H-loop/switch region; other site 887061001173 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...; Region: TM_PBP2; cd06261 887061001174 dimer interface [polypeptide binding]; other site 887061001175 conserved gate region; other site 887061001176 putative PBP binding loops; other site 887061001177 ABC-ATPase subunit interface; other site 887061001178 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061001179 Nitrate and nitrite sensing; Region: NIT; pfam08376 887061001180 ANTAR domain; Region: ANTAR; pfam03861 887061001181 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 887061001182 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 887061001183 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 887061001184 Walker A/P-loop; other site 887061001185 ATP binding site [chemical binding]; other site 887061001186 Q-loop/lid; other site 887061001187 ABC transporter signature motif; other site 887061001188 Walker B; other site 887061001189 D-loop; other site 887061001190 H-loop/switch region; other site 887061001191 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 887061001192 Carbon starvation protein CstA; Region: CstA; cl00856 887061001193 Protein of unknown function (DUF466); Region: DUF466; cl01082 887061001194 Protein of unknown function (DUF2805); Region: DUF2805; cl11923 887061001195 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 887061001196 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 887061001197 PAS fold; Region: PAS_4; pfam08448 887061001198 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 887061001199 putative active site [active] 887061001200 heme pocket [chemical binding]; other site 887061001201 PAS fold; Region: PAS_4; pfam08448 887061001202 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001203 metal binding site [ion binding]; metal-binding site 887061001204 active site 887061001205 I-site; other site 887061001206 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 887061001207 Dehydratase family; Region: ILVD_EDD; cl00340 887061001208 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 887061001209 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 887061001210 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 887061001211 active site 887061001212 phosphate binding residues; other site 887061001213 catalytic residues [active] 887061001214 Cytochrome c; Region: Cytochrom_C; cl11414 887061001215 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 887061001216 homotrimer interaction site [polypeptide binding]; other site 887061001217 putative active site [active] 887061001218 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 887061001219 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 887061001220 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 887061001221 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 887061001222 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 887061001223 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 887061001224 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 887061001225 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061001226 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 887061001227 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 887061001228 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 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 887061001229 purine monophosphate binding site [chemical binding]; other site 887061001230 dimer interface [polypeptide binding]; other site 887061001231 putative catalytic residues [active] 887061001232 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 887061001233 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 887061001234 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061001235 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 887061001236 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...; Region: DUS_like_FMN; cd02801 887061001237 FMN binding site [chemical binding]; other site 887061001238 active site 887061001239 catalytic residues [active] 887061001240 substrate binding site [chemical binding]; other site 887061001241 metabolite-proton symporter; Region: 2A0106; TIGR00883 887061001242 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 887061001243 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 887061001244 putative MPT binding site; other site 887061001245 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 887061001246 DNA polymerase I; Provisional; Region: PRK05755 887061001247 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 887061001248 active site 887061001249 metal binding site 1 [ion binding]; metal-binding site 887061001250 putative 5' ssDNA interaction site; other site 887061001251 metal binding site 3; metal-binding site 887061001252 metal binding site 2 [ion binding]; metal-binding site 887061001253 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 887061001254 putative DNA binding site [nucleotide binding]; other site 887061001255 putative metal binding site [ion binding]; other site 887061001256 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 887061001257 active site 887061001258 catalytic site [active] 887061001259 substrate binding site [chemical binding]; other site 887061001260 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 887061001261 active site 887061001262 DNA binding site [nucleotide binding] 887061001263 catalytic site [active] 887061001264 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 887061001265 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 887061001266 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 887061001267 Phosphotransferase enzyme family; Region: APH; pfam01636 887061001268 putative active site [active] 887061001269 putative substrate binding site [chemical binding]; other site 887061001270 ATP binding site [chemical binding]; other site 887061001271 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 887061001272 UvrD/REP helicase; Region: UvrD-helicase; cl14126 887061001273 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061001274 ligand binding site [chemical binding]; other site 887061001275 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 887061001276 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001277 metal binding site [ion binding]; metal-binding site 887061001278 active site 887061001279 I-site; other site 887061001280 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 887061001281 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061001282 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 trans-...; Region: HisKA; cd00082 887061001283 dimer interface [polypeptide binding]; other site 887061001284 phosphorylation site [posttranslational modification] 887061001285 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 887061001286 ATP binding site [chemical binding]; other site 887061001287 Mg2+ binding site [ion binding]; other site 887061001288 G-X-G motif; other site 887061001289 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 887061001290 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 887061001291 active site 887061001292 phosphorylation site [posttranslational modification] 887061001293 intermolecular recognition site; other site 887061001294 dimerization interface [polypeptide binding]; other site 887061001295 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...; Region: trans_reg_C; cd00383 887061001296 DNA binding site [nucleotide binding] 887061001297 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061001298 Outer membrane efflux protein; Region: OEP; pfam02321 887061001299 Outer membrane efflux protein; Region: OEP; pfam02321 887061001300 Multicopper oxidase; Region: Cu-oxidase; cl14658 887061001301 Multicopper oxidase; Region: Cu-oxidase; cl14658 887061001302 Copper binding periplasmic protein CusF; Region: CusF_Ec; cl02363 887061001303 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 887061001304 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 887061001305 ring oligomerisation interface [polypeptide binding]; other site 887061001306 ATP/Mg binding site [chemical binding]; other site 887061001307 stacking interactions; other site 887061001308 hinge regions; other site 887061001309 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...; Region: cpn10; cd00320 887061001310 oligomerisation interface [polypeptide binding]; other site 887061001311 mobile loop; other site 887061001312 roof hairpin; other site 887061001313 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 887061001314 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 887061001315 putative deacylase active site [active] 887061001316 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 887061001317 DEAD_2; Region: DEAD_2; cl14887 887061001318 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl09250 887061001319 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 887061001320 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes...; Region: Topo_IB_C; cd00659 887061001321 DNA binding site [nucleotide binding] 887061001322 active site 887061001323 Int/Topo IB signature motif; other site 887061001324 catalytic residues [active] 887061001325 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 887061001326 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061001327 DNA-binding site [nucleotide binding]; DNA binding site 887061001328 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 887061001329 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061001330 homodimer interface [polypeptide binding]; other site 887061001331 catalytic residue [active] 887061001332 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 887061001333 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 887061001334 Response regulator receiver domain; Region: Response_reg; pfam00072 887061001335 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 887061001336 active site 887061001337 phosphorylation site [posttranslational modification] 887061001338 intermolecular recognition site; other site 887061001339 dimerization interface [polypeptide binding]; other site 887061001340 PAS domain S-box; Region: sensory_box; TIGR00229 887061001341 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 887061001342 putative active site [active] 887061001343 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001344 metal binding site [ion binding]; metal-binding site 887061001345 active site 887061001346 I-site; other site 887061001347 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 887061001348 Predicted signal transduction protein [Signal transduction mechanisms]; Region: COG1639 887061001349 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061001350 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 887061001351 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 trans-...; Region: HisKA; cd00082 887061001352 dimer interface [polypeptide binding]; other site 887061001353 phosphorylation site [posttranslational modification] 887061001354 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 887061001355 ATP binding site [chemical binding]; other site 887061001356 Mg2+ binding site [ion binding]; other site 887061001357 G-X-G motif; other site 887061001358 Secretin and TonB N terminus short domain; Region: STN; pfam07660 887061001359 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061001360 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 887061001361 N-terminal plug; other site 887061001362 ligand-binding site [chemical binding]; other site 887061001363 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061001364 FecR protein; Region: FecR; pfam04773 887061001365 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061001366 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061001367 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...; Region: Sigma70_r4; cl01055 887061001368 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061001369 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061001370 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061001371 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...; Region: Sigma70_r4; cl01055 887061001372 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061001373 FecR protein; Region: FecR; pfam04773 887061001374 Secretin and TonB N terminus short domain; Region: STN; pfam07660 887061001375 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 887061001376 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 887061001377 N-terminal plug; other site 887061001378 ligand-binding site [chemical binding]; other site 887061001379 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061001380 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 887061001381 macrolide transporter subunit MacA; Provisional; Region: PRK11578 887061001382 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 887061001383 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 887061001384 Walker A/P-loop; other site 887061001385 ATP binding site [chemical binding]; other site 887061001386 Q-loop/lid; other site 887061001387 ABC transporter signature motif; other site 887061001388 Walker B; other site 887061001389 D-loop; other site 887061001390 H-loop/switch region; other site 887061001391 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 887061001392 FtsX-like permease family; Region: FtsX; pfam02687 887061001393 NodT family; Region: outer_NodT; TIGR01845 887061001394 Outer membrane efflux protein; Region: OEP; pfam02321 887061001395 Outer membrane efflux protein; Region: OEP; pfam02321 887061001396 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 887061001397 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 887061001398 inhibitor-cofactor binding pocket; inhibition site 887061001399 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061001400 catalytic residue [active] 887061001401 Beta-lactamase; Region: Beta-lactamase; cl01009 887061001402 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 887061001403 OsmC-like protein; Region: OsmC; cl00767 887061001404 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 887061001405 active site 887061001406 metal binding site [ion binding]; metal-binding site 887061001407 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 887061001408 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 887061001409 N-terminal plug; other site 887061001410 ligand-binding site [chemical binding]; other site 887061001411 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 887061001412 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 887061001413 diiron binding motif [ion binding]; other site 887061001414 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 887061001415 C-terminal peptidase (prc); Region: prc; TIGR00225 887061001416 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 887061001417 protein binding site [polypeptide binding]; other site 887061001418 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 887061001419 Catalytic dyad [active] 887061001420 Rdx family; Region: Rdx; cl01407 887061001421 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 887061001422 NlpC/P60 family; Region: NLPC_P60; cl11438 887061001423 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061001424 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 887061001425 Uncharacterized conserved protein [Function unknown]; Region: COG2308 887061001426 Domain of unknown function (DUF404); Region: DUF404; pfam04169 887061001427 Domain of unknown function (DUF407); Region: DUF407; pfam04174 887061001428 Bacterial domain of unknown function (DUF403); Region: DUF403; cl00980 887061001429 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 887061001430 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061001431 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 887061001432 Peptidase family U32; Region: Peptidase_U32; cl03113 887061001433 Collagenase; Region: DUF3656; pfam12392 887061001434 cell division protein MraZ; Reviewed; Region: PRK00326 887061001435 MraZ protein; Region: MraZ; pfam02381 887061001436 MraZ protein; Region: MraZ; pfam02381 887061001437 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 887061001438 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; cl12011 887061001439 Septum formation initiator; Region: DivIC; cl11433 887061001440 peptidoglycan synthase FtsI; Provisional; Region: PRK15105 887061001441 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 887061001442 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 887061001443 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 887061001444 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 887061001445 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061001446 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 887061001447 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 887061001448 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 undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 887061001449 Mg++ binding site [ion binding]; other site 887061001450 putative catalytic motif [active] 887061001451 putative substrate binding site [chemical binding]; other site 887061001452 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 887061001453 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061001454 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 887061001455 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 887061001456 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...; Region: GT1_MurG; cd03785 887061001457 active site 887061001458 homodimer interface [polypeptide binding]; other site 887061001459 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 887061001460 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 887061001461 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061001462 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 887061001463 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 887061001464 FAD binding domain; Region: FAD_binding_4; pfam01565 887061001465 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 887061001466 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 887061001467 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 887061001468 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061001469 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 887061001470 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 887061001471 Cell division protein FtsQ; Region: FtsQ; pfam03799 887061001472 cell division protein FtsA; Region: ftsA; TIGR01174 887061001473 Cell division protein FtsA; Region: FtsA; cl11496 887061001474 Cell division protein FtsA; Region: FtsA; cl11496 887061001475 cell division protein FtsZ; Validated; Region: PRK09330 887061001476 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...; Region: FtsZ_type1; cd02201 887061001477 nucleotide binding site [chemical binding]; other site 887061001478 SulA interaction site; other site 887061001479 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 887061001480 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 887061001481 lytic murein transglycosylase; Provisional; Region: PRK11619 887061001482 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 887061001483 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061001484 catalytic residue [active] 887061001485 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 887061001486 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 887061001487 putative NAD(P) binding site [chemical binding]; other site 887061001488 active site 887061001489 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 887061001490 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 887061001491 active site 887061001492 NTP binding site [chemical binding]; other site 887061001493 metal binding triad [ion binding]; metal-binding site 887061001494 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 887061001495 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061001496 division inhibitor protein; Provisional; Region: slmA; PRK09480 887061001497 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061001498 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 887061001499 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 887061001500 motif II; other site 887061001501 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...; Region: AAK_NAGK-C; cd04250 887061001502 feedback inhibition sensing region; other site 887061001503 homohexameric interface [polypeptide binding]; other site 887061001504 nucleotide binding site [chemical binding]; other site 887061001505 N-acetyl-L-glutamate binding site [chemical binding]; other site 887061001506 Formate--tetrahydrofolate ligase; Region: FTHFS; pfam01268 887061001507 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 887061001508 Potassium binding sites [ion binding]; other site 887061001509 Cesium cation binding sites [ion binding]; other site 887061001510 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 887061001511 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 887061001512 putative dimer interface [polypeptide binding]; other site 887061001513 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 887061001514 non-specific DNA binding site [nucleotide binding]; other site 887061001515 salt bridge; other site 887061001516 sequence-specific DNA binding site [nucleotide binding]; other site 887061001517 N-acetylglutamate synthase; Validated; Region: PRK05279 887061001518 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 N-...; Region: AAK_NAGS-ABP; cd04237 887061001519 putative feedback inhibition sensing region; other site 887061001520 putative nucleotide binding site [chemical binding]; other site 887061001521 putative substrate binding site [chemical binding]; other site 887061001522 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061001523 Coenzyme A binding pocket [chemical binding]; other site 887061001524 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 887061001525 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 887061001526 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 887061001527 putative catalytic residue [active] 887061001528 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001529 metal binding site [ion binding]; metal-binding site 887061001530 active site 887061001531 I-site; other site 887061001532 transketolase; Reviewed; Region: PRK12753 887061001533 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 887061001534 TPP-binding site [chemical binding]; other site 887061001535 dimer interface [polypeptide binding]; other site 887061001536 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 887061001537 PYR/PP interface [polypeptide binding]; other site 887061001538 dimer interface [polypeptide binding]; other site 887061001539 TPP binding site [chemical binding]; other site 887061001540 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 887061001541 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061001542 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 887061001543 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 887061001544 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 887061001545 substrate binding site [chemical binding]; other site 887061001546 hinge regions; other site 887061001547 ADP binding site [chemical binding]; other site 887061001548 catalytic site [active] 887061001549 pyruvate kinase; Provisional; Region: PRK05826 887061001550 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 887061001551 domain interfaces; other site 887061001552 active site 887061001553 hypothetical protein; Provisional; Region: PRK08185 887061001554 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...; Region: TBP_aldolase_IIB; cd00947 887061001555 intersubunit interface [polypeptide binding]; other site 887061001556 active site 887061001557 zinc binding site [ion binding]; other site 887061001558 Na+ binding site [ion binding]; other site 887061001559 Phosphate-starvation-inducible E; Region: PsiE; cl01264 887061001560 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 887061001561 ATP binding site [chemical binding]; other site 887061001562 active site 887061001563 substrate binding site [chemical binding]; other site 887061001564 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 887061001565 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 887061001566 active site clefts [active] 887061001567 zinc binding site [ion binding]; other site 887061001568 dimer interface [polypeptide binding]; other site 887061001569 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 887061001570 dimer interface [polypeptide binding]; other site 887061001571 substrate binding site [chemical binding]; other site 887061001572 metal binding sites [ion binding]; metal-binding site 887061001573 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 887061001574 ABC-2 type transporter; Region: ABC2_membrane; cl11417 887061001575 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 887061001576 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 887061001577 Walker A/P-loop; other site 887061001578 ATP binding site [chemical binding]; other site 887061001579 Q-loop/lid; other site 887061001580 ABC transporter signature motif; other site 887061001581 Walker B; other site 887061001582 D-loop; other site 887061001583 H-loop/switch region; other site 887061001584 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 887061001585 Protein of unknown function (DUF721); Region: DUF721; cl02324 887061001586 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 887061001587 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061001588 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 887061001589 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; cl14882 887061001590 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 887061001591 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 887061001592 nucleotide binding region [chemical binding]; other site 887061001593 ATP-binding site [chemical binding]; other site 887061001594 hypothetical protein; Provisional; Region: PRK10396 887061001595 SEC-C motif; Region: SEC-C; cl12132 887061001596 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 887061001597 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 887061001598 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...; Region: OAT; cd02152 887061001599 heterotetramer interface [polypeptide binding]; other site 887061001600 active site pocket [active] 887061001601 cleavage site 887061001602 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 887061001603 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...; Region: AAA; cd00009 887061001604 Walker A motif; other site 887061001605 ATP binding site [chemical binding]; other site 887061001606 Walker B motif; other site 887061001607 hypothetical protein; Provisional; Region: PRK08999 887061001608 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 887061001609 active site 887061001610 8-oxo-dGMP binding site [chemical binding]; other site 887061001611 nudix motif; other site 887061001612 metal binding site [ion binding]; metal-binding site 887061001613 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- (beta-...; Region: TMP_TenI; cd00564 887061001614 thiamine phosphate binding site [chemical binding]; other site 887061001615 active site 887061001616 pyrophosphate binding site [ion binding]; other site 887061001617 Protein of unknown function (DUF461); Region: DUF461; cl01071 887061001618 Domain of unknown function (DUF329); Region: DUF329; cl01144 887061001619 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 887061001620 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 887061001621 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 887061001622 CoA-binding site [chemical binding]; other site 887061001623 ATP-binding [chemical binding]; other site 887061001624 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 887061001625 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 887061001626 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 887061001627 octaprenyl diphosphate synthase; Provisional; Region: PRK10888 887061001628 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 887061001629 substrate binding pocket [chemical binding]; other site 887061001630 chain length determination region; other site 887061001631 substrate-Mg2+ binding site; other site 887061001632 catalytic residues [active] 887061001633 aspartate-rich region 1; other site 887061001634 active site lid residues [active] 887061001635 aspartate-rich region 2; other site 887061001636 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 887061001637 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 887061001638 GTPase CgtA; Reviewed; Region: obgE; PRK12299 887061001639 GTP1/OBG; Region: GTP1_OBG; pfam01018 887061001640 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 887061001641 G1 box; other site 887061001642 GTP/Mg2+ binding site [chemical binding]; other site 887061001643 Switch I region; other site 887061001644 G2 box; other site 887061001645 G3 box; other site 887061001646 Switch II region; other site 887061001647 G4 box; other site 887061001648 G5 box; other site 887061001649 gamma-glutamyl kinase; Provisional; Region: PRK05429 887061001650 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 887061001651 nucleotide binding site [chemical binding]; other site 887061001652 homotetrameric interface [polypeptide binding]; other site 887061001653 putative phosphate binding site [ion binding]; other site 887061001654 putative allosteric binding site; other site 887061001655 PUA domain; Region: PUA; cl00607 887061001656 AIR carboxylase; Region: AIRC; cl00310 887061001657 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 887061001658 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061001659 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 887061001660 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 887061001661 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 887061001662 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 887061001663 active site 887061001664 Riboflavin kinase; Region: Flavokinase; pfam01687 887061001665 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 887061001666 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061001667 active site 887061001668 HIGH motif; other site 887061001669 nucleotide binding site [chemical binding]; other site 887061001670 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 887061001671 active site 887061001672 KMSKS motif; other site 887061001673 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 887061001674 tRNA binding surface [nucleotide binding]; other site 887061001675 anticodon binding site; other site 887061001676 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 887061001677 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 887061001678 lipoprotein signal peptidase; Provisional; Region: PRK14787 887061001679 bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and...; Region: arch_bact_SO_family_Moco; cd02109 887061001680 Moco binding site; other site 887061001681 metal coordination site [ion binding]; other site 887061001682 SelR domain; Region: SelR; cl00369 887061001683 Protein of unknown function (DUF808); Region: DUF808; cl01002 887061001684 probable cinnamyl alcohol dehydrogenase; Region: PLN02586 887061001685 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 887061001686 putative NAD(P) binding site [chemical binding]; other site 887061001687 putative substrate binding site [chemical binding]; other site 887061001688 catalytic Zn binding site [ion binding]; other site 887061001689 structural Zn binding site [ion binding]; other site 887061001690 dimer interface [polypeptide binding]; other site 887061001691 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 887061001692 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 887061001693 tetramer interface [polypeptide binding]; other site 887061001694 heme binding pocket [chemical binding]; other site 887061001695 NADPH binding site [chemical binding]; other site 887061001696 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 887061001697 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 887061001698 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 887061001699 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 887061001700 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 887061001701 active site 887061001702 phosphorylation site [posttranslational modification] 887061001703 intermolecular recognition site; other site 887061001704 dimerization interface [polypeptide binding]; other site 887061001705 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061001706 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional; Region: PRK10841 887061001707 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 trans-...; Region: HisKA; cd00082 887061001708 phosphorylation site [posttranslational modification] 887061001709 dimer interface [polypeptide binding]; other site 887061001710 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 887061001711 ATP binding site [chemical binding]; other site 887061001712 Mg2+ binding site [ion binding]; other site 887061001713 G-X-G motif; other site 887061001714 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 887061001715 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 887061001716 N-terminal plug; other site 887061001717 ligand-binding site [chemical binding]; other site 887061001718 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061001719 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 887061001720 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...; Region: OM_channels; cl00284 887061001721 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 887061001722 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 887061001723 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061001724 Zn2+ binding site [ion binding]; other site 887061001725 Mg2+ binding site [ion binding]; other site 887061001726 PAS fold; Region: PAS_4; pfam08448 887061001727 GAF domain; Region: GAF; cl00853 887061001728 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 887061001729 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 887061001730 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001731 metal binding site [ion binding]; metal-binding site 887061001732 active site 887061001733 I-site; other site 887061001734 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 887061001735 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 887061001736 Clp amino terminal domain; Region: Clp_N; pfam02861 887061001737 Clp amino terminal domain; Region: Clp_N; pfam02861 887061001738 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...; Region: AAA; cd00009 887061001739 Walker A motif; other site 887061001740 ATP binding site [chemical binding]; other site 887061001741 Walker B motif; other site 887061001742 arginine finger; other site 887061001743 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...; Region: AAA; cd00009 887061001744 Walker A motif; other site 887061001745 ATP binding site [chemical binding]; other site 887061001746 Walker B motif; other site 887061001747 arginine finger; other site 887061001748 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 887061001749 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 887061001750 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 887061001751 NADP binding site [chemical binding]; other site 887061001752 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061001753 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 887061001754 Sel1 repeat; Region: Sel1; cl02723 887061001755 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 887061001756 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061001757 catalytic residue [active] 887061001758 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 887061001759 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH2; cd08183 887061001760 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 887061001761 putative active site [active] 887061001762 metal binding site [ion binding]; metal-binding site 887061001763 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061001764 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule...; Region: GT1_like_2; cd03814 887061001765 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 887061001766 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061001767 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 887061001768 Sulfatase; Region: Sulfatase; cl10460 887061001769 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 887061001770 active site residue [active] 887061001771 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061001772 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; cl00251 887061001773 SecA binding site; other site 887061001774 Preprotein binding site; other site 887061001775 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 887061001776 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 887061001777 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061001778 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 887061001779 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 887061001780 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_cladeC; cd03378 887061001781 active site clefts [active] 887061001782 zinc binding site [ion binding]; other site 887061001783 dimer interface [polypeptide binding]; other site 887061001784 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 887061001785 Sulfate transporter family; Region: Sulfate_transp; cl00967 887061001786 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 887061001787 anti sigma factor interaction site; other site 887061001788 regulatory phosphorylation site [posttranslational modification]; other site 887061001789 DNA utilization protein GntX; Provisional; Region: PRK11595 887061001790 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061001791 biotin synthetase; Region: bioB; TIGR00433 887061001792 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 887061001793 FeS/SAM binding site; other site 887061001794 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 887061001795 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 887061001796 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 887061001797 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061001798 catalytic residue [active] 887061001799 putative pimeloyl-BioC--CoA transferase BioH; Region: bioH; TIGR01738 887061001800 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 887061001801 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 887061001802 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 887061001803 S-adenosylmethionine binding site [chemical binding]; other site 887061001804 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 887061001805 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061001806 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061001807 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 887061001808 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 887061001809 active site 887061001810 (T/H)XGH motif; other site 887061001811 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 887061001812 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 887061001813 putative catalytic cysteine [active] 887061001814 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 887061001815 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 887061001816 Lipopolysaccharide-assembly; Region: LptE; cl01125 887061001817 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 887061001818 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 887061001819 HIGH motif; other site 887061001820 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 887061001821 active site 887061001822 KMSKS motif; other site 887061001823 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 887061001824 tRNA binding surface [nucleotide binding]; other site 887061001825 adenylate kinase; Reviewed; Region: adk; PRK00279 887061001826 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 887061001827 AMP-binding site [chemical binding]; other site 887061001828 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 887061001829 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; cl12011 887061001830 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 887061001831 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 887061001832 SurA N-terminal domain; Region: SurA_N; pfam09312 887061001833 PPIC-type PPIASE domain; Region: Rotamase; cl08278 887061001834 PPIC-type PPIASE domain; Region: Rotamase; cl08278 887061001835 OstA-like protein; Region: OstA; cl00844 887061001836 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 887061001837 Organic solvent tolerance protein; Region: OstA_C; pfam04453 887061001838 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061001839 Phosphotransferase enzyme family; Region: APH; pfam01636 887061001840 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 887061001841 Substrate binding site [chemical binding]; other site 887061001842 metal binding site [ion binding]; metal-binding site 887061001843 proline aminopeptidase P II; Provisional; Region: PRK10879 887061001844 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 887061001845 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...; Region: Prolidase; cd01087 887061001846 active site 887061001847 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061001848 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 887061001849 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 887061001850 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061001851 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 887061001852 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...; Region: DsbA_DsbC_DsbG; cd03020 887061001853 dimerization domain [polypeptide binding]; other site 887061001854 dimer interface [polypeptide binding]; other site 887061001855 catalytic residues [active] 887061001856 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061001857 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061001858 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061001859 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 887061001860 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 887061001861 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 887061001862 Walker A motif; other site 887061001863 ATP binding site [chemical binding]; other site 887061001864 Walker B motif; other site 887061001865 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 887061001866 DNA-binding site [nucleotide binding]; DNA binding site 887061001867 RNA-binding motif; other site 887061001868 isocitrate dehydrogenase; Validated; Region: PRK07362 887061001869 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 887061001870 PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-...; Region: PseudoU_synth_RluE; cd02566 887061001871 probable active site [active] 887061001872 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 887061001873 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 887061001874 catalytic triad [active] 887061001875 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 887061001876 Active site [active] 887061001877 Tetramer interface [polypeptide binding]; other site 887061001878 FMN-binding site [chemical binding]; other site 887061001879 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 887061001880 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 887061001881 putative substrate translocation pore; other site 887061001882 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 887061001883 catalytic motif [active] 887061001884 Catalytic residue [active] 887061001885 Uncharacterized ACR, COG1469; Region: DUF198; cl00642 887061001886 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 887061001887 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 with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 887061001888 TPP-binding site; other site 887061001889 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 887061001890 PYR/PP interface [polypeptide binding]; other site 887061001891 dimer interface [polypeptide binding]; other site 887061001892 TPP binding site [chemical binding]; other site 887061001893 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 887061001894 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 887061001895 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 887061001896 substrate binding pocket [chemical binding]; other site 887061001897 chain length determination region; other site 887061001898 substrate-Mg2+ binding site; other site 887061001899 catalytic residues [active] 887061001900 aspartate-rich region 1; other site 887061001901 active site lid residues [active] 887061001902 aspartate-rich region 2; other site 887061001903 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 887061001904 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 887061001905 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 887061001906 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein; Region: arCOG00543; TIGR03675 887061001907 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061001908 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061001909 putative hydrophobic ligand binding site [chemical binding]; other site 887061001910 protein interface [polypeptide binding]; other site 887061001911 gate; other site 887061001912 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061001913 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 887061001914 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061001915 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061001916 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061001917 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061001918 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...; Region: Ap4A_hydrolase_plant_like; cd03671 887061001919 putative active site [active] 887061001920 Ap4A binding site [chemical binding]; other site 887061001921 nudix motif; other site 887061001922 putative metal binding site [ion binding]; other site 887061001923 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 887061001924 ketol-acid reductoisomerase; Provisional; Region: PRK05479 887061001925 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061001926 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 887061001927 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 887061001928 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 887061001929 putative valine binding site [chemical binding]; other site 887061001930 dimer interface [polypeptide binding]; other site 887061001931 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 887061001932 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 887061001933 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 887061001934 PYR/PP interface [polypeptide binding]; other site 887061001935 dimer interface [polypeptide binding]; other site 887061001936 TPP binding site [chemical binding]; other site 887061001937 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 887061001938 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 887061001939 TPP-binding site [chemical binding]; other site 887061001940 dimer interface [polypeptide binding]; other site 887061001941 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 887061001942 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061001943 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 887061001944 Walker A motif; other site 887061001945 ATP binding site [chemical binding]; other site 887061001946 Walker B motif; other site 887061001947 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 887061001948 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 5-...; Region: QPRTase; cd01572 887061001949 dimerization interface [polypeptide binding]; other site 887061001950 active site 887061001951 putative glutathione S-transferase; Provisional; Region: PRK10357 887061001952 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 887061001953 putative C-terminal domain interface [polypeptide binding]; other site 887061001954 putative GSH binding site (G-site) [chemical binding]; other site 887061001955 putative dimer interface [polypeptide binding]; other site 887061001956 GST_C family, unknown subfamily 6; 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_C_6; cd03205 887061001957 putative N-terminal domain interface [polypeptide binding]; other site 887061001958 putative dimer interface [polypeptide binding]; other site 887061001959 putative substrate binding pocket (H-site) [chemical binding]; other site 887061001960 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 887061001961 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 887061001962 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...; Region: Nudix_Hydrolase_2; cd03675 887061001963 nudix motif; other site 887061001964 MarC family integral membrane protein; Region: MarC; cl00919 887061001965 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 887061001966 conserved cys residue [active] 887061001967 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 887061001968 active site 887061001969 dimer interface [polypeptide binding]; other site 887061001970 ribonuclease G; Provisional; Region: PRK11712 887061001971 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 887061001972 homodimer interface [polypeptide binding]; other site 887061001973 oligonucleotide binding site [chemical binding]; other site 887061001974 YGGT family; Region: YGGT; cl00508 887061001975 YGGT family; Region: YGGT; cl00508 887061001976 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 887061001977 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061001978 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 887061001979 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 887061001980 catalytic residue [active] 887061001981 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 887061001982 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 887061001983 Walker A motif; other site 887061001984 ATP binding site [chemical binding]; other site 887061001985 Walker B motif; other site 887061001986 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 887061001987 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 887061001988 Walker A motif; other site 887061001989 ATP binding site [chemical binding]; other site 887061001990 Walker B motif; other site 887061001991 Protein of unknown function DUF72; Region: DUF72; cl00777 887061001992 dihydroorotase; Provisional; Region: PRK07627 887061001993 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 887061001994 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 887061001995 active site 887061001996 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 887061001997 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 887061001998 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 887061001999 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061002000 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 887061002001 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 887061002002 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 887061002003 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 887061002004 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 887061002005 dimerization interface [polypeptide binding]; other site 887061002006 active site 887061002007 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 887061002008 Lumazine binding domain; Region: Lum_binding; pfam00677 887061002009 Lumazine binding domain; Region: Lum_binding; pfam00677 887061002010 LolC/E family; Region: lolCE; TIGR02212 887061002011 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 887061002012 FtsX-like permease family; Region: FtsX; pfam02687 887061002013 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 887061002014 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 887061002015 Walker A/P-loop; other site 887061002016 ATP binding site [chemical binding]; other site 887061002017 Q-loop/lid; other site 887061002018 ABC transporter signature motif; other site 887061002019 Walker B; other site 887061002020 D-loop; other site 887061002021 H-loop/switch region; other site 887061002022 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 887061002023 Competence protein; Region: Competence; cl00471 887061002024 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061002025 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061002026 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 887061002027 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 887061002028 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061002029 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061002030 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 887061002031 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 887061002032 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 887061002033 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 887061002034 Walker A/P-loop; other site 887061002035 ATP binding site [chemical binding]; other site 887061002036 Q-loop/lid; other site 887061002037 ABC transporter signature motif; other site 887061002038 Walker B; other site 887061002039 D-loop; other site 887061002040 H-loop/switch region; other site 887061002041 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 887061002042 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 887061002043 Trm112p-like protein; Region: Trm112p; cl01066 887061002044 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 887061002045 Ligand binding site [chemical binding]; other site 887061002046 oligomer interface [polypeptide binding]; other site 887061002047 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 887061002048 E or 'early' set of sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end; Region: E_set; cl09101 887061002049 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061002050 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 887061002051 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...; Region: ParA; cd02042 887061002052 P-loop; other site 887061002053 Magnesium ion binding site [ion binding]; other site 887061002054 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...; Region: ParA; cd02042 887061002055 Magnesium ion binding site [ion binding]; other site 887061002056 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 887061002057 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 887061002058 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 887061002059 cysteine synthases; Region: cysKM; TIGR01136 887061002060 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 887061002061 dimer interface [polypeptide binding]; other site 887061002062 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002063 catalytic residue [active] 887061002064 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 887061002065 FimV N-terminal domain; Region: FimV_core; TIGR03505 887061002066 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 887061002067 Flavin Reductases; Region: FlaRed; cl00801 887061002068 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 887061002069 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061002070 active site 887061002071 HIGH motif; other site 887061002072 nucleotide binding site [chemical binding]; other site 887061002073 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061002074 active site 887061002075 KMSKS motif; other site 887061002076 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 887061002077 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 887061002078 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061002079 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 887061002080 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 887061002081 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 887061002082 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 887061002083 E3 interaction surface; other site 887061002084 lipoyl attachment site [posttranslational modification]; other site 887061002085 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 887061002086 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061002087 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061002088 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 887061002089 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 887061002090 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 887061002091 E3 interaction surface; other site 887061002092 lipoyl attachment site [posttranslational modification]; other site 887061002093 e3 binding domain; Region: E3_binding; pfam02817 887061002094 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 887061002095 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 887061002096 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 887061002097 dimer interface [polypeptide binding]; other site 887061002098 TPP-binding site [chemical binding]; other site 887061002099 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 887061002100 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...; Region: Peptidase_M17; cd00433 887061002101 interface (dimer of trimers) [polypeptide binding]; other site 887061002102 Substrate-binding/catalytic site; other site 887061002103 Zn-binding sites [ion binding]; other site 887061002104 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061002105 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 887061002106 ligand binding site [chemical binding]; other site 887061002107 flexible hinge region; other site 887061002108 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061002109 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061002110 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061002111 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 887061002112 putative active site [active] 887061002113 putative metal binding residues [ion binding]; other site 887061002114 signature motif; other site 887061002115 putative triphosphate binding site [ion binding]; other site 887061002116 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...; Region: ParA; cd02042 887061002117 ParA-like protein; Provisional; Region: PHA02518 887061002118 P-loop; other site 887061002119 Magnesium ion binding site [ion binding]; other site 887061002120 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 887061002121 catalytic core [active] 887061002122 Sulfatase; Region: Sulfatase; cl10460 887061002123 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 887061002124 DHH family; Region: DHH; pfam01368 887061002125 DHHA1 domain; Region: DHHA1; pfam02272 887061002126 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 887061002127 substrate binding site [chemical binding]; other site 887061002128 dimer interface [polypeptide binding]; other site 887061002129 catalytic triad [active] 887061002130 Preprotein translocase SecG subunit; Region: SecG; cl09123 887061002131 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 887061002132 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 887061002133 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 887061002134 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 887061002135 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 887061002136 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of...; Region: TRX_Fd_NuoE; cd03064 887061002137 putative dimer interface [polypeptide binding]; other site 887061002138 [2Fe-2S] cluster binding site [ion binding]; other site 887061002139 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 887061002140 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 887061002141 SLBB domain; Region: SLBB; pfam10531 887061002142 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 887061002143 NADH dehydrogenase subunit G; Validated; Region: PRK09129 887061002144 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 887061002145 catalytic loop [active] 887061002146 iron binding site [ion binding]; other site 887061002147 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 887061002148 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions...; Region: MopB_NDH-1_NuoG2; cd02772 887061002149 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-; Region: MopB_CT; cl09929 887061002150 NADH dehydrogenase; Region: NADHdh; cl00469 887061002151 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 887061002152 4Fe-4S binding domain; Region: Fer4; cl02805 887061002153 4Fe-4S binding domain; Region: Fer4; cl02805 887061002154 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 887061002155 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 887061002156 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 887061002157 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 887061002158 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 887061002159 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 887061002160 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 887061002161 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 887061002162 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 887061002163 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 887061002164 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 887061002165 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...; Region: ADPRase_NUDT5; cd03424 887061002166 dimer interface [polypeptide binding]; other site 887061002167 ADP-ribose binding site [chemical binding]; other site 887061002168 active site 887061002169 nudix motif; other site 887061002170 metal binding site [ion binding]; metal-binding site 887061002171 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 887061002172 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 887061002173 putative NAD(P) binding site [chemical binding]; other site 887061002174 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 887061002175 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061002176 catalytic residue [active] 887061002177 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 887061002178 Acetamidase/Formamidase family; Region: FmdA_AmdA; cl01023 887061002179 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 887061002180 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 887061002181 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 887061002182 putative ligand binding site [chemical binding]; other site 887061002183 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 887061002184 TM-ABC transporter signature motif; other site 887061002185 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 887061002186 TM-ABC transporter signature motif; other site 887061002187 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 887061002188 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 887061002189 Walker A/P-loop; other site 887061002190 ATP binding site [chemical binding]; other site 887061002191 Q-loop/lid; other site 887061002192 ABC transporter signature motif; other site 887061002193 Walker B; other site 887061002194 D-loop; other site 887061002195 H-loop/switch region; other site 887061002196 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 887061002197 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 887061002198 Walker A/P-loop; other site 887061002199 ATP binding site [chemical binding]; other site 887061002200 Q-loop/lid; other site 887061002201 ABC transporter signature motif; other site 887061002202 Walker B; other site 887061002203 D-loop; other site 887061002204 H-loop/switch region; other site 887061002205 UreD urease accessory protein; Region: UreD; cl00530 887061002206 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 887061002207 alpha-gamma subunit interface [polypeptide binding]; other site 887061002208 beta-gamma subunit interface [polypeptide binding]; other site 887061002209 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...; Region: Urease_beta; cd00407 887061002210 gamma-beta subunit interface [polypeptide binding]; other site 887061002211 alpha-beta subunit interface [polypeptide binding]; other site 887061002212 urease subunit alpha; Reviewed; Region: ureC; PRK13207 887061002213 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 887061002214 subunit interactions [polypeptide binding]; other site 887061002215 active site 887061002216 flap region; other site 887061002217 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 C-...; Region: UreE; cd00571 887061002218 dimer interface [polypeptide binding]; other site 887061002219 catalytic residues [active] 887061002220 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 887061002221 UreF; Region: UreF; pfam01730 887061002222 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061002223 HupE / UreJ protein; Region: HupE_UreJ; cl01011 887061002224 Sodium:solute symporter family; Region: SSF; cl00456 887061002225 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 trans-...; Region: HisKA; cd00082 887061002226 dimer interface [polypeptide binding]; other site 887061002227 phosphorylation site [posttranslational modification] 887061002228 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 887061002229 ATP binding site [chemical binding]; other site 887061002230 Mg2+ binding site [ion binding]; other site 887061002231 G-X-G motif; other site 887061002232 Response regulator receiver domain; Region: Response_reg; pfam00072 887061002233 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 887061002234 active site 887061002235 phosphorylation site [posttranslational modification] 887061002236 intermolecular recognition site; other site 887061002237 dimerization interface [polypeptide binding]; other site 887061002238 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 887061002239 active site 887061002240 phosphorylation site [posttranslational modification] 887061002241 intermolecular recognition site; other site 887061002242 dimerization interface [polypeptide binding]; other site 887061002243 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...; Region: LuxR_C_like; cd06170 887061002244 DNA binding residues [nucleotide binding] 887061002245 dimerization interface [polypeptide binding]; other site 887061002246 Catalytic domain of Protein Kinases; Region: PKc; cd00180 887061002247 active site 887061002248 ATP binding site [chemical binding]; other site 887061002249 substrate binding site [chemical binding]; other site 887061002250 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 887061002251 activation loop (A-loop); other site 887061002252 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061002253 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 887061002254 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 887061002255 endonuclease III; Region: ENDO3c; smart00478 887061002256 minor groove reading motif; other site 887061002257 helix-hairpin-helix signature motif; other site 887061002258 substrate binding pocket [chemical binding]; other site 887061002259 active site 887061002260 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 887061002261 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...; Region: TGS_ThrRS_N; cd01667 887061002262 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 887061002263 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 887061002264 active site 887061002265 dimer interface [polypeptide binding]; other site 887061002266 motif 1; other site 887061002267 motif 2; other site 887061002268 motif 3; other site 887061002269 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 887061002270 anticodon binding site; other site 887061002271 translation initiation factor IF-3; Region: infC; TIGR00168 887061002272 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 887061002273 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 887061002274 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 887061002275 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 887061002276 23S rRNA binding site [nucleotide binding]; other site 887061002277 L21 binding site [polypeptide binding]; other site 887061002278 L13 binding site [polypeptide binding]; other site 887061002279 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 887061002280 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 887061002281 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 887061002282 dimer interface [polypeptide binding]; other site 887061002283 motif 1; other site 887061002284 active site 887061002285 motif 2; other site 887061002286 motif 3; other site 887061002287 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 887061002288 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 887061002289 putative tRNA-binding site [nucleotide binding]; other site 887061002290 B3/4 domain; Region: B3_4; cl11458 887061002291 tRNA synthetase B5 domain; Region: B5; cl08394 887061002292 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 887061002293 dimer interface [polypeptide binding]; other site 887061002294 motif 1; other site 887061002295 motif 3; other site 887061002296 motif 2; other site 887061002297 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 887061002298 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 higher-...; Region: HU_IHF; cd00591 887061002299 IHF - DNA interface [nucleotide binding]; other site 887061002300 IHF dimer interface [polypeptide binding]; other site 887061002301 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 887061002302 DNA binding residues [nucleotide binding] 887061002303 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061002304 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 887061002305 N-terminal plug; other site 887061002306 ligand-binding site [chemical binding]; other site 887061002307 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061002308 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 887061002309 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 887061002310 N-terminal plug; other site 887061002311 ligand-binding site [chemical binding]; other site 887061002312 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; cl14882 887061002313 ATP binding site [chemical binding]; other site 887061002314 putative Mg++ binding site [ion binding]; other site 887061002315 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 887061002316 nucleotide binding region [chemical binding]; other site 887061002317 ATP-binding site [chemical binding]; other site 887061002318 Mitochondrial degradasome RNA helicase subunit C terminal; Region: SUV3_C; pfam12513 887061002319 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 887061002320 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 887061002321 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 887061002322 Walker A motif; other site 887061002323 ATP binding site [chemical binding]; other site 887061002324 Walker B motif; other site 887061002325 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 887061002326 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061002327 Histidine kinase; Region: HisKA_3; pfam07730 887061002328 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 887061002329 ATP binding site [chemical binding]; other site 887061002330 Mg2+ binding site [ion binding]; other site 887061002331 G-X-G motif; other site 887061002332 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061002333 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 887061002334 active site 887061002335 phosphorylation site [posttranslational modification] 887061002336 intermolecular recognition site; other site 887061002337 dimerization interface [polypeptide binding]; other site 887061002338 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...; Region: LuxR_C_like; cd06170 887061002339 DNA binding residues [nucleotide binding] 887061002340 dimerization interface [polypeptide binding]; other site 887061002341 response regulator; Provisional; Region: PRK09483 887061002342 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 887061002343 active site 887061002344 phosphorylation site [posttranslational modification] 887061002345 intermolecular recognition site; other site 887061002346 dimerization interface [polypeptide binding]; other site 887061002347 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...; Region: LuxR_C_like; cd06170 887061002348 DNA binding residues [nucleotide binding] 887061002349 dimerization interface [polypeptide binding]; other site 887061002350 Histidine kinase; Region: HisKA_3; pfam07730 887061002351 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 887061002352 ATP binding site [chemical binding]; other site 887061002353 Mg2+ binding site [ion binding]; other site 887061002354 G-X-G motif; other site 887061002355 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061002356 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cd00216 887061002357 Trp docking motif; other site 887061002358 'Velcro' closure; other site 887061002359 active site 887061002360 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 887061002361 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 887061002362 Cytochrome c; Region: Cytochrom_C; cl11414 887061002363 Methanol dehydrogenase beta subunit; Region: MDH; pfam02315 887061002364 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061002365 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061002366 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061002367 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061002368 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 887061002369 metal ion-dependent adhesion site (MIDAS); other site 887061002370 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 887061002371 metal ion-dependent adhesion site (MIDAS); other site 887061002372 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061002373 putative hydrophobic ligand binding site [chemical binding]; other site 887061002374 protein interface [polypeptide binding]; other site 887061002375 gate; other site 887061002376 hypothetical protein; Provisional; Region: PRK13560 887061002377 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 887061002378 Histidine kinase; Region: HisKA_3; pfam07730 887061002379 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 887061002380 ATP binding site [chemical binding]; other site 887061002381 Mg2+ binding site [ion binding]; other site 887061002382 G-X-G motif; other site 887061002383 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061002384 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 887061002385 active site 887061002386 phosphorylation site [posttranslational modification] 887061002387 intermolecular recognition site; other site 887061002388 dimerization interface [polypeptide binding]; other site 887061002389 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...; Region: LuxR_C_like; cd06170 887061002390 DNA binding residues [nucleotide binding] 887061002391 dimerization interface [polypeptide binding]; other site 887061002392 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 887061002393 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 887061002394 FlaG protein; Region: FlaG; cl00591 887061002395 flagellar capping protein; Validated; Region: fliD; PRK08724 887061002396 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 887061002397 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 887061002398 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 887061002399 Flagellar protein FliS; Region: FliS; cl00654 887061002400 Flagellar protein FliT; Region: FliT; cl05125 887061002401 Flagellar hook-length control protein FliK; Region: Flg_hook; cl14669 887061002402 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 887061002403 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 887061002404 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 887061002405 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 887061002406 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 887061002407 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 887061002408 FliG C-terminal domain; Region: FliG_C; pfam01706 887061002409 flagellar assembly protein H; Validated; Region: fliH; PRK05687 887061002410 Flagellar assembly protein FliH; Region: FliH; pfam02108 887061002411 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 887061002412 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 887061002413 Walker A motif/ATP binding site; other site 887061002414 Walker B motif; other site 887061002415 Flagellar FliJ protein; Region: FliJ; cl09161 887061002416 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 887061002417 Flagellar hook-length control protein FliK; Region: Flg_hook; cl14669 887061002418 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 887061002419 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 887061002420 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 887061002421 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 887061002422 FliP family; Region: FliP; cl00593 887061002423 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 887061002424 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 887061002425 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 887061002426 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 887061002427 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 887061002428 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 887061002429 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 887061002430 Rod binding protein; Region: Rod-binding; cl01626 887061002431 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 887061002432 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 887061002433 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 887061002434 Flagellar L-ring protein; Region: FlgH; cl00905 887061002435 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 887061002436 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 887061002437 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 887061002438 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 887061002439 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 887061002440 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 887061002441 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 887061002442 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 887061002443 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 887061002444 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 887061002445 Flagellar hook capping protein; Region: FlgD; cl04347 887061002446 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 887061002447 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 887061002448 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 887061002449 Flagella basal body rod protein; Region: Flg_bb_rod; cl15245 887061002450 SAF domain; Region: SAF; cl00555 887061002451 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 887061002452 FlgN protein; Region: FlgN; cl09176 887061002453 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 887061002454 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 887061002455 VRR-NUC domain; Region: VRR_NUC; pfam08774 887061002456 MgtC family; Region: MgtC; cl12207 887061002457 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 887061002458 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061002459 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 887061002460 flagellar motor protein MotD; Reviewed; Region: PRK09038 887061002461 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061002462 ligand binding site [chemical binding]; other site 887061002463 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061002464 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 887061002465 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061002466 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 887061002467 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...; Region: Sigma70_r4; cd06171 887061002468 DNA binding residues [nucleotide binding] 887061002469 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 887061002470 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061002471 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 887061002472 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 887061002473 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061002474 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 887061002475 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 887061002476 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 887061002477 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 887061002478 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 887061002479 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 887061002480 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; cl12011 887061002481 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061002482 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 887061002483 N-terminal plug; other site 887061002484 ligand-binding site [chemical binding]; other site 887061002485 fec operon regulator FecR; Reviewed; Region: PRK09774 887061002486 FecR protein; Region: FecR; pfam04773 887061002487 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 887061002488 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061002489 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...; Region: Sigma70_r4; cl01055 887061002490 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 887061002491 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061002492 flagellar motor protein MotB; Validated; Region: motB; PRK09041 887061002493 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061002494 ligand binding site [chemical binding]; other site 887061002495 Response regulator receiver domain; Region: Response_reg; pfam00072 887061002496 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 887061002497 active site 887061002498 phosphorylation site [posttranslational modification] 887061002499 intermolecular recognition site; other site 887061002500 dimerization interface [polypeptide binding]; other site 887061002501 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 887061002502 putative binding surface; other site 887061002503 active site 887061002504 CheY binding; Region: CheY-binding; pfam09078 887061002505 CheY binding; Region: CheY-binding; pfam09078 887061002506 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 887061002507 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 887061002508 ATP binding site [chemical binding]; other site 887061002509 Mg2+ binding site [ion binding]; other site 887061002510 G-X-G motif; other site 887061002511 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 887061002512 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 887061002513 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 887061002514 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061002515 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061002516 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 887061002517 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 887061002518 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; cl12011 887061002519 CheD chemotactic sensory transduction; Region: CheD; cl00810 887061002520 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 887061002521 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 887061002522 active site 887061002523 phosphorylation site [posttranslational modification] 887061002524 intermolecular recognition site; other site 887061002525 dimerization interface [polypeptide binding]; other site 887061002526 CheB methylesterase; Region: CheB_methylest; pfam01339 887061002527 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 887061002528 Response regulator receiver domain; Region: Response_reg; pfam00072 887061002529 active site 887061002530 phosphorylation site [posttranslational modification] 887061002531 intermolecular recognition site; other site 887061002532 dimerization interface [polypeptide binding]; other site 887061002533 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 887061002534 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 887061002535 phosphoglucomutase; Region: PLN02307 887061002536 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one...; Region: PGM1; cd03085 887061002537 substrate binding site [chemical binding]; other site 887061002538 dimer interface [polypeptide binding]; other site 887061002539 active site 887061002540 metal binding site [ion binding]; metal-binding site 887061002541 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 887061002542 catalytic motif [active] 887061002543 Catalytic residue [active] 887061002544 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 887061002545 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 887061002546 active site 887061002547 substrate binding site [chemical binding]; other site 887061002548 metal binding site [ion binding]; metal-binding site 887061002549 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 887061002550 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; cl14056 887061002551 HemN C-terminal region; Region: HemN_C; pfam06969 887061002552 Protein of unknown function (DUF528); Region: DUF528; cl01123 887061002553 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 887061002554 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 887061002555 active site 887061002556 FMN binding site [chemical binding]; other site 887061002557 substrate binding site [chemical binding]; other site 887061002558 homotetramer interface [polypeptide binding]; other site 887061002559 catalytic residue [active] 887061002560 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 887061002561 Fumarase C-terminus; Region: Fumerase_C; cl00795 887061002562 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...; Region: SHMT; cd00378 887061002563 dimer interface [polypeptide binding]; other site 887061002564 glycine-pyridoxal phosphate binding site [chemical binding]; other site 887061002565 active site 887061002566 folate binding site [chemical binding]; other site 887061002567 ATP cone domain; Region: ATP-cone; pfam03477 887061002568 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 887061002569 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 887061002570 catalytic motif [active] 887061002571 Zn binding site [ion binding]; other site 887061002572 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 5,10-...; Region: DHFR; cl00161 887061002573 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 887061002574 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 887061002575 active site 887061002576 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 887061002577 cellulose synthase subunit BcsC; Provisional; Region: PRK11447 887061002578 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 887061002579 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 887061002580 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 887061002581 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 887061002582 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061002583 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 887061002584 Walker A motif; other site 887061002585 ATP binding site [chemical binding]; other site 887061002586 Walker B motif; other site 887061002587 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061002588 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061002589 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061002590 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 887061002591 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 887061002592 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 887061002593 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...; Region: OM_channels; cl00284 887061002594 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...; Region: OM_channels; cl00284 887061002595 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 887061002596 Initiation factor 2 subunit family; Region: IF-2B; pfam01008 887061002597 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 887061002598 intersubunit interface [polypeptide binding]; other site 887061002599 active site 887061002600 Zn2+ binding site [ion binding]; other site 887061002601 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 887061002602 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 887061002603 putative substrate binding site [chemical binding]; other site 887061002604 putative ATP binding site [chemical binding]; other site 887061002605 CTP synthetase; Validated; Region: pyrG; PRK05380 887061002606 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...; Region: CTGs; cd03113 887061002607 Catalytic site [active] 887061002608 Active site [active] 887061002609 UTP binding site [chemical binding]; other site 887061002610 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 887061002611 active site 887061002612 putative oxyanion hole; other site 887061002613 catalytic triad [active] 887061002614 NeuB family; Region: NeuB; cl00496 887061002615 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 887061002616 enolase; Provisional; Region: eno; PRK00077 887061002617 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 887061002618 dimer interface [polypeptide binding]; other site 887061002619 metal binding site [ion binding]; metal-binding site 887061002620 substrate binding pocket [chemical binding]; other site 887061002621 Septum formation initiator; Region: DivIC; cl11433 887061002622 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061002623 metal binding site [ion binding]; metal-binding site 887061002624 active site 887061002625 I-site; other site 887061002626 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 887061002627 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 887061002628 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 887061002629 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 887061002630 metal ion-dependent adhesion site (MIDAS); other site 887061002631 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 887061002632 metal ion-dependent adhesion site (MIDAS); other site 887061002633 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061002634 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061002635 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...; Region: AAA; cd00009 887061002636 Walker A motif; other site 887061002637 ATP binding site [chemical binding]; other site 887061002638 Walker B motif; other site 887061002639 arginine finger; other site 887061002640 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 887061002641 active site 1 [active] 887061002642 dimer interface [polypeptide binding]; other site 887061002643 active site 2 [active] 887061002644 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 887061002645 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 887061002646 dimer interface [polypeptide binding]; other site 887061002647 active site 887061002648 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome...; Region: Xcc1710_like; cd05560 887061002649 alanine aminotransferase; Provisional; Region: PTZ00377 887061002650 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 887061002651 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002652 homodimer interface [polypeptide binding]; other site 887061002653 catalytic residue [active] 887061002654 homoserine dehydrogenase; Provisional; Region: PRK06349 887061002655 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061002656 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 887061002657 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 887061002658 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 887061002659 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...; Region: Thr-synth_2; cd01560 887061002660 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002661 catalytic residue [active] 887061002662 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 887061002663 dimerization interface [polypeptide binding]; other site 887061002664 active site 887061002665 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 887061002666 BON domain; Region: BON; cl02771 887061002667 response regulator GlrR; Provisional; Region: PRK15115 887061002668 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 887061002669 active site 887061002670 phosphorylation site [posttranslational modification] 887061002671 intermolecular recognition site; other site 887061002672 dimerization interface [polypeptide binding]; other site 887061002673 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...; Region: AAA; cd00009 887061002674 Walker A motif; other site 887061002675 ATP binding site [chemical binding]; other site 887061002676 Walker B motif; other site 887061002677 arginine finger; other site 887061002678 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061002679 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061002680 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 trans-...; Region: HisKA; cd00082 887061002681 dimer interface [polypeptide binding]; other site 887061002682 phosphorylation site [posttranslational modification] 887061002683 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 887061002684 ATP binding site [chemical binding]; other site 887061002685 Mg2+ binding site [ion binding]; other site 887061002686 G-X-G motif; other site 887061002687 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 5,10-...; Region: DHFR; cd00209 887061002688 folate binding site [chemical binding]; other site 887061002689 NADP+ binding site [chemical binding]; other site 887061002690 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 887061002691 binding surface 887061002692 TPR motif; other site 887061002693 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 887061002694 TPR motif; other site 887061002695 binding surface 887061002696 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 887061002697 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 887061002698 arginine decarboxylase; Provisional; Region: PRK15029 887061002699 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 887061002700 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 887061002701 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061002702 catalytic residue [active] 887061002703 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 887061002704 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 887061002705 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061002706 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 887061002707 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 887061002708 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061002709 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 887061002710 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 887061002711 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 887061002712 metal binding site 2 [ion binding]; metal-binding site 887061002713 putative DNA binding helix; other site 887061002714 metal binding site 1 [ion binding]; metal-binding site 887061002715 dimer interface [polypeptide binding]; other site 887061002716 structural Zn2+ binding site [ion binding]; other site 887061002717 RNB domain; Region: RNB; pfam00773 887061002718 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; cl12011 887061002719 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 887061002720 THUMP domain; Region: THUMP; cl12076 887061002721 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; cl12011 887061002722 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 887061002723 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 887061002724 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 887061002725 dimerization interface [polypeptide binding]; other site 887061002726 ATP binding site [chemical binding]; other site 887061002727 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 887061002728 dimerization interface [polypeptide binding]; other site 887061002729 ATP binding site [chemical binding]; other site 887061002730 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 887061002731 putative active site [active] 887061002732 catalytic triad [active] 887061002733 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 887061002734 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002735 Cytochrome c; Region: Cytochrom_C; cl11414 887061002736 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 887061002737 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 887061002738 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 887061002739 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 887061002740 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 887061002741 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 887061002742 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; cl11391 887061002743 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 887061002744 motif II; other site 887061002745 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; Region: Cof-subfamily; TIGR00099 887061002746 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 887061002747 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061002748 CoA-ligase; Region: Ligase_CoA; pfam00549 887061002749 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 887061002750 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061002751 CoA-ligase; Region: Ligase_CoA; pfam00549 887061002752 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002753 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 887061002754 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002755 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 887061002756 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002757 NAD synthetase; Provisional; Region: PRK13981 887061002758 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 887061002759 multimer interface [polypeptide binding]; other site 887061002760 active site 887061002761 catalytic triad [active] 887061002762 protein interface 1 [polypeptide binding]; other site 887061002763 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...; Region: NAD_synthase; cd00553 887061002764 homodimer interface [polypeptide binding]; other site 887061002765 NAD binding pocket [chemical binding]; other site 887061002766 ATP binding pocket [chemical binding]; other site 887061002767 Mg binding site [ion binding]; other site 887061002768 active-site loop [active] 887061002769 Nitrogen regulatory protein P-II; Region: P-II; cl00412 887061002770 Protein of unknown function, DUF486; Region: DUF486; cl01236 887061002771 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 887061002772 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 887061002773 G1 box; other site 887061002774 GTP/Mg2+ binding site [chemical binding]; other site 887061002775 Switch I region; other site 887061002776 G2 box; other site 887061002777 G3 box; other site 887061002778 Switch II region; other site 887061002779 G4 box; other site 887061002780 G5 box; other site 887061002781 Nucleoside recognition; Region: Gate; cl00486 887061002782 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 887061002783 Nucleoside recognition; Region: Gate; cl00486 887061002784 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 887061002785 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 887061002786 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 C-...; Region: PDZ_serine_protease; cd00987 887061002787 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 887061002788 PPIC-type PPIASE domain; Region: Rotamase; cl08278 887061002789 BolA-like protein; Region: BolA; cl00386 887061002790 YCII-related domain; Region: YCII; cl00999 887061002791 Intracellular septation protein A; Region: IspA; cl01098 887061002792 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 887061002793 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 887061002794 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 887061002795 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 887061002796 active site 887061002797 putative substrate binding region [chemical binding]; other site 887061002798 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 887061002799 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 887061002800 active site 887061002801 HIGH motif; other site 887061002802 dimer interface [polypeptide binding]; other site 887061002803 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061002804 active site 887061002805 KMSKS motif; other site 887061002806 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 887061002807 ScpA/B protein; Region: ScpA_ScpB; cl00598 887061002808 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 887061002809 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 887061002810 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 887061002811 RNA binding surface [nucleotide binding]; other site 887061002812 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 887061002813 probable active site [active] 887061002814 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 887061002815 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 887061002816 N-terminal plug; other site 887061002817 ligand-binding site [chemical binding]; other site 887061002818 HemK family putative methylases; Region: hemK_fam; TIGR00536 887061002819 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 887061002820 S-adenosylmethionine binding site [chemical binding]; other site 887061002821 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 887061002822 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 887061002823 metal binding site [ion binding]; metal-binding site 887061002824 dimer interface [polypeptide binding]; other site 887061002825 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 887061002826 putative catalytic residues [active] 887061002827 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 887061002828 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA...; Region: LbH_THP_succinylT; cd03350 887061002829 trimer interface [polypeptide binding]; other site 887061002830 active site 887061002831 substrate binding site [chemical binding]; other site 887061002832 CoA binding site [chemical binding]; other site 887061002833 Peptidase family M48; Region: Peptidase_M48; cl12018 887061002834 potassium uptake protein; Region: kup; TIGR00794 887061002835 K+ potassium transporter; Region: K_trans; cl01227 887061002836 thiazole biosynthesis protein ThiH; Region: thiH; TIGR02351 887061002837 PEP-CTERM motif; Region: VPEP; pfam07589 887061002838 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 887061002839 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 single-strand-...; Region: ExoVII_LU_OBF; cd04489 887061002840 generic binding surface II; other site 887061002841 generic binding surface I; other site 887061002842 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 887061002843 cysteine synthases; Region: cysKM; TIGR01136 887061002844 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 887061002845 dimer interface [polypeptide binding]; other site 887061002846 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002847 catalytic residue [active] 887061002848 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 887061002849 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 887061002850 active site 887061002851 catalytic site [active] 887061002852 substrate binding site [chemical binding]; other site 887061002853 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 887061002854 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 887061002855 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 887061002856 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 887061002857 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...; Region: TM_PBP2; cd06261 887061002858 dimer interface [polypeptide binding]; other site 887061002859 conserved gate region; other site 887061002860 putative PBP binding loops; other site 887061002861 ABC-ATPase subunit interface; other site 887061002862 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061002863 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 887061002864 Walker A/P-loop; other site 887061002865 ATP binding site [chemical binding]; other site 887061002866 Q-loop/lid; other site 887061002867 ABC transporter signature motif; other site 887061002868 Walker B; other site 887061002869 D-loop; other site 887061002870 H-loop/switch region; other site 887061002871 Creatinine amidohydrolase; Region: Creatininase; cl00618 887061002872 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 887061002873 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 887061002874 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 887061002875 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 887061002876 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 887061002877 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 887061002878 Domain of unknown function (DUF1989); Region: DUF1989; cl01474 887061002879 urea carboxylase; Region: urea_carbox; TIGR02712 887061002880 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061002881 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061002882 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 887061002883 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 887061002884 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 887061002885 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 887061002886 carboxyltransferase (CT) interaction site; other site 887061002887 biotinylation site [posttranslational modification]; other site 887061002888 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 887061002889 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; cl11426 887061002890 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; cl11426 887061002891 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 887061002892 ethanolamine permease; Region: 2A0305; TIGR00908 887061002893 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 887061002894 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 887061002895 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; cl09205 887061002896 Ethanolamine ammonia-lyase light chain (EutC); Region: EutC; cl01762 887061002897 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...; Region: DnaJ; cd06257 887061002898 HSP70 interaction site [polypeptide binding]; other site 887061002899 NeuB family; Region: NeuB; cl00496 887061002900 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 887061002901 transcriptional regulator EutR; Provisional; Region: PRK10130 887061002902 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 887061002903 TRAM domain; Region: TRAM; cl01282 887061002904 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 887061002905 S-adenosylmethionine binding site [chemical binding]; other site 887061002906 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 887061002907 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061002908 Coenzyme A binding pocket [chemical binding]; other site 887061002909 Isochorismatase family; Region: Isochorismatase; pfam00857 887061002910 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 887061002911 catalytic triad [active] 887061002912 conserved cis-peptide bond; other site 887061002913 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 887061002914 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 887061002915 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 887061002916 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 887061002917 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...; Region: TM_PBP2; cl00427 887061002918 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...; Region: TM_PBP2; cd06261 887061002919 putative PBP binding loops; other site 887061002920 dimer interface [polypeptide binding]; other site 887061002921 ABC-ATPase subunit interface; other site 887061002922 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...; Region: TM_PBP2; cd06261 887061002923 dimer interface [polypeptide binding]; other site 887061002924 conserved gate region; other site 887061002925 putative PBP binding loops; other site 887061002926 ABC-ATPase subunit interface; other site 887061002927 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 887061002928 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 887061002929 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cd06181 887061002930 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 887061002931 nucleoside/Zn binding site; other site 887061002932 dimer interface [polypeptide binding]; other site 887061002933 catalytic motif [active] 887061002934 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 887061002935 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061002936 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061002937 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061002938 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061002939 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...; Region: AAA; cd00009 887061002940 Walker A motif; other site 887061002941 ATP binding site [chemical binding]; other site 887061002942 Walker B motif; other site 887061002943 arginine finger; other site 887061002944 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061002945 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 887061002946 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 887061002947 dimerization interface [polypeptide binding]; other site 887061002948 Pirin-related protein [General function prediction only]; Region: COG1741 887061002949 Cupin domain; Region: Cupin_2; cl09118 887061002950 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061002951 YceI-like domain; Region: YceI; cl01001 887061002952 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 887061002953 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 887061002954 FMN binding site [chemical binding]; other site 887061002955 active site 887061002956 substrate binding site [chemical binding]; other site 887061002957 catalytic residue [active] 887061002958 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_2; cd02138 887061002959 putative FMN binding site [chemical binding]; other site 887061002960 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 887061002961 catalytic residues [active] 887061002962 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 887061002963 putative peptidoglycan binding site; other site 887061002964 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061002965 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 887061002966 S-adenosylmethionine binding site [chemical binding]; other site 887061002967 Survival protein SurE; Region: SurE; cl00448 887061002968 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 887061002969 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061002970 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 887061002971 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 887061002972 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061002973 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 887061002974 putative metal binding site [ion binding]; other site 887061002975 LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; Region: LOTUS; cl14879 887061002976 adenylosuccinate lyase; Provisional; Region: PRK09285 887061002977 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 887061002978 tetramer interface [polypeptide binding]; other site 887061002979 active site 887061002980 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 887061002981 putative active site [active] 887061002982 heme pocket [chemical binding]; other site 887061002983 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 887061002984 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 887061002985 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061002986 metal binding site [ion binding]; metal-binding site 887061002987 active site 887061002988 I-site; other site 887061002989 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 887061002990 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 (...; Region: S24_LexA-like; cd06529 887061002991 Catalytic site [active] 887061002992 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 887061002993 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change...; Region: AcnB_Swivel; cd01576 887061002994 substrate binding site [chemical binding]; other site 887061002995 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 887061002996 substrate binding site [chemical binding]; other site 887061002997 ligand binding site [chemical binding]; other site 887061002998 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 887061002999 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 887061003000 Protein of unknown function (DUF519); Region: DUF519; cl04492 887061003001 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 887061003002 E-class dimer interface [polypeptide binding]; other site 887061003003 P-class dimer interface [polypeptide binding]; other site 887061003004 active site 887061003005 Cu2+ binding site [ion binding]; other site 887061003006 Zn2+ binding site [ion binding]; other site 887061003007 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading...; Region: EFh; cd00051 887061003008 Ca2+ binding site [ion binding]; other site 887061003009 Cation efflux family; Region: Cation_efflux; cl00316 887061003010 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 887061003011 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 887061003012 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 887061003013 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 887061003014 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 887061003015 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 887061003016 psiF repeat; Region: PsiF_repeat; pfam07769 887061003017 psiF repeat; Region: PsiF_repeat; pfam07769 887061003018 psiF repeat; Region: PsiF_repeat; pfam07769 887061003019 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...; Region: Peptidase_C39_likeD; cd02421 887061003020 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 887061003021 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 887061003022 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 887061003023 Walker A/P-loop; other site 887061003024 ATP binding site [chemical binding]; other site 887061003025 Q-loop/lid; other site 887061003026 ABC transporter signature motif; other site 887061003027 Walker B; other site 887061003028 D-loop; other site 887061003029 H-loop/switch region; other site 887061003030 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 887061003031 Outer membrane efflux protein; Region: OEP; pfam02321 887061003032 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061003033 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...; Region: LuxR_C_like; cd06170 887061003034 DNA binding residues [nucleotide binding] 887061003035 dimerization interface [polypeptide binding]; other site 887061003036 VCBS repeat; Region: VCBS_repeat; TIGR01965 887061003037 VCBS repeat; Region: VCBS_repeat; TIGR01965 887061003038 VCBS repeat; Region: VCBS_repeat; TIGR01965 887061003039 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 887061003040 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 887061003041 metal ion-dependent adhesion site (MIDAS); other site 887061003042 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; cl12108 887061003043 biofilm formation regulator HmsP; Provisional; Region: PRK11829 887061003044 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061003045 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 887061003046 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 887061003047 Bacterial protein of unknown function (DUF920); Region: DUF920; cl01479 887061003048 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061003049 Outer membrane efflux protein; Region: OEP; pfam02321 887061003050 Outer membrane efflux protein; Region: OEP; pfam02321 887061003051 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 887061003052 DNA photolyase; Region: DNA_photolyase; pfam00875 887061003053 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 887061003054 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 887061003055 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 887061003056 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 887061003057 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH...; Region: alkPPc; cd00016 887061003058 dimer interface [polypeptide binding]; other site 887061003059 Alkaline phosphatase homologues; Region: alkPPc; smart00098 887061003060 active site 887061003061 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH...; Region: alkPPc; cl12039 887061003062 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 887061003063 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 887061003064 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 887061003065 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061003066 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 887061003067 GSPII_E N-terminal domain; Region: GSPII_E_N; pfam05157 887061003068 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061003069 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 887061003070 Walker A motif; other site 887061003071 ATP binding site [chemical binding]; other site 887061003072 Walker B motif; other site 887061003073 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 887061003074 Type II secretory pathway, component HofQ [Intracellular trafficking and secretion]; Region: HofQ; COG4796 887061003075 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 887061003076 binding surface 887061003077 TPR motif; other site 887061003078 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 887061003079 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 887061003080 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 887061003081 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 887061003082 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 887061003083 Bacterial type II secretion system protein G; Region: GSPII_G; pfam08334 887061003084 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 887061003085 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061003086 catalytic residue [active] 887061003087 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...; Region: PRX_BCP; cd03017 887061003088 catalytic triad [active] 887061003089 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 887061003090 Phage integrase family; Region: Phage_integrase; pfam00589 887061003091 Int/Topo IB signature motif; other site 887061003092 active site 887061003093 DNA binding site [nucleotide binding] 887061003094 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 (...; Region: S24_LexA-like; cd06529 887061003095 Catalytic site [active] 887061003096 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 887061003097 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 887061003098 active site 887061003099 DNA binding site [nucleotide binding] 887061003100 Transposase, Mutator family; Region: Transposase_mut; pfam00872 887061003101 MULE transposase domain; Region: MULE; pfam10551 887061003102 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl01961 887061003103 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 887061003104 active site 887061003105 metal binding site [ion binding]; metal-binding site 887061003106 Chromate transporter; Region: Chromate_transp; pfam02417 887061003107 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 887061003108 Chromate transporter; Region: Chromate_transp; pfam02417 887061003109 Protein of unknown function (DUF2380); Region: DUF3280; pfam11684 887061003110 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 887061003111 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 887061003112 TPR motif; other site 887061003113 binding surface 887061003114 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 887061003115 binding surface 887061003116 TPR motif; other site 887061003117 Domain of Unknown Function (DUF3856); Region: DUF3856; pfam12968 887061003118 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 887061003119 binding surface 887061003120 TPR motif; other site 887061003121 conserved hypothetical protein; Region: TIGR02466 887061003122 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 887061003123 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 887061003124 N-terminal plug; other site 887061003125 ligand-binding site [chemical binding]; other site 887061003126 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 887061003127 Uncharacterized conserved protein [Function unknown]; Region: COG5591 887061003128 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 887061003129 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 887061003130 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 887061003131 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 887061003132 N-terminal plug; other site 887061003133 ligand-binding site [chemical binding]; other site 887061003134 ABC transporter ATPase component; Reviewed; Region: PRK11147 887061003135 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003136 Walker A/P-loop; other site 887061003137 ATP binding site [chemical binding]; other site 887061003138 Q-loop/lid; other site 887061003139 ABC transporter signature motif; other site 887061003140 Walker B; other site 887061003141 D-loop; other site 887061003142 H-loop/switch region; other site 887061003143 ABC transporter; Region: ABC_tran_2; pfam12848 887061003144 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...; Region: ABCF_EF-3; cd03221 887061003145 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 887061003146 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 887061003147 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 887061003148 active site 887061003149 phosphorylation site [posttranslational modification] 887061003150 intermolecular recognition site; other site 887061003151 dimerization interface [polypeptide binding]; other site 887061003152 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...; Region: trans_reg_C; cd00383 887061003153 DNA binding site [nucleotide binding] 887061003154 sensor protein KdpD; Provisional; Region: PRK10490 887061003155 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 887061003156 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 887061003157 Ligand Binding Site [chemical binding]; other site 887061003158 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 trans-...; Region: HisKA; cd00082 887061003159 dimer interface [polypeptide binding]; other site 887061003160 phosphorylation site [posttranslational modification] 887061003161 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 887061003162 ATP binding site [chemical binding]; other site 887061003163 Mg2+ binding site [ion binding]; other site 887061003164 G-X-G motif; other site 887061003165 K+-transporting ATPase, c chain; Region: KdpC; cl00944 887061003166 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 887061003167 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 887061003168 K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]; Region: KdpA; cl00903 887061003169 Potassium-transporting ATPase A subunit; Region: KdpA; pfam03814 887061003170 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 887061003171 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061003172 putative substrate translocation pore; other site 887061003173 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 887061003174 UvrD/REP helicase; Region: UvrD-helicase; cl14126 887061003175 UvrD/REP helicase; Region: UvrD-helicase; cl14126 887061003176 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003177 metal binding site [ion binding]; metal-binding site 887061003178 active site 887061003179 I-site; other site 887061003180 MEKHLA domain; Region: MEKHLA; pfam08670 887061003181 CHASE3 domain; Region: CHASE3; cl05000 887061003182 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003183 metal binding site [ion binding]; metal-binding site 887061003184 active site 887061003185 I-site; other site 887061003186 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 887061003187 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases...; Region: YlqF; cd01856 887061003188 GTP/Mg2+ binding site [chemical binding]; other site 887061003189 G4 box; other site 887061003190 G5 box; other site 887061003191 G1 box; other site 887061003192 Switch I region; other site 887061003193 G2 box; other site 887061003194 G3 box; other site 887061003195 Switch II region; other site 887061003196 ApbE family; Region: ApbE; cl00643 887061003197 FMN-binding domain; Region: FMN_bind; cl01081 887061003198 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; cl12011 887061003199 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 887061003200 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 887061003201 MG2 domain; Region: A2M_N; pfam01835 887061003202 Alpha-2-macroglobulin family N-terminal region; Region: A2M_N_2; pfam07703 887061003203 Alpha-2-macroglobulin family; Region: A2M; pfam00207 887061003204 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 887061003205 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 887061003206 Transglycosylase; Region: Transgly; cl07896 887061003207 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 887061003208 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 887061003209 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 887061003210 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 887061003211 ATP binding site [chemical binding]; other site 887061003212 putative Mg++ binding site [ion binding]; other site 887061003213 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; cl14882 887061003214 Helicase associated domain (HA2); Region: HA2; cl04503 887061003215 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 887061003216 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 887061003217 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061003218 NodT family; Region: outer_NodT; TIGR01845 887061003219 Outer membrane efflux protein; Region: OEP; pfam02321 887061003220 Outer membrane efflux protein; Region: OEP; pfam02321 887061003221 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 887061003222 Fusaric acid resistance protein family; Region: FUSC; pfam04632 887061003223 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 887061003224 p-hydroxybenzoic acid efflux subunit AaeA; Provisional; Region: PRK10559 887061003225 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 887061003226 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061003227 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 887061003228 dimerization interface [polypeptide binding]; other site 887061003229 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 887061003230 N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by...; Region: CIMS_N_terminal_like; cd03312 887061003231 THF binding site; other site 887061003232 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 catalyses the last step in the production of methionine by...; Region: CIMS_C_terminal_like; cd03311 887061003233 substrate binding site [chemical binding]; other site 887061003234 THF binding site; other site 887061003235 zinc-binding site [ion binding]; other site 887061003236 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 887061003237 EamA-like transporter family; Region: EamA; cl01037 887061003238 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 887061003239 ATP cone domain; Region: ATP-cone; pfam03477 887061003240 Class I ribonucleotide reductase; Region: RNR_I; cd01679 887061003241 active site 887061003242 dimer interface [polypeptide binding]; other site 887061003243 catalytic residues [active] 887061003244 effector binding site; other site 887061003245 R2 peptide binding site; other site 887061003246 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 887061003247 dimer interface [polypeptide binding]; other site 887061003248 putative radical transfer pathway; other site 887061003249 diiron center [ion binding]; other site 887061003250 tyrosyl radical; other site 887061003251 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 887061003252 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003253 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 887061003254 putative active site [active] 887061003255 putative metal-binding site [ion binding]; other site 887061003256 UvrD/REP helicase; Region: UvrD-helicase; cl14126 887061003257 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 887061003258 trimer interface [polypeptide binding]; other site 887061003259 active site 887061003260 glucose-6-phosphate 1-dehydrogenase; Provisional; Region: PRK12853 887061003261 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 887061003262 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 887061003263 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061003264 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 887061003265 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 887061003266 putative active site [active] 887061003267 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; cl12011 887061003268 Domain of unknown function DUF59; Region: DUF59; cl00941 887061003269 antiporter inner membrane protein; Provisional; Region: PRK11670 887061003270 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 887061003271 Walker A motif; other site 887061003272 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 887061003273 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 887061003274 active site 887061003275 HIGH motif; other site 887061003276 KMSKS motif; other site 887061003277 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 887061003278 tRNA binding surface [nucleotide binding]; other site 887061003279 anticodon binding site; other site 887061003280 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 887061003281 dimer interface [polypeptide binding]; other site 887061003282 putative tRNA-binding site [nucleotide binding]; other site 887061003283 comEA protein; Region: comE; TIGR01259 887061003284 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 887061003285 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 887061003286 active site 887061003287 dimer interface [polypeptide binding]; other site 887061003288 tetratricopeptide repeat protein; Provisional; Region: PRK11788 887061003289 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003290 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 887061003291 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 higher-...; Region: HU_IHF; cd00591 887061003292 IHF dimer interface [polypeptide binding]; other site 887061003293 IHF - DNA interface [nucleotide binding]; other site 887061003294 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 887061003295 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...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 887061003296 RNA binding site [nucleotide binding]; other site 887061003297 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...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 887061003298 RNA binding site [nucleotide binding]; other site 887061003299 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 887061003300 RNA binding site [nucleotide binding]; other site 887061003301 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 887061003302 RNA binding site [nucleotide binding]; other site 887061003303 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 887061003304 RNA binding site [nucleotide binding]; other site 887061003305 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 887061003306 RNA binding site [nucleotide binding]; other site 887061003307 cytidylate kinase; Provisional; Region: cmk; PRK00023 887061003308 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 887061003309 CMP-binding site; other site 887061003310 The sites determining sugar specificity; other site 887061003311 Predicted membrane protein (DUF2061); Region: DUF2061; cl01257 887061003312 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 887061003313 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 5-enolpyruvylshkimate-3-...; Region: EPSP_synthase; cd01556 887061003314 hinge; other site 887061003315 active site 887061003316 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 887061003317 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061003318 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 887061003319 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 887061003320 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 887061003321 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 887061003322 PAS domain S-box; Region: sensory_box; TIGR00229 887061003323 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 887061003324 putative active site [active] 887061003325 heme pocket [chemical binding]; other site 887061003326 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003327 metal binding site [ion binding]; metal-binding site 887061003328 active site 887061003329 I-site; other site 887061003330 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2; Region: Mfa2; pfam08842 887061003331 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 887061003332 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003333 metal binding site [ion binding]; metal-binding site 887061003334 active site 887061003335 I-site; other site 887061003336 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061003337 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061003338 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 887061003339 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 887061003340 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 887061003341 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 887061003342 hypothetical protein; Provisional; Region: PRK01254 887061003343 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; cl14056 887061003344 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 887061003345 TraB family; Region: TraB; cl12050 887061003346 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 887061003347 Response regulator receiver domain; Region: Response_reg; pfam00072 887061003348 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 887061003349 active site 887061003350 phosphorylation site [posttranslational modification] 887061003351 intermolecular recognition site; other site 887061003352 dimerization interface [polypeptide binding]; other site 887061003353 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061003354 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 887061003355 active site 887061003356 phosphorylation site [posttranslational modification] 887061003357 intermolecular recognition site; other site 887061003358 dimerization interface [polypeptide binding]; other site 887061003359 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...; Region: LuxR_C_like; cd06170 887061003360 DNA binding residues [nucleotide binding] 887061003361 dimerization interface [polypeptide binding]; other site 887061003362 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 887061003363 Ferritin-like domain; Region: Ferritin; pfam00210 887061003364 dinuclear metal binding motif [ion binding]; other site 887061003365 CHASE3 domain; Region: CHASE3; cl05000 887061003366 Histidine kinase; Region: HisKA_3; pfam07730 887061003367 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 887061003368 ATP binding site [chemical binding]; other site 887061003369 Mg2+ binding site [ion binding]; other site 887061003370 G-X-G motif; other site 887061003371 BON domain; Region: BON; cl02771 887061003372 BON domain; Region: BON; cl02771 887061003373 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 887061003374 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 887061003375 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 887061003376 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 887061003377 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 887061003378 active site 887061003379 phosphorylation site [posttranslational modification] 887061003380 intermolecular recognition site; other site 887061003381 dimerization interface [polypeptide binding]; other site 887061003382 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...; Region: trans_reg_C; cd00383 887061003383 DNA binding site [nucleotide binding] 887061003384 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 trans-...; Region: HisKA; cd00082 887061003385 dimer interface [polypeptide binding]; other site 887061003386 phosphorylation site [posttranslational modification] 887061003387 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 887061003388 ATP binding site [chemical binding]; other site 887061003389 Mg2+ binding site [ion binding]; other site 887061003390 G-X-G motif; other site 887061003391 BON domain; Region: BON; cl02771 887061003392 BON domain; Region: BON; cl02771 887061003393 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 887061003394 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 887061003395 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 887061003396 DEAD-like helicases superfamily; Region: DEXDc; smart00487 887061003397 ATP binding site [chemical binding]; other site 887061003398 Mg++ binding site [ion binding]; other site 887061003399 motif III; other site 887061003400 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 887061003401 nucleotide binding region [chemical binding]; other site 887061003402 ATP-binding site [chemical binding]; other site 887061003403 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 887061003404 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 887061003405 RNA binding surface [nucleotide binding]; other site 887061003406 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 887061003407 active site 887061003408 uracil binding [chemical binding]; other site 887061003409 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 887061003410 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 887061003411 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061003412 active site 887061003413 dimer interface [polypeptide binding]; other site 887061003414 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 887061003415 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 887061003416 DAK2 domain; Region: Dak2; cl03685 887061003417 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 887061003418 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 887061003419 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 887061003420 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 887061003421 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 887061003422 dimerization interface [polypeptide binding]; other site 887061003423 domain crossover interface; other site 887061003424 redox-dependent activation switch; other site 887061003425 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061003426 active site 887061003427 HIGH motif; other site 887061003428 nucleotide binding site [chemical binding]; other site 887061003429 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061003430 active site 887061003431 KMSKS motif; other site 887061003432 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 887061003433 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 887061003434 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 887061003435 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003436 Active site [active] 887061003437 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 887061003438 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 887061003439 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061003440 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 887061003441 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 887061003442 DNA binding site [nucleotide binding] 887061003443 active site 887061003444 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 887061003445 dimerization interface [polypeptide binding]; other site 887061003446 putative DNA binding site [nucleotide binding]; other site 887061003447 putative Zn2+ binding site [ion binding]; other site 887061003448 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_20; cd07254 887061003449 putative metal binding site [ion binding]; other site 887061003450 Low molecular weight phosphatase family; Region: LMWPc; cd00115 887061003451 Active site [active] 887061003452 Membrane transport protein; Region: Mem_trans; cl09117 887061003453 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 887061003454 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 887061003455 dimer interface [polypeptide binding]; other site 887061003456 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 887061003457 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 887061003458 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 887061003459 Outer membrane efflux protein; Region: OEP; pfam02321 887061003460 Outer membrane efflux protein; Region: OEP; pfam02321 887061003461 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 887061003462 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 887061003463 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 887061003464 active site 887061003465 DNA binding site [nucleotide binding] 887061003466 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 (...; Region: S24_LexA-like; cd06529 887061003467 Catalytic site [active] 887061003468 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 887061003469 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 887061003470 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061003471 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061003472 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 887061003473 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061003474 ligand binding site [chemical binding]; other site 887061003475 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 887061003476 Type VI secretion lipoprotein; Region: T6SS-SciN; cl01405 887061003477 Bacterial protein of unknown function (DUF876); Region: DUF876; cl01406 887061003478 Uncharacterized conserved protein [Function unknown]; Region: COG4104 887061003479 PAAR motif; Region: PAAR_motif; pfam05488 887061003480 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 887061003481 catalytic residue [active] 887061003482 Cupin domain; Region: Cupin_2; cl09118 887061003483 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cl00473 887061003484 PAS domain S-box; Region: sensory_box; TIGR00229 887061003485 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 887061003486 putative active site [active] 887061003487 heme pocket [chemical binding]; other site 887061003488 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003489 metal binding site [ion binding]; metal-binding site 887061003490 active site 887061003491 I-site; other site 887061003492 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 887061003493 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 887061003494 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 887061003495 cyclopropane fatty acyl phospholipid synthase; Provisional; Region: PRK11705 887061003496 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; cl12011 887061003497 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 887061003498 S-adenosylmethionine binding site [chemical binding]; other site 887061003499 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 887061003500 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 887061003501 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 887061003502 putative active site [active] 887061003503 heme pocket [chemical binding]; other site 887061003504 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003505 metal binding site [ion binding]; metal-binding site 887061003506 active site 887061003507 I-site; other site 887061003508 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 887061003509 Protein of unknown function (DUF779); Region: DUF779; cl01432 887061003510 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 887061003511 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 887061003512 NAD(P) binding site [chemical binding]; other site 887061003513 catalytic residues [active] 887061003514 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 887061003515 putative dimer interface [polypeptide binding]; other site 887061003516 [2Fe-2S] cluster binding site [ion binding]; other site 887061003517 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 887061003518 putative dimer interface [polypeptide binding]; other site 887061003519 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 887061003520 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 887061003521 SLBB domain; Region: SLBB; pfam10531 887061003522 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 887061003523 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 887061003524 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 887061003525 catalytic loop [active] 887061003526 iron binding site [ion binding]; other site 887061003527 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 887061003528 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)...; Region: MopB_Formate-Dh-H; cd02753 887061003529 [4Fe-4S] binding site [ion binding]; other site 887061003530 molybdopterin cofactor binding site; other site 887061003531 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...; Region: MopB_CT_Fdh-Nap-like; cd00508 887061003532 molybdopterin cofactor binding site; other site 887061003533 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 887061003534 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 887061003535 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 887061003536 substrate binding site [chemical binding]; other site 887061003537 dimer interface [polypeptide binding]; other site 887061003538 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...; Region: MECDP_synthase; cd00554 887061003539 homotrimer interaction site [polypeptide binding]; other site 887061003540 zinc binding site [ion binding]; other site 887061003541 CDP-binding sites; other site 887061003542 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061003543 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061003544 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...; Region: Biotinyl_lipoyl_domains; cl11404 887061003545 Outer membrane efflux protein; Region: OEP; pfam02321 887061003546 Outer membrane efflux protein; Region: OEP; pfam02321 887061003547 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 887061003548 dimer interface [polypeptide binding]; other site 887061003549 metal binding site [ion binding]; metal-binding site 887061003550 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 887061003551 Smr domain; Region: Smr; cl02619 887061003552 thioredoxin reductase; Provisional; Region: PRK10262 887061003553 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061003554 Ferritin-like domain; Region: Ferritin; pfam00210 887061003555 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 887061003556 dimerization interface [polypeptide binding]; other site 887061003557 DPS ferroxidase diiron center [ion binding]; other site 887061003558 ion pore; other site 887061003559 DNA translocase FtsK; Provisional; Region: PRK10263 887061003560 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003561 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 887061003562 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 887061003563 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 887061003564 recombination factor protein RarA; Reviewed; Region: PRK13342 887061003565 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...; Region: AAA; cd00009 887061003566 Walker A motif; other site 887061003567 ATP binding site [chemical binding]; other site 887061003568 Walker B motif; other site 887061003569 arginine finger; other site 887061003570 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 887061003571 seryl-tRNA synthetase; Provisional; Region: PRK05431 887061003572 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 887061003573 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...; Region: SerRS_core; cd00770 887061003574 dimer interface [polypeptide binding]; other site 887061003575 active site 887061003576 motif 1; other site 887061003577 motif 2; other site 887061003578 motif 3; other site 887061003579 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 887061003580 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 887061003581 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 887061003582 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...; Region: PBPb; cd00134 887061003583 substrate binding pocket [chemical binding]; other site 887061003584 membrane-bound complex binding site; other site 887061003585 hinge residues; other site 887061003586 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 887061003587 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061003588 catalytic residue [active] 887061003589 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 887061003590 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR1; cd08267 887061003591 putative NAD(P) binding site [chemical binding]; other site 887061003592 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 887061003593 Ly49-like protein, N-terminal region; Region: Ly49; pfam08391 887061003594 FemAB family; Region: FemAB; cl11444 887061003595 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 887061003596 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 887061003597 dimer interface [polypeptide binding]; other site 887061003598 active site 887061003599 Phosphopantetheine attachment site; Region: PP-binding; cl09936 887061003600 Esterase/lipase [General function prediction only]; Region: COG1647 887061003601 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 887061003602 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 887061003603 inhibitor-cofactor binding pocket; inhibition site 887061003604 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061003605 catalytic residue [active] 887061003606 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; cl11391 887061003607 Predicted integral membrane proteins containing uncharacterized repeats [Function unknown]; Region: COG5563 887061003608 Autotransporter beta-domain; Region: Autotransporter; cl02365 887061003609 Autotransporter beta-domain; Region: Autotransporter; cl02365 887061003610 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 887061003611 Cu(I) binding site [ion binding]; other site 887061003612 UbiA prenyltransferase family; Region: UbiA; cl00337 887061003613 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 887061003614 cytochrome c oxidase assembly protein; Provisional; Region: PTZ00127 887061003615 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061003616 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 887061003617 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 887061003618 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 887061003619 Subunit III/VIIa interface [polypeptide binding]; other site 887061003620 Phospholipid binding site [chemical binding]; other site 887061003621 Subunit I/III interface [polypeptide binding]; other site 887061003622 Subunit III/VIb interface [polypeptide binding]; other site 887061003623 Subunit III/VIa interface; other site 887061003624 Subunit III/Vb interface [polypeptide binding]; other site 887061003625 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 887061003626 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 887061003627 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 887061003628 Subunit I/III interface [polypeptide binding]; other site 887061003629 D-pathway; other site 887061003630 Subunit I/VIIc interface [polypeptide binding]; other site 887061003631 Subunit I/IV interface [polypeptide binding]; other site 887061003632 Subunit I/II interface [polypeptide binding]; other site 887061003633 Low-spin heme (heme a) binding site [chemical binding]; other site 887061003634 Subunit I/VIIa interface [polypeptide binding]; other site 887061003635 Subunit I/VIa interface [polypeptide binding]; other site 887061003636 Dimer interface; other site 887061003637 Putative water exit pathway; other site 887061003638 Binuclear center (heme a3/CuB) [ion binding]; other site 887061003639 K-pathway; other site 887061003640 Subunit I/Vb interface [polypeptide binding]; other site 887061003641 Putative proton exit pathway; other site 887061003642 Subunit I/VIb interface; other site 887061003643 Subunit I/VIc interface [polypeptide binding]; other site 887061003644 Electron transfer pathway; other site 887061003645 Subunit I/VIIIb interface [polypeptide binding]; other site 887061003646 Subunit I/VIIb interface [polypeptide binding]; other site 887061003647 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 887061003648 Cytochrome c; Region: Cytochrom_C; cl11414 887061003649 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 887061003650 Yip1 domain; Region: Yip1; cl12048 887061003651 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 887061003652 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 887061003653 FtsX-like permease family; Region: FtsX; pfam02687 887061003654 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 887061003655 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 887061003656 Walker A/P-loop; other site 887061003657 ATP binding site [chemical binding]; other site 887061003658 Q-loop/lid; other site 887061003659 ABC transporter signature motif; other site 887061003660 Walker B; other site 887061003661 D-loop; other site 887061003662 H-loop/switch region; other site 887061003663 macrolide transporter subunit MacA; Provisional; Region: PRK11578 887061003664 Outer membrane efflux protein; Region: OEP; pfam02321 887061003665 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 887061003666 Outer membrane efflux protein; Region: OEP; pfam02321 887061003667 Outer membrane efflux protein; Region: OEP; pfam02321 887061003668 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 887061003669 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003670 Walker A/P-loop; other site 887061003671 ATP binding site [chemical binding]; other site 887061003672 Q-loop/lid; other site 887061003673 ABC transporter signature motif; other site 887061003674 Walker B; other site 887061003675 D-loop; other site 887061003676 H-loop/switch region; other site 887061003677 ABC transporter; Region: ABC_tran_2; pfam12848 887061003678 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...; Region: ABCF_EF-3; cd03221 887061003679 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 887061003680 dimer interface [polypeptide binding]; other site 887061003681 FMN binding site [chemical binding]; other site 887061003682 transcription elongation factor regulatory protein; Validated; Region: PRK06342 887061003683 C-term; Region: GreA_GreB; pfam01272 887061003684 GMP synthase; Reviewed; Region: guaA; PRK00074 887061003685 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 887061003686 AMP/PPi binding site [chemical binding]; other site 887061003687 candidate oxyanion hole; other site 887061003688 catalytic triad [active] 887061003689 potential glutamine specificity residues [chemical binding]; other site 887061003690 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 887061003691 ATP Binding subdomain [chemical binding]; other site 887061003692 Ligand Binding sites [chemical binding]; other site 887061003693 Dimerization subdomain; other site 887061003694 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 887061003695 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 887061003696 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 887061003697 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...; Region: IMPDH; cd00381 887061003698 active site 887061003699 Uncharacterised protein family (UPF0125); Region: UPF0125; cl01096 887061003700 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 887061003701 putative coenzyme Q binding site [chemical binding]; other site 887061003702 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 887061003703 SmpB-tmRNA interface; other site 887061003704 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 887061003705 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 887061003706 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 887061003707 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; cl14056 887061003708 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 887061003709 elongation factor P; Validated; Region: PRK00529 887061003710 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 887061003711 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 887061003712 RNA binding site [nucleotide binding]; other site 887061003713 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 887061003714 RNA binding site [nucleotide binding]; other site 887061003715 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; cl01823 887061003716 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 887061003717 domain; Region: GreA_GreB_N; pfam03449 887061003718 C-term; Region: GreA_GreB; pfam01272 887061003719 probable DNA repair protein; Region: TIGR03623 887061003720 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 887061003721 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 887061003722 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 887061003723 UvrD/REP helicase; Region: UvrD-helicase; cl14126 887061003724 UvrD/REP helicase; Region: UvrD-helicase; cl14126 887061003725 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 887061003726 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 887061003727 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 887061003728 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 887061003729 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 887061003730 ATP binding site [chemical binding]; other site 887061003731 putative Mg++ binding site [ion binding]; other site 887061003732 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 887061003733 nucleotide binding region [chemical binding]; other site 887061003734 ATP-binding site [chemical binding]; other site 887061003735 TRCF domain; Region: TRCF; pfam03461 887061003736 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 887061003737 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 887061003738 Predicted amidohydrolase [General function prediction only]; Region: COG0388 887061003739 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 887061003740 putative active site [active] 887061003741 catalytic triad [active] 887061003742 dimer interface [polypeptide binding]; other site 887061003743 TIGR02099 family protein; Region: TIGR02099 887061003744 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 887061003745 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...; Region: ABCF_EF-3; cd03221 887061003746 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003747 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...; Region: ABCF_EF-3; cd03221 887061003748 ABC transporter; Region: ABC_tran_2; pfam12848 887061003749 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...; Region: ABCF_EF-3; cd03221 887061003750 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 887061003751 dimer interface [polypeptide binding]; other site 887061003752 DNA-binding transcriptional regulator CpxR; Provisional; Region: PRK10955 887061003753 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 887061003754 active site 887061003755 phosphorylation site [posttranslational modification] 887061003756 intermolecular recognition site; other site 887061003757 dimerization interface [polypeptide binding]; other site 887061003758 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...; Region: trans_reg_C; cd00383 887061003759 DNA binding site [nucleotide binding] 887061003760 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061003761 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 trans-...; Region: HisKA; cl00080 887061003762 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 887061003763 ATP binding site [chemical binding]; other site 887061003764 Mg2+ binding site [ion binding]; other site 887061003765 G-X-G motif; other site 887061003766 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061003767 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 887061003768 ligand binding site [chemical binding]; other site 887061003769 flexible hinge region; other site 887061003770 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061003771 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 887061003772 PilZ domain; Region: PilZ; cl01260 887061003773 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 887061003774 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 887061003775 Sulfatase; Region: Sulfatase; cl10460 887061003776 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 887061003777 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 887061003778 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 887061003779 aspartate aminotransferase; Provisional; Region: PRK08361 887061003780 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 887061003781 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061003782 homodimer interface [polypeptide binding]; other site 887061003783 catalytic residue [active] 887061003784 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...; Region: Tryp_SPc; cl00149 887061003785 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 887061003786 binding surface 887061003787 TPR motif; other site 887061003788 excinuclease ABC subunit B; Provisional; Region: PRK05298 887061003789 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 887061003790 ATP binding site [chemical binding]; other site 887061003791 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 887061003792 nucleotide binding region [chemical binding]; other site 887061003793 ATP-binding site [chemical binding]; other site 887061003794 Ultra-violet resistance protein B; Region: UvrB; pfam12344 887061003795 UvrB/uvrC motif; Region: UVR; pfam02151 887061003796 ribonuclease E; Reviewed; Region: rne; PRK10811 887061003797 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 887061003798 homodimer interface [polypeptide binding]; other site 887061003799 oligonucleotide binding site [chemical binding]; other site 887061003800 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 887061003801 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 887061003802 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...; Region: PseudoU_synth_RluCD_like; cd02869 887061003803 active site 887061003804 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061003805 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 887061003806 motif II; other site 887061003807 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)...; Region: Rieske; cl00938 887061003808 iron-sulfur cluster [ion binding]; other site 887061003809 [2Fe-2S] cluster binding site [ion binding]; other site 887061003810 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 887061003811 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 887061003812 tandem repeat interface [polypeptide binding]; other site 887061003813 oligomer interface [polypeptide binding]; other site 887061003814 active site residues [active] 887061003815 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 887061003816 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 887061003817 active site 887061003818 dimer interface [polypeptide binding]; other site 887061003819 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 887061003820 dimer interface [polypeptide binding]; other site 887061003821 active site 887061003822 glycogen branching enzyme; Provisional; Region: PRK05402 887061003823 Glycogen branching enzyme N-terminus domain. Glycogen branching enzyme (AKA 1,4 alpha glucan branching enzyme) catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a...; Region: Glycogen_branching_enzyme_N_term; cd02855 887061003824 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061003825 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; cl02706 887061003826 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 887061003827 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 887061003828 ligand binding site [chemical binding]; other site 887061003829 oligomer interface [polypeptide binding]; other site 887061003830 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 rate-...; Region: LbH_G1P_AT_C; cd04651 887061003831 dimer interface [polypeptide binding]; other site 887061003832 N-terminal domain interface [polypeptide binding]; other site 887061003833 sulfate 1 binding site; other site 887061003834 Alpha-amylase/alpha-mannosidase [Carbohydrate transport and metabolism]; Region: COG1449 887061003835 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 887061003836 Glycosyl hydrolases family 38 N-terminal domain; Region: Glyco_hydro_38; pfam01074 887061003837 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 887061003838 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 887061003839 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 887061003840 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 887061003841 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain...; Region: CBS_pair_GGDEF_assoc; cd04598 887061003842 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003843 metal binding site [ion binding]; metal-binding site 887061003844 active site 887061003845 I-site; other site 887061003846 Glycosyl hydrolases family 17; Region: Glyco_hydro_17; cl02191 887061003847 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 887061003848 active site 887061003849 Glycosyl hydrolases family 17; Region: Glyco_hydro_17; cl02191 887061003850 YdjC-like protein; Region: YdjC; cl01344 887061003851 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 887061003852 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 887061003853 Ligand binding site [chemical binding]; other site 887061003854 Putative Catalytic site [active] 887061003855 DXD motif; other site 887061003856 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 887061003857 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 887061003858 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 887061003859 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 887061003860 Localisation of periplasmic protein complexes; Region: AMIN; pfam11741 887061003861 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 887061003862 active site 887061003863 metal binding site [ion binding]; metal-binding site 887061003864 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 887061003865 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061003866 Beta-Casp domain; Region: Beta-Casp; pfam10996 887061003867 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 887061003868 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 887061003869 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 887061003870 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 887061003871 ATP binding site [chemical binding]; other site 887061003872 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 887061003873 Protein of unknown function (DUF817); Region: DUF817; cl01520 887061003874 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 887061003875 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 887061003876 dimer interface [polypeptide binding]; other site 887061003877 substrate binding site [chemical binding]; other site 887061003878 ATP binding site [chemical binding]; other site 887061003879 IPP transferase; Region: IPPT; cl00403 887061003880 aspartate aminotransferase; Provisional; Region: PRK08361 887061003881 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 887061003882 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061003883 homodimer interface [polypeptide binding]; other site 887061003884 catalytic residue [active] 887061003885 Predicted permeases [General function prediction only]; Region: RarD; COG2962 887061003886 EamA-like transporter family; Region: EamA; cl01037 887061003887 Intradiol dioxygenase supgroup. Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. They break the catechol C1-C2 bond and utilize Fe3+, as opposed to the...; Region: intradiol_dioxygenase_like; cd03457 887061003888 putative active site [active] 887061003889 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 887061003890 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061003891 ATP binding site [chemical binding]; other site 887061003892 Walker B motif; other site 887061003893 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 887061003894 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-...; Region: CBS_pair; cl10010 887061003895 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003896 metal binding site [ion binding]; metal-binding site 887061003897 active site 887061003898 I-site; other site 887061003899 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 887061003900 binding surface 887061003901 TPR motif; other site 887061003902 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 887061003903 binding surface 887061003904 TPR motif; other site 887061003905 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 887061003906 binding surface 887061003907 TPR motif; other site 887061003908 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 887061003909 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061003910 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 887061003911 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; cl12011 887061003912 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 887061003913 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 887061003914 S-adenosylmethionine binding site [chemical binding]; other site 887061003915 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 887061003916 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; cl12011 887061003917 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 887061003918 S-adenosylmethionine binding site [chemical binding]; other site 887061003919 Protein of unknown function (DUF1365); Region: DUF1365; cl01388 887061003920 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061003921 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 887061003922 Di-iron ligands [ion binding]; other site 887061003923 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 887061003924 Lipocalin / cytosolic fatty-acid binding protein family; Region: Lipocalin; cl01150 887061003925 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 887061003926 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 887061003927 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 887061003928 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 887061003929 S-adenosylmethionine binding site [chemical binding]; other site 887061003930 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 887061003931 DNA binding residues [nucleotide binding] 887061003932 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 887061003933 B12 binding site [chemical binding]; other site 887061003934 Anti-sigma-K factor rskA; Region: RskA; cl02208 887061003935 RNA polymerase sigma factor; Provisional; Region: PRK12514 887061003936 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061003937 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...; Region: Sigma70_r4; cl01055 887061003938 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061003939 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061003940 Trp docking motif; other site 887061003941 'Velcro' closure; other site 887061003942 active site 887061003943 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 Gram-...; Region: OMPLA; cl00248 887061003944 dimerization interface [polypeptide binding]; other site 887061003945 substrate binding site [chemical binding]; other site 887061003946 active site 887061003947 calcium binding site [ion binding]; other site 887061003948 Cache domain; Region: Cache_1; pfam02743 887061003949 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061003950 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061003951 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061003952 PEP-CTERM motif; Region: VPEP; pfam07589 887061003953 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 887061003954 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 887061003955 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 887061003956 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 887061003957 Walker A/P-loop; other site 887061003958 ATP binding site [chemical binding]; other site 887061003959 Q-loop/lid; other site 887061003960 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 887061003961 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 887061003962 ABC transporter signature motif; other site 887061003963 Walker B; other site 887061003964 D-loop; other site 887061003965 H-loop/switch region; other site 887061003966 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 887061003967 FtsZ protein binding site [polypeptide binding]; other site 887061003968 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 887061003969 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 887061003970 nucleotide binding pocket [chemical binding]; other site 887061003971 K-X-D-G motif; other site 887061003972 catalytic site [active] 887061003973 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 887061003974 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 887061003975 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 887061003976 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 887061003977 Dimer interface [polypeptide binding]; other site 887061003978 BRCT sequence motif; other site 887061003979 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 887061003980 active site 887061003981 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 887061003982 Moco binding site; other site 887061003983 metal coordination site [ion binding]; other site 887061003984 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 887061003985 DoxX; Region: DoxX; cl00976 887061003986 Conserved TM helix; Region: TM_helix; pfam05552 887061003987 Conserved TM helix; Region: TM_helix; pfam05552 887061003988 Uncharacterised BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 887061003989 Cation efflux family; Region: Cation_efflux; cl00316 887061003990 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_1; cd09140 887061003991 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 887061003992 putative active site [active] 887061003993 putative active site [active] 887061003994 catalytic site [active] 887061003995 catalytic site [active] 887061003996 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_2; cd09143 887061003997 phospholipase D alpha; Region: PLN02270 887061003998 putative active site [active] 887061003999 catalytic site [active] 887061004000 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 887061004001 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 887061004002 putative catalytic site [active] 887061004003 putative metal binding site [ion binding]; other site 887061004004 putative phosphate binding site [ion binding]; other site 887061004005 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading...; Region: EFh; cd00051 887061004006 Ca2+ binding site [ion binding]; other site 887061004007 Predicted outer membrane protein [Function unknown]; Region: COG3652 887061004008 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 887061004009 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 887061004010 inhibitor site; inhibition site 887061004011 active site 887061004012 dimer interface [polypeptide binding]; other site 887061004013 catalytic residue [active] 887061004014 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 887061004015 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 887061004016 NADP binding site [chemical binding]; other site 887061004017 active site 887061004018 steroid binding site; other site 887061004019 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061004020 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061004021 Predicted outer membrane protein [Function unknown]; Region: COG3652 887061004022 short chain dehydrogenase; Provisional; Region: PRK06701 887061004023 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 887061004024 NAD binding site [chemical binding]; other site 887061004025 metal binding site [ion binding]; metal-binding site 887061004026 active site 887061004027 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061004028 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 887061004029 active site 887061004030 phosphorylation site [posttranslational modification] 887061004031 intermolecular recognition site; other site 887061004032 dimerization interface [polypeptide binding]; other site 887061004033 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...; Region: LuxR_C_like; cl10457 887061004034 Protein of unknown function (DUF1345); Region: DUF1345; cl01753 887061004035 YceI-like domain; Region: YceI; cl01001 887061004036 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 887061004037 The Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily belongs to the M14 family of metallocarboxypeptidases (MCPs), and includes ASTE, which catalyzes the fifth and last step in arginine catabolism by the arginine...; Region: M14_ASTE_ASPA_like; cd06230 887061004038 active site 887061004039 Zn-binding site [ion binding]; other site 887061004040 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 887061004041 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 887061004042 metal-binding site [ion binding] 887061004043 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 887061004044 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; cl11391 887061004045 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 887061004046 DNA-binding site [nucleotide binding]; DNA binding site 887061004047 RNA-binding motif; other site 887061004048 CsbD-like; Region: CsbD; cl01272 887061004049 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...; Region: LuxR_C_like; cd06170 887061004050 DNA binding residues [nucleotide binding] 887061004051 dimerization interface [polypeptide binding]; other site 887061004052 Sodium:solute symporter family; Region: SSF; cl00456 887061004053 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 887061004054 VRR-NUC domain; Region: VRR_NUC; pfam08774 887061004055 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 887061004056 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 887061004057 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 887061004058 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061004059 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 887061004060 active site 887061004061 phosphorylation site [posttranslational modification] 887061004062 intermolecular recognition site; other site 887061004063 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...; Region: LuxR_C_like; cd06170 887061004064 DNA binding residues [nucleotide binding] 887061004065 dimerization interface [polypeptide binding]; other site 887061004066 ferredoxin-NADP reductase; Provisional; Region: PRK10926 887061004067 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 887061004068 FAD binding pocket [chemical binding]; other site 887061004069 FAD binding motif [chemical binding]; other site 887061004070 phosphate binding motif [ion binding]; other site 887061004071 beta-alpha-beta structure motif; other site 887061004072 NAD binding pocket [chemical binding]; other site 887061004073 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 887061004074 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 887061004075 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 887061004076 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 887061004077 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 887061004078 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 887061004079 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 887061004080 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 887061004081 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 887061004082 catalytic loop [active] 887061004083 iron binding site [ion binding]; other site 887061004084 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 887061004085 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 887061004086 Ligand binding site [chemical binding]; other site 887061004087 metal binding site [ion binding]; metal-binding site 887061004088 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 887061004089 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 887061004090 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061004091 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061004092 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061004093 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 887061004094 putative effector binding pocket; other site 887061004095 dimerization interface [polypeptide binding]; other site 887061004096 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061004097 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 887061004098 active site 887061004099 PilZ domain; Region: PilZ; cl01260 887061004100 DNA polymerase III subunit delta'; Validated; Region: PRK06964 887061004101 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061004102 thymidylate kinase; Validated; Region: tmk; PRK00698 887061004103 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...; Region: TMPK; cd01672 887061004104 TMP-binding site; other site 887061004105 ATP-binding site [chemical binding]; other site 887061004106 YceG-like family; Region: YceG; pfam02618 887061004107 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 887061004108 dimerization interface [polypeptide binding]; other site 887061004109 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 887061004110 Aminotransferase class IV; Region: Aminotran_4; pfam01063 887061004111 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004112 catalytic residue [active] 887061004113 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 887061004114 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 887061004115 dimer interface [polypeptide binding]; other site 887061004116 active site 887061004117 Phosphopantetheine attachment site; Region: PP-binding; cl09936 887061004118 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 887061004119 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 887061004120 NAD(P) binding site [chemical binding]; other site 887061004121 homotetramer interface [polypeptide binding]; other site 887061004122 homodimer interface [polypeptide binding]; other site 887061004123 active site 887061004124 Acyl transferase domain; Region: Acyl_transf_1; cl08282 887061004125 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 887061004126 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 887061004127 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 887061004128 dimer interface [polypeptide binding]; other site 887061004129 active site 887061004130 CoA binding pocket [chemical binding]; other site 887061004131 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 887061004132 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 887061004133 pyruvate carboxylase subunit A; Validated; Region: PRK07178 887061004134 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061004135 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061004136 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 887061004137 pyruvate carboxylase subunit B; Validated; Region: PRK09282 887061004138 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 887061004139 active site 887061004140 metal binding site [ion binding]; metal-binding site 887061004141 homodimer binding site [polypeptide binding]; other site 887061004142 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 887061004143 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 887061004144 carboxyltransferase (CT) interaction site; other site 887061004145 biotinylation site [posttranslational modification]; other site 887061004146 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 887061004147 active site 887061004148 dimer interface [polypeptide binding]; other site 887061004149 Uncharacterized conserved protein [Function unknown]; Region: COG5316 887061004150 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 887061004151 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 887061004152 RNA/DNA hybrid binding site [nucleotide binding]; other site 887061004153 active site 887061004154 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 887061004155 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 887061004156 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 887061004157 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...; Region: LbH_UDP-GlcNAc_AT; cd03351 887061004158 active site 887061004159 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 887061004160 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 887061004161 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 887061004162 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-2,3-...; Region: LbH_LpxD; cd03352 887061004163 trimer interface [polypeptide binding]; other site 887061004164 active site 887061004165 UDP-GlcNAc binding site [chemical binding]; other site 887061004166 lipid binding site [chemical binding]; lipid-binding site 887061004167 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 887061004168 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 887061004169 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 887061004170 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 887061004171 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 887061004172 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 887061004173 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 887061004174 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 887061004175 Surface antigen; Region: Bac_surface_Ag; cl03097 887061004176 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 887061004177 zinc metallopeptidase RseP; Provisional; Region: PRK10779 887061004178 active site 887061004179 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...; Region: PDZ_metalloprotease; cd00989 887061004180 protein binding site [polypeptide binding]; other site 887061004181 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...; Region: PDZ_metalloprotease; cd00989 887061004182 protein binding site [polypeptide binding]; other site 887061004183 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 887061004184 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 887061004185 putative substrate binding region [chemical binding]; other site 887061004186 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 887061004187 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 887061004188 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 887061004189 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 887061004190 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 887061004191 catalytic residue [active] 887061004192 putative FPP diphosphate binding site; other site 887061004193 putative FPP binding hydrophobic cleft; other site 887061004194 dimer interface [polypeptide binding]; other site 887061004195 putative IPP diphosphate binding site; other site 887061004196 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 887061004197 hinge region; other site 887061004198 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...; Region: AAK_UMPK-PyrH-Ec; cd04254 887061004199 putative nucleotide binding site [chemical binding]; other site 887061004200 uridine monophosphate binding site [chemical binding]; other site 887061004201 homohexameric interface [polypeptide binding]; other site 887061004202 elongation factor Ts; Provisional; Region: tsf; PRK09377 887061004203 Elongation factor TS; Region: EF_TS; pfam00889 887061004204 Elongation factor TS; Region: EF_TS; pfam00889 887061004205 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 887061004206 rRNA interaction site [nucleotide binding]; other site 887061004207 S8 interaction site; other site 887061004208 putative laminin-1 binding site; other site 887061004209 methionine aminopeptidase; Reviewed; Region: PRK07281 887061004210 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 887061004211 active site 887061004212 PII uridylyl-transferase; Provisional; Region: PRK03059 887061004213 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 887061004214 metal binding triad; other site 887061004215 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 887061004216 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061004217 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 887061004218 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 887061004219 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 887061004220 active site 887061004221 DNA polymerase IV; Validated; Region: PRK02406 887061004222 DNA binding site [nucleotide binding] 887061004223 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 887061004224 classical (c) SDRs; Region: SDR_c; cd05233 887061004225 NAD(P) binding site [chemical binding]; other site 887061004226 active site 887061004227 Cupin domain; Region: Cupin_2; cl09118 887061004228 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(...; Region: Pep_deformylase; cd00487 887061004229 active site 887061004230 catalytic residues [active] 887061004231 metal binding site [ion binding]; metal-binding site 887061004232 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 887061004233 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 887061004234 active site lid residues [active] 887061004235 substrate binding pocket [chemical binding]; other site 887061004236 catalytic residues [active] 887061004237 substrate-Mg2+ binding site; other site 887061004238 aspartate-rich region 1; other site 887061004239 aspartate-rich region 2; other site 887061004240 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 887061004241 catalytic residues [active] 887061004242 substrate binding pocket [chemical binding]; other site 887061004243 substrate-Mg2+ binding site; other site 887061004244 aspartate-rich region 1; other site 887061004245 aspartate-rich region 2; other site 887061004246 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061004247 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 887061004248 Membrane protein of unknown function; Region: DUF360; cl00850 887061004249 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061004250 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 887061004251 NAD(P) binding site [chemical binding]; other site 887061004252 active site 887061004253 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 887061004254 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061004255 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 887061004256 motif II; other site 887061004257 DNA repair protein RadA; Provisional; Region: PRK11823 887061004258 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 887061004259 Walker A motif/ATP binding site; other site 887061004260 ATP binding site [chemical binding]; other site 887061004261 Walker B motif; other site 887061004262 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 887061004263 alanine racemase; Reviewed; Region: alr; PRK00053 887061004264 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 887061004265 active site 887061004266 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 887061004267 substrate binding site [chemical binding]; other site 887061004268 catalytic residues [active] 887061004269 dimer interface [polypeptide binding]; other site 887061004270 replicative DNA helicase; Region: DnaB; TIGR00665 887061004271 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 887061004272 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 887061004273 Walker A motif; other site 887061004274 ATP binding site [chemical binding]; other site 887061004275 Walker B motif; other site 887061004276 DNA binding loops [nucleotide binding] 887061004277 cystathionine beta-lyase; Provisional; Region: PRK07050 887061004278 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 887061004279 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061004280 catalytic residue [active] 887061004281 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 887061004282 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 887061004283 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 887061004284 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 887061004285 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 887061004286 dimer interface [polypeptide binding]; other site 887061004287 ssDNA binding site [nucleotide binding]; other site 887061004288 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061004289 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 887061004290 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 887061004291 Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism; Energy production and conversion]; Region: COG1892; cl14656 887061004292 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 887061004293 glycogen synthase; Provisional; Region: glgA; PRK00654 887061004294 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 887061004295 ADP-binding pocket [chemical binding]; other site 887061004296 homodimer interface [polypeptide binding]; other site 887061004297 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 887061004298 putative active site [active] 887061004299 putative substrate binding site [chemical binding]; other site 887061004300 catalytic site [active] 887061004301 dimer interface [polypeptide binding]; other site 887061004302 Peptidase family M48; Region: Peptidase_M48; cl12018 887061004303 GTPase RsgA; Reviewed; Region: PRK00098 887061004304 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 887061004305 GTPase/OB domain interface [polypeptide binding]; other site 887061004306 GTPase/Zn-binding domain interface [polypeptide binding]; other site 887061004307 GTP/Mg2+ binding site [chemical binding]; other site 887061004308 G4 box; other site 887061004309 G5 box; other site 887061004310 G1 box; other site 887061004311 Switch I region; other site 887061004312 G2 box; other site 887061004313 G3 box; other site 887061004314 Switch II region; other site 887061004315 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 887061004316 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 887061004317 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 887061004318 active site 887061004319 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 887061004320 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 887061004321 NADP binding site [chemical binding]; other site 887061004322 active site 887061004323 putative substrate binding site [chemical binding]; other site 887061004324 Cupin domain; Region: Cupin_2; cl09118 887061004325 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 887061004326 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 887061004327 substrate binding site [chemical binding]; other site 887061004328 tetramer interface [polypeptide binding]; other site 887061004329 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 887061004330 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 887061004331 NAD binding site [chemical binding]; other site 887061004332 substrate binding site [chemical binding]; other site 887061004333 homodimer interface [polypeptide binding]; other site 887061004334 active site 887061004335 Proteobacterial; Region: dnaQ_proteo; TIGR01406 887061004336 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 887061004337 active site 887061004338 substrate binding site [chemical binding]; other site 887061004339 catalytic site [active] 887061004340 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 887061004341 RNA/DNA hybrid binding site [nucleotide binding]; other site 887061004342 active site 887061004343 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; cl12011 887061004344 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061004345 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 887061004346 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061004347 catalytic residue [active] 887061004348 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 887061004349 putative peptidoglycan binding site; other site 887061004350 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 887061004351 putative peptidoglycan binding site; other site 887061004352 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 887061004353 putative peptidoglycan binding site; other site 887061004354 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 887061004355 The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold; Region: PBP2_AppA_like; cd08514 887061004356 peptide binding site [polypeptide binding]; other site 887061004357 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 887061004358 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...; Region: TM_PBP2; cd06261 887061004359 dimer interface [polypeptide binding]; other site 887061004360 conserved gate region; other site 887061004361 putative PBP binding loops; other site 887061004362 ABC-ATPase subunit interface; other site 887061004363 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 887061004364 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...; Region: TM_PBP2; cd06261 887061004365 dimer interface [polypeptide binding]; other site 887061004366 conserved gate region; other site 887061004367 putative PBP binding loops; other site 887061004368 ABC-ATPase subunit interface; other site 887061004369 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 887061004370 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 887061004371 NAD binding site [chemical binding]; other site 887061004372 homotetramer interface [polypeptide binding]; other site 887061004373 homodimer interface [polypeptide binding]; other site 887061004374 substrate binding site [chemical binding]; other site 887061004375 active site 887061004376 periplasmic folding chaperone; Provisional; Region: PRK10788 887061004377 PPIC-type PPIASE domain; Region: Rotamase; cl08278 887061004378 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 higher-...; Region: HU_IHF; cd00591 887061004379 IHF dimer interface [polypeptide binding]; other site 887061004380 IHF - DNA interface [nucleotide binding]; other site 887061004381 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 887061004382 Found in ATP-dependent protease La (LON); Region: LON; cl01056 887061004383 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...; Region: AAA; cd00009 887061004384 Walker A motif; other site 887061004385 ATP binding site [chemical binding]; other site 887061004386 Walker B motif; other site 887061004387 arginine finger; other site 887061004388 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 887061004389 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 887061004390 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 887061004391 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061004392 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...; Region: AAA; cd00009 887061004393 Walker A motif; other site 887061004394 ATP binding site [chemical binding]; other site 887061004395 Walker B motif; other site 887061004396 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 887061004397 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 887061004398 oligomer interface [polypeptide binding]; other site 887061004399 active site residues [active] 887061004400 trigger factor; Provisional; Region: tig; PRK01490 887061004401 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 887061004402 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 887061004403 Phage integrase family; Region: Phage_integrase; pfam00589 887061004404 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 887061004405 DNA binding site [nucleotide binding] 887061004406 Int/Topo IB signature motif; other site 887061004407 active site 887061004408 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 887061004409 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 887061004410 active site 887061004411 DNA binding site [nucleotide binding] 887061004412 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 887061004413 Outer membrane efflux protein; Region: OEP; pfam02321 887061004414 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061004415 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061004416 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004417 metal binding site [ion binding]; metal-binding site 887061004418 active site 887061004419 I-site; other site 887061004420 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; cd00488 887061004421 aromatic arch; other site 887061004422 DCoH dimer interaction site [polypeptide binding]; other site 887061004423 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 887061004424 DCoH tetramer interaction site [polypeptide binding]; other site 887061004425 substrate binding site [chemical binding]; other site 887061004426 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 887061004427 substrate binding site [chemical binding]; other site 887061004428 aminodeoxychorismate synthase subunit I; Provisional; Region: pabB; PRK15465 887061004429 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 887061004430 chorismate binding enzyme; Region: Chorismate_bind; cl10555 887061004431 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 887061004432 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061004433 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 887061004434 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 887061004435 active site 887061004436 Formaldehyde-activating enzyme (Fae); Region: Fae; cl00774 887061004437 Formaldehyde-activating enzyme (Fae); Region: Fae; cl00774 887061004438 Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with...; Region: SIS_PHI; cd05005 887061004439 tetramer interface [polypeptide binding]; other site 887061004440 active site 887061004441 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for...; Region: KGPDC_HPS; cd04726 887061004442 active site 887061004443 dimer interface [polypeptide binding]; other site 887061004444 magnesium binding site [ion binding]; other site 887061004445 transaldolase-like protein; Provisional; Region: PTZ00411 887061004446 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 887061004447 active site 887061004448 dimer interface [polypeptide binding]; other site 887061004449 catalytic residue [active] 887061004450 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 887061004451 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 887061004452 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061004453 Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5)...; Region: MCH; cd00545 887061004454 trimer interface I [polypeptide binding]; other site 887061004455 putative substrate binding pocket [chemical binding]; other site 887061004456 trimer interface II [polypeptide binding]; other site 887061004457 Predicted ATP-dependent carboligase related to biotin carboxylase [General function prediction only]; Region: COG2232 887061004458 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061004459 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; Region: Mpt_N; pfam09176 887061004460 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061004461 NAD(P) binding pocket [chemical binding]; other site 887061004462 Predicted archaeal sugar kinases [General function prediction only]; Region: COG1907 887061004463 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 887061004464 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 887061004465 The MopB_FmdB-FwdB CD contains the molybdenum/tungsten formylmethanofuran dehydrogenases, subunit B (FmdB/FwdB), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea...; Region: MopB_FmdB-FwdB; cd02761 887061004466 formylmethanofuran dehydrogenase subunit B; Region: one_C_dehyd_B; TIGR03129 887061004467 putative [4Fe-4S] binding site [ion binding]; other site 887061004468 putative molybdopterin cofactor binding site [chemical binding]; other site 887061004469 formylmethanofuran dehydrogenase subunit A; Region: one_C_dehyd_A; TIGR03121 887061004470 Formylmethanofuran dehydrogenase (FMDH) subunit A; Methanogenic bacteria and archea derive the energy for autotrophic growth from methanogenesis, the reduction of CO2 with molecular hydrogen as the electron donor. FMDH catalyzes the first step in...; Region: FMDH_A; cd01304 887061004471 active site 887061004472 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional; Region: PRK02114 887061004473 lobe; Region: FTR; pfam01913 887061004474 FTR, proximal lobe; Region: FTR_C; pfam02741 887061004475 FwdC/FmdC. This domain of unknown function is found in the subunit C of formylmethanofuran dehydrogenase, an enzyme that catalyzes the first step in methane formation from CO2 in methanogenic archaea, hyperthermophiles and bacteria. There are two...; Region: FwdC/FmdC; cd00980 887061004476 putative subunit interface; other site 887061004477 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061004478 ligand binding site [chemical binding]; other site 887061004479 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 887061004480 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 887061004481 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 887061004482 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061004483 Domain of unknown function DUF302; Region: DUF302; cl01364 887061004484 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 887061004485 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061004486 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 887061004487 substrate binding site [chemical binding]; other site 887061004488 dimerization interface [polypeptide binding]; other site 887061004489 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 887061004490 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 887061004491 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 887061004492 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 887061004493 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 887061004494 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 887061004495 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 887061004496 Active Sites [active] 887061004497 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 887061004498 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 887061004499 Active Sites [active] 887061004500 sulfate adenylyltransferase, large subunit; Region: CysN; TIGR02034 887061004501 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 887061004502 CysD dimerization site [polypeptide binding]; other site 887061004503 G1 box; other site 887061004504 putative GEF interaction site [polypeptide binding]; other site 887061004505 GTP/Mg2+ binding site [chemical binding]; other site 887061004506 Switch I region; other site 887061004507 G2 box; other site 887061004508 G3 box; other site 887061004509 Switch II region; other site 887061004510 G4 box; other site 887061004511 G5 box; other site 887061004512 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...; Region: CysN_NodQ_II; cd03695 887061004513 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...; Region: CysN_NoDQ_III; cd04095 887061004514 Ferredoxin [Energy production and conversion]; Region: COG1146 887061004515 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 887061004516 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 887061004517 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 887061004518 ATP binding site [chemical binding]; other site 887061004519 putative Mg++ binding site [ion binding]; other site 887061004520 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 887061004521 nucleotide binding region [chemical binding]; other site 887061004522 ATP-binding site [chemical binding]; other site 887061004523 RQC domain; Region: RQC; pfam09382 887061004524 HRDC domain; Region: HRDC; cl02578 887061004525 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 887061004526 putative substrate translocation pore; other site 887061004527 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061004528 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 887061004529 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 887061004530 FeS/SAM binding site; other site 887061004531 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 887061004532 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 887061004533 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 887061004534 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061004535 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061004536 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 887061004537 NeuB family; Region: NeuB; cl00496 887061004538 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 887061004539 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 887061004540 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004541 homodimer interface [polypeptide binding]; other site 887061004542 catalytic residue [active] 887061004543 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004544 metal binding site [ion binding]; metal-binding site 887061004545 active site 887061004546 I-site; other site 887061004547 Chorismate mutase type II; Region: CM_2; cl00693 887061004548 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 887061004549 Prephenate dehydratase; Region: PDT; pfam00800 887061004550 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 887061004551 putative L-Phe binding site [chemical binding]; other site 887061004552 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...; Region: PSAT_like; cd00611 887061004553 homodimer interface [polypeptide binding]; other site 887061004554 substrate-cofactor binding pocket; other site 887061004555 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004556 catalytic residue [active] 887061004557 DNA gyrase subunit A; Validated; Region: PRK05560 887061004558 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...; Region: TOP4c; cd00187 887061004559 CAP-like domain; other site 887061004560 Active site [active] 887061004561 primary dimer interface [polypeptide binding]; other site 887061004562 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004563 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004564 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004565 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004566 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004567 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004568 peroxidase; Provisional; Region: PRK15000 887061004569 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...; Region: PRX_Typ2cys; cd03015 887061004570 dimer interface [polypeptide binding]; other site 887061004571 decamer (pentamer of dimers) interface [polypeptide binding]; other site 887061004572 catalytic triad [active] 887061004573 peroxidatic and resolving cysteines [active] 887061004574 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 887061004575 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 887061004576 homodimer interface [polypeptide binding]; other site 887061004577 substrate-cofactor binding pocket; other site 887061004578 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004579 catalytic residue [active] 887061004580 amidophosphoribosyltransferase; Provisional; Region: PRK09246 887061004581 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 887061004582 active site 887061004583 tetramer interface [polypeptide binding]; other site 887061004584 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061004585 Colicin V production protein; Region: Colicin_V; cl00567 887061004586 rare lipoprotein A; Provisional; Region: PRK10672 887061004587 Sporulation related domain; Region: SPOR; cl10051 887061004588 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 887061004589 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 887061004590 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 887061004591 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...; Region: Tryptophan_synthase_alpha; cd04724 887061004592 substrate binding site [chemical binding]; other site 887061004593 active site 887061004594 catalytic residues [active] 887061004595 heterodimer interface [polypeptide binding]; other site 887061004596 tryptophan synthase, beta chain; Region: PLN02618 887061004597 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 887061004598 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004599 catalytic residue [active] 887061004600 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 887061004601 active site 887061004602 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 887061004603 active site 887061004604 dimerization interface 3.5A [polypeptide binding]; other site 887061004605 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 887061004606 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 887061004607 FimV N-terminal domain; Region: FimV_core; TIGR03505 887061004608 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 887061004609 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 887061004610 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061004611 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 887061004612 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 887061004613 isocitrate dehydrogenase; Validated; Region: PRK06451 887061004614 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 3-...; Region: IPMI_Swivel; cd01577 887061004615 substrate binding site [chemical binding]; other site 887061004616 Entericidin EcnA/B family; Region: Entericidin; cl02322 887061004617 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 887061004618 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 887061004619 substrate binding site [chemical binding]; other site 887061004620 ligand binding site [chemical binding]; other site 887061004621 Protein of unknown function (DUF520); Region: DUF520; cl00723 887061004622 DinB superfamily; Region: DinB_2; cl00986 887061004623 Protein of unknown function (DUF1255); Region: DUF1255; cl01202 887061004624 argininosuccinate synthase; Provisional; Region: PLN00200 887061004625 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 887061004626 ANP binding site [chemical binding]; other site 887061004627 Substrate Binding Site II [chemical binding]; other site 887061004628 Substrate Binding Site I [chemical binding]; other site 887061004629 ornithine carbamoyltransferase; Provisional; Region: PRK00779 887061004630 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 887061004631 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 887061004632 acetylornithine aminotransferase; Provisional; Region: PRK02627 887061004633 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 887061004634 inhibitor-cofactor binding pocket; inhibition site 887061004635 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004636 catalytic residue [active] 887061004637 Predicted membrane protein [Function unknown]; Region: COG3748 887061004638 Protein of unknown function (DUF989); Region: DUF989; pfam06181 887061004639 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 887061004640 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 887061004641 [2Fe-2S] cluster binding site [ion binding]; other site 887061004642 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 887061004643 alpha subunit interface [polypeptide binding]; other site 887061004644 active site 887061004645 substrate binding site [chemical binding]; other site 887061004646 Fe binding site [ion binding]; other site 887061004647 EamA-like transporter family; Region: EamA; cl01037 887061004648 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 887061004649 response regulator; Provisional; Region: PRK09483 887061004650 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 887061004651 active site 887061004652 phosphorylation site [posttranslational modification] 887061004653 intermolecular recognition site; other site 887061004654 dimerization interface [polypeptide binding]; other site 887061004655 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...; Region: LuxR_C_like; cd06170 887061004656 DNA binding residues [nucleotide binding] 887061004657 dimerization interface [polypeptide binding]; other site 887061004658 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061004659 PAS domain S-box; Region: sensory_box; TIGR00229 887061004660 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 887061004661 putative active site [active] 887061004662 heme pocket [chemical binding]; other site 887061004663 Histidine kinase; Region: HisKA_3; pfam07730 887061004664 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 887061004665 ATP binding site [chemical binding]; other site 887061004666 Mg2+ binding site [ion binding]; other site 887061004667 G-X-G motif; other site 887061004668 Cache domain; Region: Cache_1; pfam02743 887061004669 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061004670 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061004671 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061004672 HPP family; Region: HPP; pfam04982 887061004673 Integral membrane protein TerC family; Region: TerC; cl10468 887061004674 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 887061004675 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 887061004676 metal binding triad; other site 887061004677 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 887061004678 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 887061004679 metal binding triad; other site 887061004680 acetyl-CoA synthetase; Provisional; Region: PRK00174 887061004681 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 887061004682 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 887061004683 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061004684 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 887061004685 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 887061004686 N-terminal plug; other site 887061004687 ligand-binding site [chemical binding]; other site 887061004688 fec operon regulator FecR; Reviewed; Region: PRK09774 887061004689 FecR protein; Region: FecR; pfam04773 887061004690 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061004691 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061004692 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...; Region: Sigma70_r4; cl01055 887061004693 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 887061004694 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 887061004695 dimerization interface [polypeptide binding]; other site 887061004696 putative DNA binding site [nucleotide binding]; other site 887061004697 putative Zn2+ binding site [ion binding]; other site 887061004698 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061004699 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 887061004700 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 887061004701 G1 box; other site 887061004702 putative GEF interaction site [polypeptide binding]; other site 887061004703 GTP/Mg2+ binding site [chemical binding]; other site 887061004704 Switch I region; other site 887061004705 G2 box; other site 887061004706 G3 box; other site 887061004707 Switch II region; other site 887061004708 G4 box; other site 887061004709 G5 box; other site 887061004710 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 887061004711 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061004712 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 887061004713 ligand binding site [chemical binding]; other site 887061004714 flexible hinge region; other site 887061004715 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061004716 Response regulator receiver domain; Region: Response_reg; pfam00072 887061004717 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 887061004718 active site 887061004719 phosphorylation site [posttranslational modification] 887061004720 intermolecular recognition site; other site 887061004721 dimerization interface [polypeptide binding]; other site 887061004722 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 887061004723 GAF domain; Region: GAF; cl00853 887061004724 Phytochrome region; Region: PHY; pfam00360 887061004725 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 trans-...; Region: HisKA; cd00082 887061004726 dimer interface [polypeptide binding]; other site 887061004727 phosphorylation site [posttranslational modification] 887061004728 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 887061004729 ATP binding site [chemical binding]; other site 887061004730 Mg2+ binding site [ion binding]; other site 887061004731 G-X-G motif; other site 887061004732 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 887061004733 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 887061004734 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 887061004735 Membrane bound L-sorbosone dehydrogenase; Region: SNDH; pfam12303 887061004736 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 887061004737 CHASE domain; Region: CHASE; cl01369 887061004738 PAS fold; Region: PAS_3; pfam08447 887061004739 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 887061004740 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004741 metal binding site [ion binding]; metal-binding site 887061004742 active site 887061004743 I-site; other site 887061004744 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 887061004745 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 887061004746 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061004747 DNA-binding site [nucleotide binding]; DNA binding site 887061004748 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 887061004749 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004750 homodimer interface [polypeptide binding]; other site 887061004751 catalytic residue [active] 887061004752 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 887061004753 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 887061004754 putative molybdopterin cofactor binding site [chemical binding]; other site 887061004755 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT)...; Region: MopB_CT_ydeP; cd02787 887061004756 putative molybdopterin cofactor binding site; other site 887061004757 Phosphotransferase enzyme family; Region: APH; pfam01636 887061004758 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061004759 active site 887061004760 ATP binding site [chemical binding]; other site 887061004761 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...; Region: GSH_Peroxidase; cd00340 887061004762 catalytic residues [active] 887061004763 dimer interface [polypeptide binding]; other site 887061004764 Uncharacterized membrane protein, required for N-linked glycosylation [General function prediction only]; Region: COG1287 887061004765 cyclase homology domain; Region: CHD; cd07302 887061004766 nucleotidyl binding site; other site 887061004767 metal binding site [ion binding]; metal-binding site 887061004768 dimer interface [polypeptide binding]; other site 887061004769 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 887061004770 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...; Region: AAA; cd00009 887061004771 Walker A motif; other site 887061004772 ATP binding site [chemical binding]; other site 887061004773 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061004774 Walker B motif; other site 887061004775 arginine finger; other site 887061004776 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 887061004777 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14969 887061004778 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 887061004779 recombination protein RecR; Reviewed; Region: recR; PRK00076 887061004780 RecR protein; Region: RecR; pfam02132 887061004781 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 887061004782 putative active site [active] 887061004783 putative metal-binding site [ion binding]; other site 887061004784 tetramer interface [polypeptide binding]; other site 887061004785 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061004786 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 887061004787 motif II; other site 887061004788 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 887061004789 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 887061004790 S-adenosylmethionine binding site [chemical binding]; other site 887061004791 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 887061004792 active site 887061004793 putative substrate binding pocket [chemical binding]; other site 887061004794 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061004795 ligand binding site [chemical binding]; other site 887061004796 Protein of unknown function (DUF556); Region: DUF556; cl00822 887061004797 Protein of unknown function (DUF447); Region: DUF447; cl01035 887061004798 dihydropteroate synthase-related protein; Region: TIGR00284 887061004799 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 887061004800 substrate binding pocket [chemical binding]; other site 887061004801 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 887061004802 dimer interface [polypeptide binding]; other site 887061004803 inhibitor binding site; inhibition site 887061004804 Archaeal flavoproteins [Energy production and conversion]; Region: COG1036 887061004805 Flavoprotein; Region: Flavoprotein; cl08021 887061004806 adenylosuccinate synthetase; Provisional; Region: PRK01117 887061004807 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 r-...; Region: AdSS; cd03108 887061004808 GDP-binding site [chemical binding]; other site 887061004809 ACT binding site; other site 887061004810 IMP binding site; other site 887061004811 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 887061004812 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 887061004813 dimer interface [polypeptide binding]; other site 887061004814 motif 1; other site 887061004815 active site 887061004816 motif 2; other site 887061004817 motif 3; other site 887061004818 FtsH protease regulator HflC; Provisional; Region: PRK11029 887061004819 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 887061004820 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 887061004821 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 887061004822 HflK protein; Region: hflK; TIGR01933 887061004823 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 887061004824 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 887061004825 G1 box; other site 887061004826 GTP/Mg2+ binding site [chemical binding]; other site 887061004827 Switch I region; other site 887061004828 G2 box; other site 887061004829 G3 box; other site 887061004830 Switch II region; other site 887061004831 G4 box; other site 887061004832 G5 box; other site 887061004833 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 887061004834 Sm1 motif; other site 887061004835 intra - hexamer interaction site; other site 887061004836 inter - hexamer interaction site [polypeptide binding]; other site 887061004837 nucleotide binding pocket [chemical binding]; other site 887061004838 Sm2 motif; other site 887061004839 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 887061004840 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 887061004841 active site 887061004842 HIGH motif; other site 887061004843 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 887061004844 active site 887061004845 KMSKS motif; other site 887061004846 NodT family; Region: outer_NodT; TIGR01845 887061004847 Outer membrane efflux protein; Region: OEP; pfam02321 887061004848 Outer membrane efflux protein; Region: OEP; pfam02321 887061004849 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 887061004850 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 887061004851 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061004852 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061004853 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 887061004854 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061004855 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 887061004856 putative active site [active] 887061004857 heme pocket [chemical binding]; other site 887061004858 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 887061004859 putative active site [active] 887061004860 heme pocket [chemical binding]; other site 887061004861 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004862 metal binding site [ion binding]; metal-binding site 887061004863 active site 887061004864 I-site; other site 887061004865 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 887061004866 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 887061004867 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 887061004868 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 887061004869 FeS/SAM binding site; other site 887061004870 TRAM domain; Region: TRAM; cl01282 887061004871 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 887061004872 ZIP Zinc transporter; Region: Zip; pfam02535 887061004873 PEP-CTERM motif; Region: VPEP; pfam07589 887061004874 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 887061004875 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 887061004876 N-terminal plug; other site 887061004877 ligand-binding site [chemical binding]; other site 887061004878 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 887061004879 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 887061004880 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 887061004881 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 887061004882 RNA binding surface [nucleotide binding]; other site 887061004883 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...; Region: PseudoU_synth_RluCD_like; cd02869 887061004884 active site 887061004885 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 887061004886 GTP-binding protein Der; Reviewed; Region: PRK00093 887061004887 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 887061004888 G1 box; other site 887061004889 GTP/Mg2+ binding site [chemical binding]; other site 887061004890 Switch I region; other site 887061004891 G2 box; other site 887061004892 Switch II region; other site 887061004893 G3 box; other site 887061004894 G4 box; other site 887061004895 G5 box; other site 887061004896 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 887061004897 G1 box; other site 887061004898 GTP/Mg2+ binding site [chemical binding]; other site 887061004899 Switch I region; other site 887061004900 G2 box; other site 887061004901 G3 box; other site 887061004902 Switch II region; other site 887061004903 G4 box; other site 887061004904 G5 box; other site 887061004905 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 887061004906 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061004907 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061004908 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 887061004909 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 887061004910 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 887061004911 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 887061004912 Walker A/P-loop; other site 887061004913 ATP binding site [chemical binding]; other site 887061004914 Q-loop/lid; other site 887061004915 ABC transporter signature motif; other site 887061004916 Walker B; other site 887061004917 D-loop; other site 887061004918 H-loop/switch region; other site 887061004919 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 887061004920 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 887061004921 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 887061004922 Walker A/P-loop; other site 887061004923 ATP binding site [chemical binding]; other site 887061004924 Q-loop/lid; other site 887061004925 ABC transporter signature motif; other site 887061004926 Walker B; other site 887061004927 D-loop; other site 887061004928 H-loop/switch region; other site 887061004929 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 887061004930 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 887061004931 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 887061004932 dimer interface [polypeptide binding]; other site 887061004933 motif 1; other site 887061004934 active site 887061004935 motif 2; other site 887061004936 motif 3; other site 887061004937 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 887061004938 anticodon binding site; other site 887061004939 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 887061004940 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 887061004941 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 887061004942 cytoskeletal protein RodZ; Provisional; Region: PRK10856 887061004943 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 887061004944 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 887061004945 binding surface 887061004946 TPR motif; other site 887061004947 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 887061004948 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 887061004949 FeS/SAM binding site; other site 887061004950 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 887061004951 active site 887061004952 multimer interface [polypeptide binding]; other site 887061004953 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 887061004954 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 887061004955 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 887061004956 ribonuclease R; Region: RNase_R; TIGR02063 887061004957 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 887061004958 RNB domain; Region: RNB; pfam00773 887061004959 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...; Region: S1_RNase_R; cd04471 887061004960 RNA binding site [nucleotide binding]; other site 887061004961 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061004962 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 887061004963 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 887061004964 NAD(P) binding site [chemical binding]; other site 887061004965 homodimer interface [polypeptide binding]; other site 887061004966 substrate binding site [chemical binding]; other site 887061004967 active site 887061004968 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 887061004969 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl11406 887061004970 NAD(P) binding site [chemical binding]; other site 887061004971 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 887061004972 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 887061004973 tropinone reductase; Provisional; Region: PRK09242 887061004974 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 887061004975 NADP binding site [chemical binding]; other site 887061004976 homodimer interface [polypeptide binding]; other site 887061004977 active site 887061004978 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 887061004979 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 887061004980 FeS/SAM binding site; other site 887061004981 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 887061004982 RNA binding surface [nucleotide binding]; other site 887061004983 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 887061004984 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 887061004985 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 887061004986 MoaE homodimer interface [polypeptide binding]; other site 887061004987 MoaD interaction [polypeptide binding]; other site 887061004988 active site residues [active] 887061004989 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 887061004990 MoaE interaction surface [polypeptide binding]; other site 887061004991 MoeB interaction surface [polypeptide binding]; other site 887061004992 thiocarboxylated glycine; other site 887061004993 chromosome segregation protein; Provisional; Region: PRK02224 887061004994 RmuC family; Region: RmuC; pfam02646 887061004995 CHASE2 domain; Region: CHASE2; cl01732 887061004996 Bacterial SH3 domain; Region: SH3_3; cl02551 887061004997 Peptidase family M48; Region: Peptidase_M48; cl12018 887061004998 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 887061004999 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 887061005000 G1 box; other site 887061005001 putative GEF interaction site [polypeptide binding]; other site 887061005002 GTP/Mg2+ binding site [chemical binding]; other site 887061005003 Switch I region; other site 887061005004 G2 box; other site 887061005005 G3 box; other site 887061005006 Switch II region; other site 887061005007 G4 box; other site 887061005008 G5 box; other site 887061005009 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 887061005010 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...; Region: BipA_TypA_C; cd03710 887061005011 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 887061005012 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 887061005013 ATP binding site [chemical binding]; other site 887061005014 Mg++ binding site [ion binding]; other site 887061005015 motif III; other site 887061005016 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 887061005017 nucleotide binding region [chemical binding]; other site 887061005018 ATP-binding site [chemical binding]; other site 887061005019 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 887061005020 DEAD-like helicases superfamily; Region: DEXDc; smart00487 887061005021 ATP binding site [chemical binding]; other site 887061005022 Mg++ binding site [ion binding]; other site 887061005023 motif III; other site 887061005024 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 887061005025 nucleotide binding region [chemical binding]; other site 887061005026 ATP-binding site [chemical binding]; other site 887061005027 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...; Region: Trunc_globin; cd00454 887061005028 apolar tunnel; other site 887061005029 heme binding site [chemical binding]; other site 887061005030 dimerization interface [polypeptide binding]; other site 887061005031 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 887061005032 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061005033 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061005034 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061005035 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 887061005036 active site 887061005037 phosphorylation site [posttranslational modification] 887061005038 intermolecular recognition site; other site 887061005039 dimerization interface [polypeptide binding]; other site 887061005040 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...; Region: AAA; cd00009 887061005041 Walker A motif; other site 887061005042 ATP binding site [chemical binding]; other site 887061005043 Walker B motif; other site 887061005044 arginine finger; other site 887061005045 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061005046 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061005047 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 887061005048 N-terminal plug; other site 887061005049 ligand-binding site [chemical binding]; other site 887061005050 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 887061005051 FtsX-like permease family; Region: FtsX; pfam02687 887061005052 FtsX-like permease family; Region: FtsX; pfam02687 887061005053 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 887061005054 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 887061005055 Walker A/P-loop; other site 887061005056 ATP binding site [chemical binding]; other site 887061005057 Q-loop/lid; other site 887061005058 ABC transporter signature motif; other site 887061005059 Walker B; other site 887061005060 D-loop; other site 887061005061 H-loop/switch region; other site 887061005062 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 887061005063 active site 887061005064 catalytic triad [active] 887061005065 oxyanion hole [active] 887061005066 switch loop; other site 887061005067 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 887061005068 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 887061005069 Ligand Binding Site [chemical binding]; other site 887061005070 B3/4 domain; Region: B3_4; cl11458 887061005071 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 887061005072 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 887061005073 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 887061005074 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 887061005075 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...; Region: DnaE_OBF; cd04485 887061005076 generic binding surface II; other site 887061005077 generic binding surface I; other site 887061005078 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 887061005079 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 887061005080 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 887061005081 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 887061005082 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 887061005083 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 887061005084 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 887061005085 ATP binding site [chemical binding]; other site 887061005086 Mg2+ binding site [ion binding]; other site 887061005087 G-X-G motif; other site 887061005088 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 887061005089 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005090 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 887061005091 active site 887061005092 phosphorylation site [posttranslational modification] 887061005093 intermolecular recognition site; other site 887061005094 dimerization interface [polypeptide binding]; other site 887061005095 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061005096 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061005097 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 887061005098 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005099 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 887061005100 active site 887061005101 phosphorylation site [posttranslational modification] 887061005102 intermolecular recognition site; other site 887061005103 dimerization interface [polypeptide binding]; other site 887061005104 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005105 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 887061005106 active site 887061005107 phosphorylation site [posttranslational modification] 887061005108 intermolecular recognition site; other site 887061005109 dimerization interface [polypeptide binding]; other site 887061005110 Uncharacterized conserved protein [Function unknown]; Region: COG3287 887061005111 FIST N domain; Region: FIST; pfam08495 887061005112 FIST C domain; Region: FIST_C; pfam10442 887061005113 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 887061005114 dimer interface [polypeptide binding]; other site 887061005115 catalytic triad [active] 887061005116 peroxidatic and resolving cysteines [active] 887061005117 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 887061005118 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 887061005119 Autotransporter beta-domain; Region: Autotransporter; cl02365 887061005120 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...; Region: OM_channels; cl00284 887061005121 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...; Region: OM_channels; cl00284 887061005122 fec operon regulator FecR; Reviewed; Region: PRK09774 887061005123 FecR protein; Region: FecR; pfam04773 887061005124 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061005125 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005126 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...; Region: Sigma70_r4; cl01055 887061005127 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 887061005128 homodimer interface [polypeptide binding]; other site 887061005129 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 887061005130 active site pocket [active] 887061005131 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 887061005132 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061005133 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061005134 Gram-negative bacterial tonB protein; Region: TonB; cl10048 887061005135 Hemin uptake protein hemP; Region: hemP; cl10043 887061005136 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 887061005137 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 887061005138 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 887061005139 RNA binding surface [nucleotide binding]; other site 887061005140 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 887061005141 heat shock protein 90; Provisional; Region: PRK05218 887061005142 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 887061005143 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; cl01792 887061005144 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-...; Region: YgdL_like; cd00755 887061005145 putative ATP binding site [chemical binding]; other site 887061005146 putative substrate interface [chemical binding]; other site 887061005147 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 887061005148 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 887061005149 active site 887061005150 hydrophilic channel; other site 887061005151 dimerization interface [polypeptide binding]; other site 887061005152 catalytic residues [active] 887061005153 active site lid [active] 887061005154 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 887061005155 Recombination protein O N terminal; Region: RecO_N; pfam11967 887061005156 Recombination protein O C terminal; Region: RecO_C; pfam02565 887061005157 GTPase Era; Reviewed; Region: era; PRK00089 887061005158 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 887061005159 G1 box; other site 887061005160 GTP/Mg2+ binding site [chemical binding]; other site 887061005161 Switch I region; other site 887061005162 G2 box; other site 887061005163 Switch II region; other site 887061005164 G3 box; other site 887061005165 G4 box; other site 887061005166 G5 box; other site 887061005167 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...; Region: KH-I; cl00098 887061005168 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 887061005169 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 post-...; Region: RIBOc; cd00593 887061005170 dimerization interface [polypeptide binding]; other site 887061005171 active site 887061005172 metal binding site [ion binding]; metal-binding site 887061005173 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...; Region: DSRM; cd00048 887061005174 dsRNA binding site [nucleotide binding]; other site 887061005175 signal peptidase I; Provisional; Region: PRK10861 887061005176 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 887061005177 Catalytic site [active] 887061005178 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 887061005179 GTP-binding protein LepA; Provisional; Region: PRK05433 887061005180 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 887061005181 G1 box; other site 887061005182 putative GEF interaction site [polypeptide binding]; other site 887061005183 GTP/Mg2+ binding site [chemical binding]; other site 887061005184 Switch I region; other site 887061005185 G2 box; other site 887061005186 G3 box; other site 887061005187 Switch II region; other site 887061005188 G4 box; other site 887061005189 G5 box; other site 887061005190 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-...; Region: lepA_II; cd03699 887061005191 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 887061005192 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 887061005193 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 887061005194 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...; Region: Tryp_SPc; cl00149 887061005195 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 C-...; Region: PDZ_serine_protease; cd00987 887061005196 protein binding site [polypeptide binding]; other site 887061005197 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 C-...; Region: PDZ_serine_protease; cd00987 887061005198 protein binding site [polypeptide binding]; other site 887061005199 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 887061005200 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 887061005201 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 887061005202 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005203 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...; Region: Sigma70_r4; cd06171 887061005204 DNA binding residues [nucleotide binding] 887061005205 L-aspartate oxidase; Provisional; Region: PRK09077 887061005206 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061005207 domain; Region: Succ_DH_flav_C; pfam02910 887061005208 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 887061005209 hypothetical protein; Provisional; Region: PRK05409 887061005210 Protein of unknown function (DUF692); Region: DUF692; cl01263 887061005211 RNA polymerase sigma factor; Provisional; Region: PRK12520 887061005212 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005213 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...; Region: Sigma70_r4; cl01055 887061005214 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 887061005215 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4398 887061005216 FIST C domain; Region: FIST_C; pfam10442 887061005217 endonuclease III; Provisional; Region: PRK10702 887061005218 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 887061005219 minor groove reading motif; other site 887061005220 helix-hairpin-helix signature motif; other site 887061005221 substrate binding pocket [chemical binding]; other site 887061005222 active site 887061005223 FES domain; Region: FES; smart00525 887061005224 electron transport complex protein RnfB; Provisional; Region: PRK05113 887061005225 4Fe-4S binding domain; Region: Fer4; cl02805 887061005226 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 887061005227 dihydrodipicolinate synthase; Region: dapA; TIGR00674 887061005228 dimer interface [polypeptide binding]; other site 887061005229 active site 887061005230 catalytic residue [active] 887061005231 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 887061005232 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061005233 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 887061005234 type III secretion outer membrane pore, YscC/HrcC family; Region: type_III_yscC; TIGR02516 887061005235 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 887061005236 Cupin superfamily protein; Region: Cupin_4; pfam08007 887061005237 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...; Region: PRX_BCP; cd03017 887061005238 catalytic triad [active] 887061005239 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 887061005240 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 887061005241 Ligand binding site [chemical binding]; other site 887061005242 Putative Catalytic site [active] 887061005243 DXD motif; other site 887061005244 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 887061005245 active site 887061005246 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 887061005247 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 887061005248 active site 887061005249 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 887061005250 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 887061005251 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 887061005252 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061005253 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061005254 'Velcro' closure; other site 887061005255 Trp docking motif; other site 887061005256 active site 887061005257 Core-2/I-Branching enzyme; Region: Branch; pfam02485 887061005258 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 887061005259 catalytic residues [active] 887061005260 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 887061005261 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 887061005262 MutS domain I; Region: MutS_I; pfam01624 887061005263 MutS domain II; Region: MutS_II; pfam05188 887061005264 MutS family domain IV; Region: MutS_IV; pfam05190 887061005265 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 887061005266 Walker A/P-loop; other site 887061005267 ATP binding site [chemical binding]; other site 887061005268 Q-loop/lid; other site 887061005269 ABC transporter signature motif; other site 887061005270 Walker B; other site 887061005271 D-loop; other site 887061005272 H-loop/switch region; other site 887061005273 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 887061005274 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061005275 catalytic residue [active] 887061005276 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 887061005277 active site 887061005278 tetramer interface [polypeptide binding]; other site 887061005279 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 887061005280 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 887061005281 NAD binding site [chemical binding]; other site 887061005282 homodimer interface [polypeptide binding]; other site 887061005283 active site 887061005284 substrate binding site [chemical binding]; other site 887061005285 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 887061005286 Cupin domain; Region: Cupin_2; cl09118 887061005287 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 887061005288 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 887061005289 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 887061005290 DXD motif; other site 887061005291 colanic acid biosynthesis glycosyltransferase WcaL; Provisional; Region: PRK15427 887061005292 This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor; Region: GT1_amsK_like; cd03799 887061005293 putative ADP-binding pocket [chemical binding]; other site 887061005294 O-Antigen ligase; Region: Wzy_C; cl04850 887061005295 Protein of unknown function (DUF3485); Region: DUF3485; cl11827 887061005296 eight transmembrane protein EpsH (proposed exosortase); Region: 8TM_EpsH; cl10495 887061005297 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 887061005298 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 887061005299 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 887061005300 Nucleotide binding site [chemical binding]; other site 887061005301 P loop; other site 887061005302 DTAP/Switch II; other site 887061005303 Switch I; other site 887061005304 chain length determinant protein EpsF; Region: EpsF; TIGR03017 887061005305 Chain length determinant protein; Region: Wzz; cl01623 887061005306 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 887061005307 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 887061005308 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 887061005309 SLBB domain; Region: SLBB; pfam10531 887061005310 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 887061005311 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 887061005312 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 887061005313 ligand binding site [chemical binding]; other site 887061005314 flexible hinge region; other site 887061005315 transcriptional regulator EpsA; Region: EpsA; TIGR03020 887061005316 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...; Region: LuxR_C_like; cd06170 887061005317 DNA binding residues [nucleotide binding] 887061005318 dimerization interface [polypeptide binding]; other site 887061005319 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 887061005320 Bacterial sugar transferase; Region: Bac_transf; cl00939 887061005321 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 887061005322 active site 887061005323 dimerization interface [polypeptide binding]; other site 887061005324 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 887061005325 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 887061005326 serine O-acetyltransferase; Region: cysE; TIGR01172 887061005327 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 L-...; Region: LbH_SAT; cd03354 887061005328 trimer interface [polypeptide binding]; other site 887061005329 active site 887061005330 substrate binding site [chemical binding]; other site 887061005331 CoA binding site [chemical binding]; other site 887061005332 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061005333 Rrf2 family protein; Region: rrf2_super; TIGR00738 887061005334 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 887061005335 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 887061005336 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061005337 catalytic residue [active] 887061005338 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 887061005339 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 887061005340 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061005341 catalytic residue [active] 887061005342 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 887061005343 trimerization site [polypeptide binding]; other site 887061005344 active site 887061005345 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 887061005346 co-chaperone HscB; Provisional; Region: hscB; PRK03578 887061005347 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...; Region: DnaJ; cl02542 887061005348 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 887061005349 chaperone protein HscA; Provisional; Region: hscA; PRK05183 887061005350 tellurium resistance terB-like protein; Region: terB_like; cl11965 887061005351 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 887061005352 catalytic loop [active] 887061005353 iron binding site [ion binding]; other site 887061005354 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 887061005355 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061005356 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 887061005357 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 887061005358 active site 887061005359 phosphorylation site [posttranslational modification] 887061005360 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 887061005361 dimerization domain swap beta strand [polypeptide binding]; other site 887061005362 regulatory protein interface [polypeptide binding]; other site 887061005363 active site 887061005364 regulatory phosphorylation site [posttranslational modification]; other site 887061005365 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 887061005366 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 887061005367 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 887061005368 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 887061005369 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 887061005370 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 887061005371 putative substrate binding site [chemical binding]; other site 887061005372 putative ATP binding site [chemical binding]; other site 887061005373 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 887061005374 P-loop; other site 887061005375 active site 887061005376 phosphorylation site [posttranslational modification] 887061005377 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA...; Region: PTS_IIB_fructose; cd05569 887061005378 P-loop; other site 887061005379 active site 887061005380 phosphorylation site [posttranslational modification] 887061005381 Phosphotransferase system, EIIC; Region: PTS_EIIC; cl00557 887061005382 The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-...; Region: Maltoporin-like; cd01346 887061005383 trimer interface; other site 887061005384 sugar binding site [chemical binding]; other site 887061005385 fructose-1,6-bisphosphatase family protein; Region: PLN02628 887061005386 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-1,7-...; Region: FBPase; cd00354 887061005387 AMP binding site [chemical binding]; other site 887061005388 metal binding site [ion binding]; metal-binding site 887061005389 active site 887061005390 putative diguanylate cyclase; Provisional; Region: PRK09776 887061005391 MASE1; Region: MASE1; pfam05231 887061005392 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 887061005393 putative active site [active] 887061005394 heme pocket [chemical binding]; other site 887061005395 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 887061005396 putative active site [active] 887061005397 heme pocket [chemical binding]; other site 887061005398 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 887061005399 putative active site [active] 887061005400 heme pocket [chemical binding]; other site 887061005401 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061005402 metal binding site [ion binding]; metal-binding site 887061005403 active site 887061005404 I-site; other site 887061005405 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 887061005406 Polymer-forming cytoskeletal; Region: Bactofilin; cl09137 887061005407 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 887061005408 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-...; Region: LysRS_N; cd04322 887061005409 dimer interface [polypeptide binding]; other site 887061005410 putative anticodon binding site; other site 887061005411 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 887061005412 motif 1; other site 887061005413 active site 887061005414 motif 2; other site 887061005415 motif 3; other site 887061005416 peptide chain release factor 2; Validated; Region: prfB; PRK00578 887061005417 RF-1 domain; Region: RF-1; cl02875 887061005418 RF-1 domain; Region: RF-1; cl02875 887061005419 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 887061005420 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 887061005421 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...; Region: TM_PBP2; cd06261 887061005422 dimer interface [polypeptide binding]; other site 887061005423 conserved gate region; other site 887061005424 putative PBP binding loops; other site 887061005425 ABC-ATPase subunit interface; other site 887061005426 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...; Region: TM_PBP2; cd06261 887061005427 dimer interface [polypeptide binding]; other site 887061005428 conserved gate region; other site 887061005429 putative PBP binding loops; other site 887061005430 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4590 887061005431 ABC-ATPase subunit interface; other site 887061005432 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14252 887061005433 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 887061005434 Walker A/P-loop; other site 887061005435 ATP binding site [chemical binding]; other site 887061005436 Q-loop/lid; other site 887061005437 ABC transporter signature motif; other site 887061005438 Walker B; other site 887061005439 D-loop; other site 887061005440 H-loop/switch region; other site 887061005441 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 887061005442 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 887061005443 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005444 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-...; Region: GT1_UGDG_like; cd03817 887061005445 putative ADP-binding pocket [chemical binding]; other site 887061005446 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 887061005447 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 887061005448 Cupin domain; Region: Cupin_2; cl09118 887061005449 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061005450 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 887061005451 active site 887061005452 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 887061005453 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 UDP-N-...; Region: GlmM; cd05802 887061005454 active site 887061005455 substrate binding site [chemical binding]; other site 887061005456 metal binding site [ion binding]; metal-binding site 887061005457 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 887061005458 dihydropteroate synthase; Region: DHPS; TIGR01496 887061005459 substrate binding pocket [chemical binding]; other site 887061005460 dimer interface [polypeptide binding]; other site 887061005461 inhibitor binding site; inhibition site 887061005462 FtsH Extracellular; Region: FtsH_ext; pfam06480 887061005463 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 887061005464 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...; Region: AAA; cd00009 887061005465 Walker A motif; other site 887061005466 ATP binding site [chemical binding]; other site 887061005467 Walker B motif; other site 887061005468 arginine finger; other site 887061005469 Peptidase family M41; Region: Peptidase_M41; pfam01434 887061005470 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; cl12011 887061005471 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 887061005472 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 887061005473 domain; Region: GreA_GreB_N; pfam03449 887061005474 C-term; Region: GreA_GreB; pfam01272 887061005475 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 887061005476 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061005477 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061005478 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 887061005479 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061005480 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061005481 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 887061005482 IMP binding site; other site 887061005483 dimer interface [polypeptide binding]; other site 887061005484 interdomain contacts; other site 887061005485 partial ornithine binding site; other site 887061005486 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 887061005487 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 887061005488 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 887061005489 catalytic site [active] 887061005490 subunit interface [polypeptide binding]; other site 887061005491 dihydrodipicolinate reductase; Provisional; Region: PRK00048 887061005492 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061005493 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 887061005494 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 887061005495 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 887061005496 metal binding site 2 [ion binding]; metal-binding site 887061005497 putative DNA binding helix; other site 887061005498 metal binding site 1 [ion binding]; metal-binding site 887061005499 dimer interface [polypeptide binding]; other site 887061005500 structural Zn2+ binding site [ion binding]; other site 887061005501 recombination and repair protein; Provisional; Region: PRK10869 887061005502 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...; Region: ABC_RecN; cd03241 887061005503 Walker A/P-loop; other site 887061005504 ATP binding site [chemical binding]; other site 887061005505 Q-loop/lid; other site 887061005506 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...; Region: ABC_RecN; cd03241 887061005507 ABC transporter signature motif; other site 887061005508 Walker B; other site 887061005509 D-loop; other site 887061005510 H-loop/switch region; other site 887061005511 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 887061005512 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 887061005513 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 887061005514 Sulfatase; Region: Sulfatase; cl10460 887061005515 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 887061005516 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 887061005517 HrcA protein C terminal domain; Region: HrcA; pfam01628 887061005518 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 887061005519 Flagellar protein YcgR; Region: YcgR_2; pfam12945 887061005520 PilZ domain; Region: PilZ; cl01260 887061005521 ferrochelatase; Reviewed; Region: hemH; PRK00035 887061005522 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 887061005523 C-terminal domain interface [polypeptide binding]; other site 887061005524 active site 887061005525 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 887061005526 active site 887061005527 N-terminal domain interface [polypeptide binding]; other site 887061005528 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 887061005529 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 887061005530 NADP binding site [chemical binding]; other site 887061005531 homopentamer interface [polypeptide binding]; other site 887061005532 substrate binding site [chemical binding]; other site 887061005533 active site 887061005534 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 887061005535 dimer interface [polypeptide binding]; other site 887061005536 active site 887061005537 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 887061005538 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 887061005539 putative ribose interaction site [chemical binding]; other site 887061005540 putative ADP binding site [chemical binding]; other site 887061005541 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061005542 active site 887061005543 nucleotide binding site [chemical binding]; other site 887061005544 HIGH motif; other site 887061005545 KMSKS motif; other site 887061005546 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 887061005547 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 887061005548 putative active site [active] 887061005549 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005550 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 887061005551 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 887061005552 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005553 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 887061005554 putative ADP-binding pocket [chemical binding]; other site 887061005555 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061005556 active site 887061005557 ATP binding site [chemical binding]; other site 887061005558 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061005559 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 887061005560 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 887061005561 active site 887061005562 intersubunit interface [polypeptide binding]; other site 887061005563 catalytic residue [active] 887061005564 Dehydratase family; Region: ILVD_EDD; cl00340 887061005565 6-phosphogluconate dehydratase; Region: edd; TIGR01196 887061005566 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 887061005567 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 887061005568 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061005569 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 887061005570 active site 887061005571 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061005572 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 887061005573 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005574 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 887061005575 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 887061005576 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 887061005577 putative active site [active] 887061005578 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 887061005579 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 887061005580 dimer interface [polypeptide binding]; other site 887061005581 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 887061005582 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 887061005583 chaperone protein DnaJ; Provisional; Region: PRK10767 887061005584 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...; Region: DnaJ; cd06257 887061005585 HSP70 interaction site [polypeptide binding]; other site 887061005586 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 887061005587 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 887061005588 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 887061005589 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 887061005590 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 887061005591 putative active site [active] 887061005592 O-Antigen ligase; Region: Wzy_C; cl04850 887061005593 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 887061005594 putative active site [active] 887061005595 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005596 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 887061005597 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005598 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 887061005599 putative ADP-binding pocket [chemical binding]; other site 887061005600 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 887061005601 Protein of unknown function (DUF1022); Region: DUF1022; pfam06258 887061005602 2-isopropylmalate synthase; Validated; Region: PRK03739 887061005603 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 887061005604 active site 887061005605 catalytic residues [active] 887061005606 metal binding site [ion binding]; metal-binding site 887061005607 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 887061005608 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 887061005609 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 887061005610 substrate binding pocket [chemical binding]; other site 887061005611 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 887061005612 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 887061005613 dimer interface [polypeptide binding]; other site 887061005614 active site 887061005615 metal binding site [ion binding]; metal-binding site 887061005616 glutathione binding site [chemical binding]; other site 887061005617 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061005618 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 887061005619 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...; Region: PBPb; cd00134 887061005620 substrate binding pocket [chemical binding]; other site 887061005621 membrane-bound complex binding site; other site 887061005622 hinge residues; other site 887061005623 hypothetical protein; Provisional; Region: PRK13795 887061005624 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 887061005625 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 887061005626 active site 887061005627 (T/H)XGH motif; other site 887061005628 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 887061005629 S-adenosylmethionine binding site [chemical binding]; other site 887061005630 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 887061005631 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 887061005632 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 887061005633 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 887061005634 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 887061005635 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 887061005636 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 887061005637 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 887061005638 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 887061005639 P loop; other site 887061005640 GTP binding site [chemical binding]; other site 887061005641 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 887061005642 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061005643 Walker A/P-loop; other site 887061005644 ATP binding site [chemical binding]; other site 887061005645 Q-loop/lid; other site 887061005646 ABC transporter signature motif; other site 887061005647 Walker B; other site 887061005648 D-loop; other site 887061005649 H-loop/switch region; other site 887061005650 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 887061005651 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 887061005652 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 887061005653 dimerization interface [polypeptide binding]; other site 887061005654 active site 887061005655 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 887061005656 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 887061005657 FAD binding pocket [chemical binding]; other site 887061005658 FAD binding motif [chemical binding]; other site 887061005659 phosphate binding motif [ion binding]; other site 887061005660 beta-alpha-beta structure motif; other site 887061005661 NAD binding pocket [chemical binding]; other site 887061005662 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 887061005663 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 887061005664 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 887061005665 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 887061005666 Ligand binding site [chemical binding]; other site 887061005667 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 887061005668 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 887061005669 putative dimerization interface [polypeptide binding]; other site 887061005670 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 887061005671 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061005672 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 887061005673 PhnA protein; Region: PhnA; pfam03831 887061005674 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; cl12011 887061005675 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 887061005676 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 887061005677 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 887061005678 homodimer interface [polypeptide binding]; other site 887061005679 substrate-cofactor binding pocket; other site 887061005680 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061005681 catalytic residue [active] 887061005682 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 887061005683 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 887061005684 Walker A/P-loop; other site 887061005685 ATP binding site [chemical binding]; other site 887061005686 Q-loop/lid; other site 887061005687 ABC transporter signature motif; other site 887061005688 Walker B; other site 887061005689 D-loop; other site 887061005690 H-loop/switch region; other site 887061005691 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 887061005692 putative ligand binding site [chemical binding]; other site 887061005693 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 887061005694 TM-ABC transporter signature motif; other site 887061005695 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 887061005696 TM-ABC transporter signature motif; other site 887061005697 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 887061005698 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 887061005699 Walker A/P-loop; other site 887061005700 ATP binding site [chemical binding]; other site 887061005701 Q-loop/lid; other site 887061005702 ABC transporter signature motif; other site 887061005703 Walker B; other site 887061005704 D-loop; other site 887061005705 H-loop/switch region; other site 887061005706 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 887061005707 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 887061005708 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 887061005709 active site 887061005710 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 887061005711 dimer interface [polypeptide binding]; other site 887061005712 non-prolyl cis peptide bond; other site 887061005713 insertion regions; other site 887061005714 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061005715 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 887061005716 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 887061005717 Flavin binding site [chemical binding]; other site 887061005718 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061005719 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061005720 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 887061005721 NodT family; Region: outer_NodT; TIGR01845 887061005722 Outer membrane efflux protein; Region: OEP; pfam02321 887061005723 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061005724 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 887061005725 Protein export membrane protein; Region: SecD_SecF; cl14618 887061005726 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 887061005727 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 887061005728 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 887061005729 active site 887061005730 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 887061005731 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 887061005732 active site 887061005733 dimer interface [polypeptide binding]; other site 887061005734 non-prolyl cis peptide bond; other site 887061005735 insertion regions; other site 887061005736 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 887061005737 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 887061005738 Flavin binding site [chemical binding]; other site 887061005739 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 887061005740 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...; Region: AAA; cd00009 887061005741 Walker A motif; other site 887061005742 ATP binding site [chemical binding]; other site 887061005743 Walker B motif; other site 887061005744 arginine finger; other site 887061005745 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061005746 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 887061005747 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 887061005748 dimerization interface [polypeptide binding]; other site 887061005749 active site 887061005750 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 887061005751 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...; Region: PBPb; cd00134 887061005752 substrate binding pocket [chemical binding]; other site 887061005753 membrane-bound complex binding site; other site 887061005754 hinge residues; other site 887061005755 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061005756 metal binding site [ion binding]; metal-binding site 887061005757 active site 887061005758 I-site; other site 887061005759 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 887061005760 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 887061005761 active site 887061005762 nucleophile elbow; other site 887061005763 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061005764 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 887061005765 N-terminal plug; other site 887061005766 ligand-binding site [chemical binding]; other site 887061005767 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 887061005768 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 887061005769 N-terminal plug; other site 887061005770 ligand-binding site [chemical binding]; other site 887061005771 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 887061005772 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 887061005773 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; cl01544 887061005774 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 887061005775 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 887061005776 putative substrate translocation pore; other site 887061005777 Cytochrome c; Region: Cytochrom_C; cl11414 887061005778 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 887061005779 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; cl01930 887061005780 hypothetical protein; Provisional; Region: PRK10649 887061005781 Sulfatase; Region: Sulfatase; cl10460 887061005782 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 887061005783 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061005784 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 887061005785 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061005786 Coenzyme A binding pocket [chemical binding]; other site 887061005787 Protein of unknown function (DUF330); Region: DUF330; cl01135 887061005788 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 887061005789 mce related protein; Region: MCE; cl03606 887061005790 mce related protein; Region: MCE; cl03606 887061005791 mce related protein; Region: MCE; cl03606 887061005792 Paraquat-inducible protein A; Region: PqiA; pfam04403 887061005793 Paraquat-inducible protein A; Region: PqiA; pfam04403 887061005794 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 887061005795 Autotransporter beta-domain; Region: Autotransporter; cl02365 887061005796 EamA-like transporter family; Region: EamA; cl01037 887061005797 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 887061005798 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 887061005799 intersubunit interface [polypeptide binding]; other site 887061005800 active site 887061005801 Zn2+ binding site [ion binding]; other site 887061005802 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 887061005803 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061005804 Q-loop/lid; other site 887061005805 ABC transporter signature motif; other site 887061005806 Walker B; other site 887061005807 D-loop; other site 887061005808 H-loop/switch region; other site 887061005809 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 887061005810 hypothetical protein; Validated; Region: PRK09039 887061005811 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061005812 Outer membrane efflux protein; Region: OEP; pfam02321 887061005813 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061005814 putative hydrophobic ligand binding site [chemical binding]; other site 887061005815 protein interface [polypeptide binding]; other site 887061005816 gate; other site 887061005817 putative transcriptional regulator; Provisional; Region: PRK11640 887061005818 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061005819 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 887061005820 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 887061005821 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005822 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...; Region: Sigma70_r4; cd06171 887061005823 DNA binding residues [nucleotide binding] 887061005824 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; cl01253 887061005825 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 887061005826 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs)...; Region: Era_like; cd00880 887061005827 Switch II region; other site 887061005828 G3 box; other site 887061005829 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 887061005830 G4 box; other site 887061005831 G5 box; other site 887061005832 Protein of unknown function (DUF971); Region: DUF971; cl01414 887061005833 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 887061005834 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 887061005835 S-adenosylmethionine binding site [chemical binding]; other site 887061005836 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; cl12011 887061005837 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 887061005838 SCP-2 sterol transfer family; Region: SCP2; cl01225 887061005839 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 887061005840 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 887061005841 active site 887061005842 substrate binding site [chemical binding]; other site 887061005843 ATP binding site [chemical binding]; other site 887061005844 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061005845 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 887061005846 Sodium:solute symporter family; Region: SSF; cl00456 887061005847 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 887061005848 H2TH interface [polypeptide binding]; other site 887061005849 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 887061005850 DNA binding site [nucleotide binding] 887061005851 putative catalytic residues [active] 887061005852 turnover-facilitating residue; other site 887061005853 intercalation triad [nucleotide binding]; other site 887061005854 8OG recognition residue [nucleotide binding]; other site 887061005855 putative reading head residues; other site 887061005856 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 887061005857 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 887061005858 gliding-associated putative ABC transporter substrate-binding component GldG; Region: GldG; TIGR03521 887061005859 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 887061005860 ABC-2 type transporter; Region: ABC2_membrane; cl11417 887061005861 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 887061005862 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061005863 Walker A/P-loop; other site 887061005864 ATP binding site [chemical binding]; other site 887061005865 Q-loop/lid; other site 887061005866 ABC transporter signature motif; other site 887061005867 Walker B; other site 887061005868 D-loop; other site 887061005869 H-loop/switch region; other site 887061005870 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 887061005871 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 887061005872 TPR motif; other site 887061005873 binding surface 887061005874 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 887061005875 TPR motif; other site 887061005876 binding surface 887061005877 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 887061005878 binding surface 887061005879 TPR motif; other site 887061005880 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 887061005881 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 887061005882 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 887061005883 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 887061005884 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK04923 887061005885 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061005886 Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this...; Region: Ribosomal_L25_TL5_CTC; cd00495 887061005887 5S rRNA interface [nucleotide binding]; other site 887061005888 CTC domain interface; other site 887061005889 L16 interface [polypeptide binding]; other site 887061005890 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 887061005891 putative active site [active] 887061005892 catalytic residue [active] 887061005893 GTP-binding protein YchF; Reviewed; Region: PRK09601 887061005894 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 887061005895 G1 box; other site 887061005896 GTP/Mg2+ binding site [chemical binding]; other site 887061005897 Switch I region; other site 887061005898 G2 box; other site 887061005899 Switch II region; other site 887061005900 G3 box; other site 887061005901 G4 box; other site 887061005902 G5 box; other site 887061005903 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 887061005904 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 887061005905 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 887061005906 cofactor binding site; other site 887061005907 DNA binding site [nucleotide binding] 887061005908 substrate interaction site [chemical binding]; other site 887061005909 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; cl12011 887061005910 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 887061005911 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061005912 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 887061005913 dimerization interface [polypeptide binding]; other site 887061005914 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 887061005915 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 887061005916 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 887061005917 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 887061005918 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 887061005919 Staphylococcal nuclease homologues; Region: SNc; smart00318 887061005920 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 887061005921 Catalytic site; other site 887061005922 putative metal dependent hydrolase; Provisional; Region: PRK11598 887061005923 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 887061005924 Sulfatase; Region: Sulfatase; cl10460 887061005925 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 887061005926 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 887061005927 Phage-related baseplate assembly protein; Region: Phage_base_V; cl11432 887061005928 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 887061005929 DoxX; Region: DoxX; cl00976 887061005930 Pirin-related protein [General function prediction only]; Region: COG1741 887061005931 Cupin domain; Region: Cupin_2; cl09118 887061005932 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 887061005933 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061005934 LysR family transcriptional regulator; Provisional; Region: PRK14997 887061005935 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061005936 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 887061005937 putative effector binding pocket; other site 887061005938 dimerization interface [polypeptide binding]; other site 887061005939 LexA repressor; Validated; Region: PRK00215 887061005940 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 (...; Region: S24_LexA-like; cd06529 887061005941 Catalytic site [active] 887061005942 FemAB family; Region: FemAB; cl11444 887061005943 Protein of unknown function, DUF482; Region: DUF482; pfam04339 887061005944 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading...; Region: EFh; cd00051 887061005945 Ca2+ binding site [ion binding]; other site 887061005946 osmolarity response regulator; Provisional; Region: ompR; PRK09468 887061005947 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 887061005948 active site 887061005949 phosphorylation site [posttranslational modification] 887061005950 intermolecular recognition site; other site 887061005951 dimerization interface [polypeptide binding]; other site 887061005952 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...; Region: trans_reg_C; cd00383 887061005953 DNA binding site [nucleotide binding] 887061005954 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061005955 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 trans-...; Region: HisKA; cd00082 887061005956 dimer interface [polypeptide binding]; other site 887061005957 phosphorylation site [posttranslational modification] 887061005958 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 887061005959 ATP binding site [chemical binding]; other site 887061005960 Mg2+ binding site [ion binding]; other site 887061005961 G-X-G motif; other site 887061005962 siroheme synthase; Provisional; Region: cysG; PRK10637 887061005963 precorrin-2 dehydrogenase; Validated; Region: PRK06719 887061005964 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 887061005965 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 887061005966 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 887061005967 ChuX-like family; Region: DUF1008; cl01509 887061005968 ChuX-like family; Region: DUF1008; cl01509 887061005969 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 887061005970 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 887061005971 putative hemin binding site; other site 887061005972 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...; Region: TM_ABC_iron-siderophores_like; cd06550 887061005973 ABC-ATPase subunit interface; other site 887061005974 dimer interface [polypeptide binding]; other site 887061005975 putative PBP binding regions; other site 887061005976 ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG4559 887061005977 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 887061005978 Walker A/P-loop; other site 887061005979 ATP binding site [chemical binding]; other site 887061005980 Q-loop/lid; other site 887061005981 ABC transporter signature motif; other site 887061005982 Walker B; other site 887061005983 D-loop; other site 887061005984 H-loop/switch region; other site 887061005985 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 887061005986 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 887061005987 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; cl14056 887061005988 TRAM domain; Region: TRAM; cl01282 887061005989 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 887061005990 PhoH-like protein; Region: PhoH; cl12134 887061005991 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 887061005992 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 887061005993 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 887061005994 Transporter associated domain; Region: CorC_HlyC; pfam03471 887061005995 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 887061005996 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 887061005997 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 887061005998 putative active site [active] 887061005999 catalytic triad [active] 887061006000 putative dimer interface [polypeptide binding]; other site 887061006001 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 887061006002 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 887061006003 dimer interface [polypeptide binding]; other site 887061006004 motif 1; other site 887061006005 active site 887061006006 motif 2; other site 887061006007 motif 3; other site 887061006008 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 887061006009 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 887061006010 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 887061006011 active site 887061006012 motif I; other site 887061006013 motif II; other site 887061006014 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 887061006015 putative acyl-acceptor binding pocket; other site 887061006016 Protein of unknown function DUF45; Region: DUF45; cl00636 887061006017 Predicted transcriptional regulator [Transcription]; Region: COG1959 887061006018 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061006019 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 887061006020 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 887061006021 heme-binding site [chemical binding]; other site 887061006022 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 887061006023 FAD binding pocket [chemical binding]; other site 887061006024 FAD binding motif [chemical binding]; other site 887061006025 phosphate binding motif [ion binding]; other site 887061006026 beta-alpha-beta structure motif; other site 887061006027 NAD binding pocket [chemical binding]; other site 887061006028 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 887061006029 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 887061006030 Ferritin-like domain; Region: Ferritin; pfam00210 887061006031 heme binding site [chemical binding]; other site 887061006032 ferroxidase pore; other site 887061006033 ferroxidase diiron center [ion binding]; other site 887061006034 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 887061006035 Ferritin-like domain; Region: Ferritin; pfam00210 887061006036 heme binding site [chemical binding]; other site 887061006037 ferroxidase pore; other site 887061006038 ferroxidase diiron center [ion binding]; other site 887061006039 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 887061006040 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 887061006041 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 887061006042 metal-binding site [ion binding] 887061006043 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 887061006044 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; cl11391 887061006045 FixH; Region: FixH; cl01254 887061006046 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 887061006047 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 alpha-; Region: HCP_like; cl14655 887061006048 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 887061006049 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 887061006050 Cytochrome c; Region: Cytochrom_C; cl11414 887061006051 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of...; Region: cbb3_Oxidase_CcoQ; cl00282 887061006052 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 887061006053 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the...; Region: cbb3_Oxidase_I; cd01661 887061006054 Low-spin heme binding site [chemical binding]; other site 887061006055 Putative water exit pathway; other site 887061006056 Binuclear center (active site) [active] 887061006057 Putative proton exit pathway; other site 887061006058 Surface antigen; Region: Surface_Ag_2; cl01155 887061006059 branched-chain amino acid aminotransferase; Provisional; Region: PRK12479 887061006060 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 alpha-...; Region: BCAT_beta_family; cd01557 887061006061 homodimer interface [polypeptide binding]; other site 887061006062 substrate-cofactor binding pocket; other site 887061006063 catalytic residue [active] 887061006064 Zinc-finger domain; Region: zf-CHCC; cl01821 887061006065 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 887061006066 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 887061006067 Uncharacterized small protein (DUF2292); Region: DUF2292; cl02371 887061006068 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 887061006069 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 887061006070 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 887061006071 TOBE domain; Region: TOBE_2; cl01440 887061006072 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 887061006073 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 887061006074 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061006075 catalytic residue [active] 887061006076 serine O-acetyltransferase; Region: cysE; TIGR01172 887061006077 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 L-...; Region: LbH_SAT; cd03354 887061006078 trimer interface [polypeptide binding]; other site 887061006079 active site 887061006080 substrate binding site [chemical binding]; other site 887061006081 CoA binding site [chemical binding]; other site 887061006082 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 887061006083 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 887061006084 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 887061006085 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...; Region: TM_PBP2; cd06261 887061006086 dimer interface [polypeptide binding]; other site 887061006087 conserved gate region; other site 887061006088 putative PBP binding loops; other site 887061006089 ABC-ATPase subunit interface; other site 887061006090 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...; Region: TM_PBP2; cd06261 887061006091 dimer interface [polypeptide binding]; other site 887061006092 conserved gate region; other site 887061006093 putative PBP binding loops; other site 887061006094 ABC-ATPase subunit interface; other site 887061006095 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 887061006096 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 solute-...; Region: ABC_CysA_sulfate_importer; cd03296 887061006097 Walker A/P-loop; other site 887061006098 ATP binding site [chemical binding]; other site 887061006099 Q-loop/lid; other site 887061006100 ABC transporter signature motif; other site 887061006101 Walker B; other site 887061006102 D-loop; other site 887061006103 H-loop/switch region; other site 887061006104 TOBE-like domain; Region: TOBE_3; pfam12857 887061006105 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 887061006106 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 887061006107 YeeE/YedE family (DUF395); Region: DUF395; cl01018 887061006108 YeeE/YedE family (DUF395); Region: DUF395; cl01018 887061006109 poly(A) polymerase; Region: pcnB; TIGR01942 887061006110 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 887061006111 active site 887061006112 NTP binding site [chemical binding]; other site 887061006113 metal binding triad [ion binding]; metal-binding site 887061006114 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 887061006115 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 887061006116 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 887061006117 catalytic center binding site [active] 887061006118 ATP binding site [chemical binding]; other site 887061006119 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 887061006120 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7...; Region: dNK; cd01673 887061006121 Substrate-binding site [chemical binding]; other site 887061006122 Substrate specificity [chemical binding]; other site 887061006123 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 887061006124 oligomerization interface [polypeptide binding]; other site 887061006125 active site 887061006126 metal binding site [ion binding]; metal-binding site 887061006127 Pantoate-beta-alanine ligase; Region: PanC; cd00560 887061006128 pantoate--beta-alanine ligase; Region: panC; TIGR00018 887061006129 active site 887061006130 ATP-binding site [chemical binding]; other site 887061006131 pantoate-binding site; other site 887061006132 HXXH motif; other site 887061006133 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 887061006134 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 887061006135 substrate binding pocket [chemical binding]; other site 887061006136 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 887061006137 tetramerization interface [polypeptide binding]; other site 887061006138 active site 887061006139 Domain of unknown function DUF143; Region: DUF143; cl00519 887061006140 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 887061006141 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 887061006142 DNA photolyase; Region: DNA_photolyase; pfam00875 887061006143 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 887061006144 MFS transporter, sugar porter (SP) family; Region: SP; TIGR00879 887061006145 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 887061006146 putative substrate translocation pore; other site 887061006147 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 887061006148 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-1,7-...; Region: FBPase; cd00354 887061006149 AMP binding site [chemical binding]; other site 887061006150 metal binding site [ion binding]; metal-binding site 887061006151 active site 887061006152 VacJ like lipoprotein; Region: VacJ; cl01073 887061006153 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 887061006154 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 887061006155 Protein of unknown function (DUF615); Region: DUF615; cl01147 887061006156 Site-specific recombinase; Region: SpecificRecomb; pfam10136 887061006157 Site-specific recombinase [DNA replication, recombination, and repair]; Region: COG4389 887061006158 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 C-...; Region: PDZ_serine_protease; cd00987 887061006159 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 887061006160 MPT binding site; other site 887061006161 trimer interface [polypeptide binding]; other site 887061006162 thiamine monophosphate kinase; Provisional; Region: PRK05731 887061006163 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 887061006164 ATP binding site [chemical binding]; other site 887061006165 dimerization interface [polypeptide binding]; other site 887061006166 Predicted integral membrane proteins containing uncharacterized repeats [Function unknown]; Region: COG5563 887061006167 probable extracellular repeat, HAF family; Region: HAF_rpt; TIGR02913 887061006168 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 887061006169 tetramer interfaces [polypeptide binding]; other site 887061006170 binuclear metal-binding site [ion binding]; other site 887061006171 Competence-damaged protein; Region: CinA; cl00666 887061006172 recombinase A; Provisional; Region: recA; PRK09354 887061006173 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 887061006174 hexamer interface [polypeptide binding]; other site 887061006175 Walker A motif; other site 887061006176 ATP binding site [chemical binding]; other site 887061006177 Walker B motif; other site 887061006178 RecX family; Region: RecX; cl00936 887061006179 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 887061006180 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...; Region: AlaRS_core; cd00673 887061006181 motif 1; other site 887061006182 active site 887061006183 motif 2; other site 887061006184 motif 3; other site 887061006185 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 887061006186 aspartate kinase; Reviewed; Region: PRK06635 887061006187 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 887061006188 putative nucleotide binding site [chemical binding]; other site 887061006189 putative catalytic residues [active] 887061006190 putative Mg ion binding site [ion binding]; other site 887061006191 putative aspartate binding site [chemical binding]; other site 887061006192 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 887061006193 putative allosteric regulatory site; other site 887061006194 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 887061006195 putative allosteric regulatory residue; other site 887061006196 hydroperoxidase II; Provisional; Region: katE; PRK11249 887061006197 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 887061006198 tetramer interface [polypeptide binding]; other site 887061006199 heme binding pocket [chemical binding]; other site 887061006200 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 887061006201 domain interactions; other site 887061006202 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 887061006203 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 887061006204 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 887061006205 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061006206 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061006207 Malic enzyme, N-terminal domain; Region: malic; pfam00390 887061006208 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 887061006209 putative NAD(P) binding site [chemical binding]; other site 887061006210 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061006211 HlyD family secretion protein; Region: HlyD_2; pfam12700 887061006212 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 887061006213 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061006214 Outer membrane efflux protein; Region: OEP; pfam02321 887061006215 Outer membrane efflux protein; Region: OEP; pfam02321 887061006216 CHASE3 domain; Region: CHASE3; cl05000 887061006217 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 trans-...; Region: HisKA; cd00082 887061006218 dimer interface [polypeptide binding]; other site 887061006219 phosphorylation site [posttranslational modification] 887061006220 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 887061006221 ATP binding site [chemical binding]; other site 887061006222 Mg2+ binding site [ion binding]; other site 887061006223 G-X-G motif; other site 887061006224 Response regulator receiver domain; Region: Response_reg; pfam00072 887061006225 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 887061006226 active site 887061006227 phosphorylation site [posttranslational modification] 887061006228 intermolecular recognition site; other site 887061006229 dimerization interface [polypeptide binding]; other site 887061006230 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 887061006231 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 887061006232 active site 887061006233 phosphorylation site [posttranslational modification] 887061006234 intermolecular recognition site; other site 887061006235 dimerization interface [polypeptide binding]; other site 887061006236 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 887061006237 PAS fold; Region: PAS_4; pfam08448 887061006238 bacterio-opsin activator; Provisional; Region: PRK13558 887061006239 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 887061006240 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006241 metal binding site [ion binding]; metal-binding site 887061006242 active site 887061006243 I-site; other site 887061006244 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 887061006245 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 887061006246 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 887061006247 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 887061006248 HPP family; Region: HPP; pfam04982 887061006249 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-...; Region: CBS_pair; cl10010 887061006250 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 887061006251 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 887061006252 dinuclear metal binding motif [ion binding]; other site 887061006253 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061006254 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061006255 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 887061006256 dimer interface [polypeptide binding]; other site 887061006257 Domain of unknown function (DUF299); Region: DUF299; cl00780 887061006258 phosphoenolpyruvate synthase; Validated; Region: PRK06464 887061006259 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 887061006260 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 887061006261 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 887061006262 Protein of unknown function, DUF481; Region: DUF481; cl01213 887061006263 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 887061006264 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 887061006265 active site 887061006266 motif I; other site 887061006267 motif II; other site 887061006268 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 887061006269 active site 887061006270 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 887061006271 BON domain; Region: BON; cl02771 887061006272 YaeQ protein; Region: YaeQ; cl01913 887061006273 signal recognition particle protein; Provisional; Region: PRK10867 887061006274 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 887061006275 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 887061006276 P loop; other site 887061006277 GTP binding site [chemical binding]; other site 887061006278 Signal peptide binding domain; Region: SRP_SPB; pfam02978 887061006279 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 887061006280 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; cl11391 887061006281 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 887061006282 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 887061006283 2-isopropylmalate synthase; Validated; Region: PRK00915 887061006284 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 887061006285 active site 887061006286 catalytic residues [active] 887061006287 metal binding site [ion binding]; metal-binding site 887061006288 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; pfam08502 887061006289 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 887061006290 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 887061006291 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 887061006292 Preprotein translocase subunit; Region: YajC; cl00806 887061006293 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 887061006294 Protein export membrane protein; Region: SecD_SecF; cl14618 887061006295 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 887061006296 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 887061006297 Protein export membrane protein; Region: SecD_SecF; cl14618 887061006298 Domain of unknown function DUF21; Region: DUF21; pfam01595 887061006299 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 887061006300 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 887061006301 Transporter associated domain; Region: CorC_HlyC; pfam03471 887061006302 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 887061006303 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 887061006304 Clp amino terminal domain; Region: Clp_N; pfam02861 887061006305 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...; Region: AAA; cd00009 887061006306 Walker A motif; other site 887061006307 ATP binding site [chemical binding]; other site 887061006308 Walker B motif; other site 887061006309 arginine finger; other site 887061006310 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...; Region: AAA; cd00009 887061006311 Walker A motif; other site 887061006312 ATP binding site [chemical binding]; other site 887061006313 Walker B motif; other site 887061006314 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 887061006315 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 887061006316 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061006317 GST_C family, unknown subfamily 5; 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_C_5; cd03196 887061006318 putative N-terminal domain interface [polypeptide binding]; other site 887061006319 putative dimer interface [polypeptide binding]; other site 887061006320 putative substrate binding pocket (H-site) [chemical binding]; other site 887061006321 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 887061006322 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...; Region: DHOD_2_like; cd04738 887061006323 quinone interaction residues [chemical binding]; other site 887061006324 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 887061006325 active site 887061006326 catalytic residues [active] 887061006327 FMN binding site [chemical binding]; other site 887061006328 substrate binding site [chemical binding]; other site 887061006329 Nitrogen regulatory protein P-II; Region: P-II; cl00412 887061006330 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061006331 Nitrogen regulatory protein P-II; Region: P-II; cl00412 887061006332 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061006333 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061006334 Outer membrane efflux protein; Region: OEP; pfam02321 887061006335 Outer membrane efflux protein; Region: OEP; pfam02321 887061006336 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 887061006337 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 887061006338 active site 887061006339 HIGH motif; other site 887061006340 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 887061006341 KMSKS motif; other site 887061006342 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 887061006343 tRNA binding surface [nucleotide binding]; other site 887061006344 anticodon binding site; other site 887061006345 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 887061006346 binding surface 887061006347 TPR motif; other site 887061006348 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 887061006349 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 887061006350 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 887061006351 substrate binding site [chemical binding]; other site 887061006352 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 887061006353 substrate binding site [chemical binding]; other site 887061006354 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 887061006355 putative active site [active] 887061006356 putative metal binding site [ion binding]; other site 887061006357 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cd00060 887061006358 phosphopeptide binding site; other site 887061006359 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 rRNA-...; Region: NusB_Sun; cl00223 887061006360 putative RNA binding site [nucleotide binding]; other site 887061006361 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 887061006362 homopentamer interface [polypeptide binding]; other site 887061006363 active site 887061006364 Oxalate/Formate Antiporter; Region: 2A0111; TIGR00890 887061006365 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 887061006366 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 887061006367 active site 887061006368 phosphorylation site [posttranslational modification] 887061006369 intermolecular recognition site; other site 887061006370 dimerization interface [polypeptide binding]; other site 887061006371 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...; Region: trans_reg_C; cd00383 887061006372 DNA binding site [nucleotide binding] 887061006373 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 887061006374 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 887061006375 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 887061006376 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 trans-...; Region: HisKA; cd00082 887061006377 dimer interface [polypeptide binding]; other site 887061006378 phosphorylation site [posttranslational modification] 887061006379 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 887061006380 ATP binding site [chemical binding]; other site 887061006381 Mg2+ binding site [ion binding]; other site 887061006382 G-X-G motif; other site 887061006383 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 887061006384 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 887061006385 FAD binding domain; Region: FAD_binding_4; pfam01565 887061006386 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 887061006387 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 887061006388 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 887061006389 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...; Region: TlpA_like_family; cd02966 887061006390 catalytic residues [active] 887061006391 Uncharacterised protein family (UPF0093); Region: UPF0093; cl00863 887061006392 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061006393 putative hydrophobic ligand binding site [chemical binding]; other site 887061006394 protein interface [polypeptide binding]; other site 887061006395 gate; other site 887061006396 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061006397 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061006398 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 887061006399 substrate binding site [chemical binding]; other site 887061006400 ATP binding site [chemical binding]; other site 887061006401 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 887061006402 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 887061006403 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 887061006404 putative acyl-acceptor binding pocket; other site 887061006405 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 887061006406 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 887061006407 active site 887061006408 metal binding site [ion binding]; metal-binding site 887061006409 Cytochrome c; Region: Cytochrom_C; cl11414 887061006410 Cytochrome c; Region: Cytochrom_C; cl11414 887061006411 Sulfatase; Region: Sulfatase; cl10460 887061006412 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 887061006413 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 887061006414 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 887061006415 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 887061006416 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061006417 catalytic residue [active] 887061006418 prolyl-tRNA synthetase; Provisional; Region: PRK09194 887061006419 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...; Region: ProRS_core_prok; cd00779 887061006420 dimer interface [polypeptide binding]; other site 887061006421 motif 1; other site 887061006422 active site 887061006423 motif 2; other site 887061006424 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 single-...; Region: ProRS-INS; cd04334 887061006425 putative deacylase active site [active] 887061006426 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...; Region: class_II_aaRS-like_core; cl00268 887061006427 active site 887061006428 motif 3; other site 887061006429 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-...; Region: ProRS_anticodon_short; cd00861 887061006430 anticodon binding site; other site 887061006431 Domain of unknown function (DUF477); Region: DUF477; cl01535 887061006432 Domain of unknown function (DUF477); Region: DUF477; cl01535 887061006433 LemA family; Region: LemA; cl00742 887061006434 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 887061006435 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 887061006436 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061006437 Coenzyme A binding pocket [chemical binding]; other site 887061006438 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 887061006439 RF-1 domain; Region: RF-1; cl02875 887061006440 Protein of unknown function (DUF3820); Region: DUF3820; cl01411 887061006441 EamA-like transporter family; Region: EamA; cl01037 887061006442 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 887061006443 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 887061006444 ring oligomerisation interface [polypeptide binding]; other site 887061006445 ATP/Mg binding site [chemical binding]; other site 887061006446 stacking interactions; other site 887061006447 hinge regions; other site 887061006448 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...; Region: cpn10; cd00320 887061006449 oligomerisation interface [polypeptide binding]; other site 887061006450 mobile loop; other site 887061006451 roof hairpin; other site 887061006452 Domain of unknown function DUF; Region: DUF202; cl09954 887061006453 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 887061006454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061006455 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 887061006456 transcriptional regulator; Provisional; Region: PRK10632 887061006457 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061006458 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 887061006459 putative effector binding pocket; other site 887061006460 dimerization interface [polypeptide binding]; other site 887061006461 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 887061006462 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; cl14882 887061006463 DEAD_2; Region: DEAD_2; cl14887 887061006464 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl09250 887061006465 pyrrolysine biosynthesis protein PylC; Region: pyrrolys_PylC; TIGR03909 887061006466 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 887061006467 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings...; Region: proteasome_beta_bacterial; cd03765 887061006468 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 887061006469 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...; Region: Aldo_ket_red; cd06660 887061006470 active site 887061006471 catalytic tetrad [active] 887061006472 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 887061006473 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...; Region: Trunc_globin; cd00454 887061006474 apolar tunnel; other site 887061006475 heme binding site [chemical binding]; other site 887061006476 dimerization interface [polypeptide binding]; other site 887061006477 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 887061006478 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 connected by an extended linker. The...; Region: HAMP; cd06225 887061006479 dimerization interface [polypeptide binding]; other site 887061006480 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006481 metal binding site [ion binding]; metal-binding site 887061006482 active site 887061006483 I-site; other site 887061006484 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 887061006485 Dihydroorotase [Nucleotide transport and metabolism]; Region: PyrC; COG0418 887061006486 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 887061006487 active site 887061006488 substrate binding pocket [chemical binding]; other site 887061006489 dimer interface [polypeptide binding]; other site 887061006490 Predicted methyltransferases [General function prediction only]; Region: COG0313 887061006491 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 887061006492 LppC putative lipoprotein; Region: LppC; pfam04348 887061006493 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 887061006494 putative ligand binding site [chemical binding]; other site 887061006495 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 887061006496 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 887061006497 dimer interface [polypeptide binding]; other site 887061006498 active site 887061006499 BON domain; Region: BON; cl02771 887061006500 BON domain; Region: BON; cl02771 887061006501 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 887061006502 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...; Region: TlpA_like_family; cd02966 887061006503 catalytic residues [active] 887061006504 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 887061006505 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 887061006506 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 887061006507 catalytic residues [active] 887061006508 transcription termination factor Rho; Provisional; Region: rho; PRK09376 887061006509 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 887061006510 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...; Region: Rho_CSD; cd04459 887061006511 RNA binding site [nucleotide binding]; other site 887061006512 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...; Region: rho_factor; cd01128 887061006513 multimer interface [polypeptide binding]; other site 887061006514 Walker A motif; other site 887061006515 ATP binding site [chemical binding]; other site 887061006516 Walker B motif; other site 887061006517 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 887061006518 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 887061006519 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061006520 molybdenum ABC transporter, ATP-binding protein; Region: modC_ABC; TIGR02142 887061006521 Walker A/P-loop; other site 887061006522 ATP binding site [chemical binding]; other site 887061006523 Q-loop/lid; other site 887061006524 ABC transporter signature motif; other site 887061006525 Walker B; other site 887061006526 D-loop; other site 887061006527 H-loop/switch region; other site 887061006528 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...; Region: TM_PBP2; cd06261 887061006529 dimer interface [polypeptide binding]; other site 887061006530 conserved gate region; other site 887061006531 putative PBP binding loops; other site 887061006532 ABC-ATPase subunit interface; other site 887061006533 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 887061006534 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 887061006535 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061006536 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 887061006537 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 887061006538 FeS/SAM binding site; other site 887061006539 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 887061006540 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 887061006541 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 887061006542 GTP binding site [chemical binding]; other site 887061006543 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa...; Region: MobB; cd03116 887061006544 Walker A motif; other site 887061006545 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 887061006546 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 887061006547 dimer interface [polypeptide binding]; other site 887061006548 putative functional site; other site 887061006549 putative MPT binding site; other site 887061006550 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_9; cd07245 887061006551 dimer interface [polypeptide binding]; other site 887061006552 putative metal binding site [ion binding]; other site 887061006553 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061006554 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 887061006555 N-terminal plug; other site 887061006556 ligand-binding site [chemical binding]; other site 887061006557 Predicted secreted protein [Function unknown]; Region: COG5501; cl02313 887061006558 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 887061006559 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 887061006560 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061006561 Gram-negative bacterial tonB protein; Region: TonB; cl10048 887061006562 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061006563 adaptive-response sensory kinase; Validated; Region: PRK09303 887061006564 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 trans-...; Region: HisKA; cl00080 887061006565 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 887061006566 ATP binding site [chemical binding]; other site 887061006567 G-X-G motif; other site 887061006568 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...; Region: PRX_BCP; cd03017 887061006569 catalytic triad [active] 887061006570 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 887061006571 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 887061006572 putative active site [active] 887061006573 PhoH-like protein; Region: PhoH; cl12134 887061006574 lysophospholipid transporter LplT; Provisional; Region: PRK11195 887061006575 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 887061006576 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061006577 Cytochrome c; Region: Cytochrom_C; cl11414 887061006578 Cytochrome c; Region: Cytochrom_C; cl11414 887061006579 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 887061006580 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...; Region: PBPb; cd00134 887061006581 substrate binding pocket [chemical binding]; other site 887061006582 membrane-bound complex binding site; other site 887061006583 hinge residues; other site 887061006584 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061006585 'Velcro' closure; other site 887061006586 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 887061006587 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 887061006588 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 887061006589 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 887061006590 ligand binding site [chemical binding]; other site 887061006591 flexible hinge region; other site 887061006592 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 887061006593 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 887061006594 active site residue [active] 887061006595 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 887061006596 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 887061006597 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 887061006598 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 887061006599 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 887061006600 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 887061006601 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 887061006602 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061006603 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 887061006604 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...; Region: Sigma70_r4; cd06171 887061006605 DNA binding residues [nucleotide binding] 887061006606 DNA primase; Validated; Region: dnaG; PRK05667 887061006607 CHC2 zinc finger; Region: zf-CHC2; cl02597 887061006608 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 887061006609 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 887061006610 active site 887061006611 metal binding site [ion binding]; metal-binding site 887061006612 interdomain interaction site; other site 887061006613 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 887061006614 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 887061006615 GatB domain; Region: GatB_Yqey; cl11497 887061006616 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 887061006617 UGMP family protein; Validated; Region: PRK09604 887061006618 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 887061006619 Domain of unknown function (DUF205); Region: DUF205; cl00410 887061006620 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...; Region: DHNA_DHNTPE; cd00534 887061006621 homooctamer interface [polypeptide binding]; other site 887061006622 active site 887061006623 TIGR03790 family protein; Region: TIGR03790 887061006624 SEC-C motif; Region: SEC-C; cl12132 887061006625 hypothetical protein; Provisional; Region: PRK04233 887061006626 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 887061006627 N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid...; Region: INT_XerDC; cd00798 887061006628 Int/Topo IB signature motif; other site 887061006629 active site 887061006630 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 887061006631 DNA binding site [nucleotide binding] 887061006632 active site 887061006633 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 887061006634 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 887061006635 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 887061006636 RimM N-terminal domain; Region: RimM; pfam01782 887061006637 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...; Region: PRCH; cl09959 887061006638 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 887061006639 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 887061006640 Ligand Binding Site [chemical binding]; other site 887061006641 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 887061006642 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 887061006643 FeS/SAM binding site; other site 887061006644 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 887061006645 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 887061006646 TPR motif; other site 887061006647 binding surface 887061006648 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061006649 ligand binding site [chemical binding]; other site 887061006650 translocation protein TolB; Provisional; Region: tolB; PRK02889 887061006651 TolB amino-terminal domain; Region: TolB_N; pfam04052 887061006652 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061006653 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061006654 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061006655 TolA protein; Region: tolA_full; TIGR02794 887061006656 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 887061006657 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061006658 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061006659 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...; Region: 4HBT; cd00586 887061006660 active site 887061006661 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 887061006662 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...; Region: AAA; cd00009 887061006663 Walker A motif; other site 887061006664 ATP binding site [chemical binding]; other site 887061006665 Walker B motif; other site 887061006666 arginine finger; other site 887061006667 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 887061006668 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 887061006669 RuvA N terminal domain; Region: RuvA_N; pfam01330 887061006670 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 887061006671 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 887061006672 active site 887061006673 putative DNA-binding cleft [nucleotide binding]; other site 887061006674 dimer interface [polypeptide binding]; other site 887061006675 Domain of unknown function DUF28; Region: DUF28; cl00361 887061006676 EamA-like transporter family; Region: EamA; cl01037 887061006677 EamA-like transporter family; Region: EamA; cl01037 887061006678 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 887061006679 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061006680 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-...; Region: CBS_pair_10; cd04623 887061006681 FOG: CBS domain [General function prediction only]; Region: COG0517 887061006682 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 887061006683 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 887061006684 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061006685 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061006686 Uncharacterised protein family UPF0047; Region: UPF0047; cl00439 887061006687 Formaldehyde-activating enzyme (Fae); Region: Fae; cl00774 887061006688 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 887061006689 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 887061006690 catalytic triad [active] 887061006691 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 887061006692 Domain of Unknown Function with PDB structure; Region: DUF3857; pfam12969 887061006693 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061006694 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061006695 Lipoprotein NlpI, contains TPR repeats [General function prediction only]; Region: NlpI; COG4785 887061006696 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 887061006697 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 887061006698 catalytic residue [active] 887061006699 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...; Region: GltS_FMN; cd02808 887061006700 Conserved region in glutamate synthase; Region: Glu_synthase; pfam01645 887061006701 active site 887061006702 FMN binding site [chemical binding]; other site 887061006703 substrate binding site [chemical binding]; other site 887061006704 3Fe-4S cluster binding site [ion binding]; other site 887061006705 GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran...; Region: GXGXG; cl00239 887061006706 domain_subunit interface; other site 887061006707 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 887061006708 Glutamine amidotransferases class-II (Gn-AT)_GlxB-type. GlxB is a glutamine amidotransferase-like protein of unknown function found in bacteria and archaea. GlxB has a structural fold similar to that of other class II glutamine amidotransferases...; Region: GlxB; cd01907 887061006709 putative active site [active] 887061006710 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 887061006711 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 887061006712 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 887061006713 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 887061006714 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 887061006715 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061006716 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 887061006717 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 887061006718 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 887061006719 Sarcosine oxidase, delta subunit family; Region: SoxD; cl01767 887061006720 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 887061006721 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 887061006722 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 887061006723 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 887061006724 non-specific DNA binding site [nucleotide binding]; other site 887061006725 salt bridge; other site 887061006726 sequence-specific DNA binding site [nucleotide binding]; other site 887061006727 Cupin domain; Region: Cupin_2; cl09118 887061006728 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 887061006729 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061006730 Coenzyme A binding pocket [chemical binding]; other site 887061006731 Domain of unknown function DUF140; Region: DUF140; cl00510 887061006732 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 887061006733 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061006734 Walker A/P-loop; other site 887061006735 ATP binding site [chemical binding]; other site 887061006736 Q-loop/lid; other site 887061006737 ABC transporter signature motif; other site 887061006738 Walker B; other site 887061006739 D-loop; other site 887061006740 H-loop/switch region; other site 887061006741 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 887061006742 mce related protein; Region: MCE; cl03606 887061006743 Protein of unknown function (DUF330); Region: DUF330; cl01135 887061006744 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 887061006745 Phospholipase D delta; Region: PLN03008 887061006746 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 887061006747 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Region: PLDc_vPLD1_2_like_2; cd09105 887061006748 phospholipase D; Region: PLN02866 887061006749 putative active site [active] 887061006750 catalytic site [active] 887061006751 CCC1-related family of proteins; Region: CCC1_like; cl00278 887061006752 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 887061006753 PAS fold; Region: PAS; pfam00989 887061006754 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 887061006755 putative active site [active] 887061006756 heme pocket [chemical binding]; other site 887061006757 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006758 metal binding site [ion binding]; metal-binding site 887061006759 active site 887061006760 I-site; other site 887061006761 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 887061006762 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 887061006763 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 887061006764 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 887061006765 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 887061006766 putative active site [active] 887061006767 putative metal binding site [ion binding]; other site 887061006768 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 887061006769 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 887061006770 active site 887061006771 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 887061006772 GAF domain; Region: GAF; cl00853 887061006773 PAS domain S-box; Region: sensory_box; TIGR00229 887061006774 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 887061006775 putative active site [active] 887061006776 heme pocket [chemical binding]; other site 887061006777 PAS domain S-box; Region: sensory_box; TIGR00229 887061006778 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 887061006779 putative active site [active] 887061006780 heme pocket [chemical binding]; other site 887061006781 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006782 metal binding site [ion binding]; metal-binding site 887061006783 active site 887061006784 I-site; other site 887061006785 PEP-CTERM motif; Region: VPEP; pfam07589 887061006786 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061006787 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 887061006788 N-terminal plug; other site 887061006789 ligand-binding site [chemical binding]; other site 887061006790 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 887061006791 putative active site [active] 887061006792 catalytic site [active] 887061006793 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 887061006794 putative active site [active] 887061006795 catalytic site [active] 887061006796 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 887061006797 putative catalytic site [active] 887061006798 putative metal binding site [ion binding]; other site 887061006799 putative phosphate binding site [ion binding]; other site 887061006800 Quinolinate synthetase A protein; Region: NadA; cl00420 887061006801 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_7; cd04664 887061006802 nudix motif; other site 887061006803 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061006804 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 887061006805 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 887061006806 binding surface 887061006807 TPR motif; other site 887061006808 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 887061006809 binding surface 887061006810 TPR motif; other site 887061006811 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 887061006812 binding surface 887061006813 TPR motif; other site 887061006814 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 887061006815 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 887061006816 dimer interface [polypeptide binding]; other site 887061006817 anticodon binding site; other site 887061006818 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 887061006819 homodimer interface [polypeptide binding]; other site 887061006820 motif 1; other site 887061006821 active site 887061006822 motif 2; other site 887061006823 GAD domain; Region: GAD; pfam02938 887061006824 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 887061006825 motif 3; other site 887061006826 Protein of unknown function (DUF502); Region: DUF502; cl01107 887061006827 Zinc ribbon domain; Region: CxxC_CxxC_SSSS; cl00993 887061006828 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 887061006829 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 887061006830 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 887061006831 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 887061006832 Ligand binding site [chemical binding]; other site 887061006833 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 887061006834 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 887061006835 Cysteine-rich domain; Region: CCG; pfam02754 887061006836 Trimethylamine dehydrogenase (TMADH) and histamine dehydrogenase (HD) FMN-binding domain. TMADH is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. The protein forms a...; Region: TMADH_HD_FMN; cd02929 887061006837 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 887061006838 FMN binding site [chemical binding]; other site 887061006839 active site 887061006840 homodimer interface [polypeptide binding]; other site 887061006841 putative catalytic residue [active] 887061006842 4Fe-4S cluster binding site [ion binding]; other site 887061006843 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061006844 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 887061006845 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 887061006846 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 887061006847 transcriptional regulator NarL; Provisional; Region: PRK10651 887061006848 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 887061006849 active site 887061006850 phosphorylation site [posttranslational modification] 887061006851 intermolecular recognition site; other site 887061006852 dimerization interface [polypeptide binding]; other site 887061006853 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...; Region: LuxR_C_like; cd06170 887061006854 DNA binding residues [nucleotide binding] 887061006855 dimerization interface [polypeptide binding]; other site 887061006856 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 887061006857 Histidine kinase; Region: HisKA_3; pfam07730 887061006858 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 887061006859 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061006860 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 887061006861 putative active site [active] 887061006862 heme pocket [chemical binding]; other site 887061006863 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 887061006864 putative active site [active] 887061006865 heme pocket [chemical binding]; other site 887061006866 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 887061006867 PAS fold; Region: PAS_3; pfam08447 887061006868 putative active site [active] 887061006869 heme pocket [chemical binding]; other site 887061006870 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 887061006871 Protein of unknown function (DUF3445); Region: DUF3445; pfam11927 887061006872 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 887061006873 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-...; Region: PDR_like; cd06185 887061006874 FMN-binding pocket [chemical binding]; other site 887061006875 flavin binding motif; other site 887061006876 phosphate binding motif [ion binding]; other site 887061006877 beta-alpha-beta structure motif; other site 887061006878 NAD binding pocket [chemical binding]; other site 887061006879 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 887061006880 catalytic loop [active] 887061006881 iron binding site [ion binding]; other site 887061006882 Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]; Region: GcvT; COG0404 887061006883 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 887061006884 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 887061006885 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 887061006886 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 887061006887 PAS fold; Region: PAS_3; pfam08447 887061006888 putative active site [active] 887061006889 heme pocket [chemical binding]; other site 887061006890 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006891 metal binding site [ion binding]; metal-binding site 887061006892 active site 887061006893 I-site; other site 887061006894 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 887061006895 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 887061006896 Protein of unknown function (DUF3375); Region: DUF3375; pfam11855 887061006897 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 trans-...; Region: HisKA; cd00082 887061006898 dimer interface [polypeptide binding]; other site 887061006899 phosphorylation site [posttranslational modification] 887061006900 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 887061006901 ATP binding site [chemical binding]; other site 887061006902 Mg2+ binding site [ion binding]; other site 887061006903 G-X-G motif; other site 887061006904 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 887061006905 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 887061006906 active site 887061006907 phosphorylation site [posttranslational modification] 887061006908 intermolecular recognition site; other site 887061006909 dimerization interface [polypeptide binding]; other site 887061006910 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...; Region: trans_reg_C; cd00383 887061006911 DNA binding site [nucleotide binding] 887061006912 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 887061006913 putative hydrophobic ligand binding site [chemical binding]; other site 887061006914 Molybdenum cofactor biosynthesis protein F; Region: MoaF; pfam10703 887061006915 transcriptional regulator; Provisional; Region: PRK10632 887061006916 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061006917 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 887061006918 putative effector binding pocket; other site 887061006919 putative dimerization interface [polypeptide binding]; other site 887061006920 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 887061006921 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061006922 NAD(P) binding site [chemical binding]; other site 887061006923 active site 887061006924 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 887061006925 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 887061006926 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061006927 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 887061006928 NodT family; Region: outer_NodT; TIGR01845 887061006929 Outer membrane efflux protein; Region: OEP; pfam02321 887061006930 Outer membrane efflux protein; Region: OEP; pfam02321 887061006931 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061006932 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 887061006933 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061006934 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 887061006935 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 887061006936 dimer interface [polypeptide binding]; other site 887061006937 ssDNA binding site [nucleotide binding]; other site 887061006938 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061006939 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 887061006940 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061006941 putative substrate translocation pore; other site 887061006942 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 887061006943 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 887061006944 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 887061006945 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 887061006946 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061006947 Transglycosylase; Region: Transgly; cl07896 887061006948 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 887061006949 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 887061006950 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 887061006951 shikimate binding site; other site 887061006952 NAD(P) binding site [chemical binding]; other site 887061006953 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 887061006954 active site residue [active] 887061006955 glutamine synthetase; Provisional; Region: glnA; PRK09469 887061006956 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 887061006957 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 887061006958 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 887061006959 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 887061006960 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 trans-...; Region: HisKA; cd00082 887061006961 dimer interface [polypeptide binding]; other site 887061006962 phosphorylation site [posttranslational modification] 887061006963 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 887061006964 ATP binding site [chemical binding]; other site 887061006965 Mg2+ binding site [ion binding]; other site 887061006966 G-X-G motif; other site 887061006967 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 887061006968 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 887061006969 active site 887061006970 phosphorylation site [posttranslational modification] 887061006971 intermolecular recognition site; other site 887061006972 dimerization interface [polypeptide binding]; other site 887061006973 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...; Region: AAA; cd00009 887061006974 Walker A motif; other site 887061006975 ATP binding site [chemical binding]; other site 887061006976 Walker B motif; other site 887061006977 arginine finger; other site 887061006978 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061006979 type III secretion low calcium response chaperone LcrH/SycD; Region: LcrH_SycD; TIGR02552 887061006980 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 887061006981 binding surface 887061006982 TPR motif; other site 887061006983 Macrocin-O-methyltransferase (TylF); Region: TylF; pfam05711 887061006984 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 887061006985 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 887061006986 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 887061006987 active site 887061006988 dimer interface [polypeptide binding]; other site 887061006989 metal binding site [ion binding]; metal-binding site 887061006990 shikimate kinase; Reviewed; Region: aroK; PRK00131 887061006991 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...; Region: SK; cd00464 887061006992 ADP binding site [chemical binding]; other site 887061006993 magnesium binding site [ion binding]; other site 887061006994 putative shikimate binding site; other site 887061006995 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 887061006996 Secretin and TonB N terminus short domain; Region: STN; pfam07660 887061006997 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 887061006998 Bacterial type II and III secretion system protein; Region: Secretin; cl02829 887061006999 Pilus assembly protein, PilP; Region: PilP; cl01235 887061007000 Pilus assembly protein, PilO; Region: PilO; cl01234 887061007001 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 887061007002 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 887061007003 Competence protein A; Region: Competence_A; pfam11104 887061007004 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 887061007005 Transglycosylase; Region: Transgly; cl07896 887061007006 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 887061007007 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 887061007008 dimer interface [polypeptide binding]; other site 887061007009 allosteric magnesium binding site [ion binding]; other site 887061007010 active site 887061007011 aspartate-rich active site metal binding site; other site 887061007012 Schiff base residues; other site 887061007013 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 887061007014 active site 887061007015 ribulose/triose binding site [chemical binding]; other site 887061007016 phosphate binding site [ion binding]; other site 887061007017 substrate (anthranilate) binding pocket [chemical binding]; other site 887061007018 product (indole) binding pocket [chemical binding]; other site 887061007019 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 887061007020 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 887061007021 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 887061007022 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 887061007023 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 887061007024 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 887061007025 glutamine binding [chemical binding]; other site 887061007026 catalytic triad [active] 887061007027 anthranilate synthase component I; Provisional; Region: PRK13565 887061007028 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 887061007029 chorismate binding enzyme; Region: Chorismate_bind; cl10555 887061007030 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061007031 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; cl11391 887061007032 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 887061007033 motif II; other site 887061007034 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...; Region: RPE; cd00429 887061007035 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 887061007036 substrate binding site [chemical binding]; other site 887061007037 hexamer interface [polypeptide binding]; other site 887061007038 metal binding site [ion binding]; metal-binding site 887061007039 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 887061007040 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 887061007041 tRNA; other site 887061007042 putative tRNA binding site [nucleotide binding]; other site 887061007043 putative NADP binding site [chemical binding]; other site 887061007044 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 887061007045 peptide chain release factor 1; Validated; Region: prfA; PRK00591 887061007046 RF-1 domain; Region: RF-1; cl02875 887061007047 RF-1 domain; Region: RF-1; cl02875 887061007048 Predicted membrane protein (DUF2127); Region: DUF2127; cl01785 887061007049 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 887061007050 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; cl12011 887061007051 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 887061007052 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 887061007053 trimer interface [polypeptide binding]; other site 887061007054 putative metal binding site [ion binding]; other site 887061007055 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 887061007056 Homoserine acetyltransferase [Amino acid transport and metabolism]; Region: MET2; COG2021 887061007057 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; cl12011 887061007058 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 887061007059 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 887061007060 muropeptide transporter; Reviewed; Region: ampG; PRK11902 887061007061 putative substrate translocation pore; other site 887061007062 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 887061007063 putative active site [active] 887061007064 putative DNA binding site [nucleotide binding]; other site 887061007065 putative phosphate binding site [ion binding]; other site 887061007066 putative catalytic site [active] 887061007067 metal binding site A [ion binding]; metal-binding site 887061007068 putative AP binding site [nucleotide binding]; other site 887061007069 putative metal binding site B [ion binding]; other site 887061007070 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 887061007071 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 887061007072 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 887061007073 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 887061007074 GatB domain; Region: GatB_Yqey; cl11497 887061007075 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 887061007076 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; cl11426 887061007077 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 887061007078 rod shape-determining protein MreB; Provisional; Region: PRK13927 887061007079 Cell division protein FtsA; Region: FtsA; cl11496 887061007080 rod shape-determining protein MreC; Provisional; Region: PRK13922 887061007081 rod shape-determining protein MreC; Region: MreC; pfam04085 887061007082 rod shape-determining protein MreD; Region: MreD; cl01087 887061007083 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 887061007084 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 887061007085 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 887061007086 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 887061007087 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 887061007088 Sporulation related domain; Region: SPOR; cl10051 887061007089 Beta-lactamase; Region: Beta-lactamase; cl01009 887061007090 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 887061007091 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 887061007092 branched-chain amino acid aminotransferase; Provisional; Region: PRK12479 887061007093 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and D-...; Region: D-AAT_like; cd01558 887061007094 homodimer interface [polypeptide binding]; other site 887061007095 substrate-cofactor binding pocket; other site 887061007096 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061007097 catalytic residue [active] 887061007098 Protein of unknown function (DUF493); Region: DUF493; cl01102 887061007099 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 887061007100 lipoyl synthase; Provisional; Region: PRK05481 887061007101 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 887061007102 FeS/SAM binding site; other site 887061007103 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 887061007104 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061007105 DNA-binding site [nucleotide binding]; DNA binding site 887061007106 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 887061007107 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061007108 homodimer interface [polypeptide binding]; other site 887061007109 Dehydrogenases with pyrrolo-quinoline quinone (PQQ) as cofactor, like ethanol, methanol, and membrane bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller; Region: PQQ_DH; cl11493 887061007110 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061007111 Trp docking motif; other site 887061007112 'Velcro' closure; other site 887061007113 active site 887061007114 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; cl01558 887061007115 phosphoribosylamine--glycine ligase; Provisional; Region: PRK13790 887061007116 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061007117 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 887061007118 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 887061007119 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 887061007120 S-adenosylmethionine binding site [chemical binding]; other site 887061007121 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 887061007122 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061007123 trehalose synthase; Region: treS_nterm; TIGR02456 887061007124 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061007125 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; cl01286 887061007126 Maltooligosyl trehalose synthase (MTSase) N-terminus domain. MTSase and maltooligosyl trehalose trehalohydrolase (MTHase) work together to produce trehalose. MTSase is responsible for converting the alpha-1,4-glucosidic linkage to an alpha,alpha-1,1-...; Region: MTHase_N_term; cd02853 887061007127 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 887061007128 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061007129 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 887061007130 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 887061007131 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061007132 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 887061007133 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061007134 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...; Region: HIT_like; cl00228 887061007135 nucleotide binding site/active site [active] 887061007136 HIT family signature motif; other site 887061007137 catalytic residue [active] 887061007138 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:; Region: TRX_Fd_family; cd02980 887061007139 dimer interface [polypeptide binding]; other site 887061007140 [2Fe-2S] cluster binding site [ion binding]; other site 887061007141 Gram-negative bacterial tonB protein; Region: TonB; cl10048 887061007142 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 887061007143 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 887061007144 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061007145 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 887061007146 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 887061007147 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 887061007148 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061007149 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 887061007150 N-terminal plug; other site 887061007151 ligand-binding site [chemical binding]; other site 887061007152 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 887061007153 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 887061007154 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 887061007155 substrate binding pocket [chemical binding]; other site 887061007156 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 887061007157 B12 binding site [chemical binding]; other site 887061007158 cobalt ligand [ion binding]; other site 887061007159 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 887061007160 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_2; cd02433 887061007161 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 887061007162 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061007163 Membrane fusogenic activity; Region: BMFP; cl01115 887061007164 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 887061007165 Nitrogen regulatory protein P-II; Region: P-II; cl00412 887061007166 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 887061007167 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 887061007168 Glutamate-cysteine ligase; Region: GshA; pfam08886 887061007169 glutathione synthetase; Provisional; Region: PRK05246 887061007170 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 887061007171 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 887061007172 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 887061007173 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 887061007174 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 887061007175 Prokaryotic N-terminal methylation motif; Region: N_methyl; cl06830 887061007176 Type II transport protein GspH; Region: GspH; pfam12019 887061007177 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 887061007178 diaminopimelate decarboxylase; Region: lysA; TIGR01048 887061007179 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 887061007180 active site 887061007181 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 887061007182 substrate binding site [chemical binding]; other site 887061007183 catalytic residues [active] 887061007184 dimer interface [polypeptide binding]; other site 887061007185 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 887061007186 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 887061007187 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 887061007188 putative active site [active] 887061007189 putative substrate binding site [chemical binding]; other site 887061007190 putative cosubstrate binding site; other site 887061007191 catalytic site [active] 887061007192 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; cl01368 887061007193 CobD/Cbib protein; Region: CobD_Cbib; cl00561 887061007194 LytB protein; Region: LYTB; cl00507 887061007195 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 887061007196 DoxX; Region: DoxX; cl00976 887061007197 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061007198 Coenzyme A binding pocket [chemical binding]; other site 887061007199 Formaldehyde-activating enzyme (Fae); Region: Fae; cl00774 887061007200 putative transporter; Provisional; Region: PRK11660 887061007201 Sulfate transporter family; Region: Sulfate_transp; cl00967 887061007202 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 887061007203 adenine DNA glycosylase; Provisional; Region: PRK10880 887061007204 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 887061007205 minor groove reading motif; other site 887061007206 helix-hairpin-helix signature motif; other site 887061007207 substrate binding pocket [chemical binding]; other site 887061007208 active site 887061007209 FES domain; Region: FES; smart00525 887061007210 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 887061007211 DNA binding and oxoG recognition site [nucleotide binding] 887061007212 AsmA family; Region: AsmA; pfam05170 887061007213 putative assembly protein; Provisional; Region: PRK10833 887061007214 AsmA family; Region: AsmA; pfam05170 887061007215 Predicted membrane protein [Function unknown]; Region: COG3164 887061007216 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 887061007217 Bacitracin resistance protein BacA; Region: BacA; cl00858 887061007218 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 887061007219 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 887061007220 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 887061007221 RNA binding surface [nucleotide binding]; other site 887061007222 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PSSA_1; cd02555 887061007223 active site 887061007224 ThiC family; Region: ThiC; cl08031 887061007225 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 887061007226 TPR motif; other site 887061007227 binding surface 887061007228 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 887061007229 classical (c) SDRs; Region: SDR_c; cd05233 887061007230 NAD(P) binding site [chemical binding]; other site 887061007231 active site 887061007232 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 887061007233 heme binding pocket [chemical binding]; other site 887061007234 heme ligand [chemical binding]; other site 887061007235 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 887061007236 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 887061007237 Thermostable hemolysin; Region: T_hemolysin; pfam12261 887061007238 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 trans-...; Region: HisKA; cd00082 887061007239 dimer interface [polypeptide binding]; other site 887061007240 phosphorylation site [posttranslational modification] 887061007241 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 887061007242 ATP binding site [chemical binding]; other site 887061007243 Mg2+ binding site [ion binding]; other site 887061007244 G-X-G motif; other site 887061007245 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061007246 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 887061007247 active site 887061007248 phosphorylation site [posttranslational modification] 887061007249 intermolecular recognition site; other site 887061007250 dimerization interface [polypeptide binding]; other site 887061007251 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...; Region: AAA; cd00009 887061007252 Walker A motif; other site 887061007253 ATP binding site [chemical binding]; other site 887061007254 Walker B motif; other site 887061007255 arginine finger; other site 887061007256 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 887061007257 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 887061007258 S-adenosylmethionine binding site [chemical binding]; other site 887061007259 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 887061007260 Isochorismatase family; Region: Isochorismatase; pfam00857 887061007261 catalytic triad [active] 887061007262 dimer interface [polypeptide binding]; other site 887061007263 conserved cis-peptide bond; other site 887061007264 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 887061007265 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 887061007266 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 887061007267 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 887061007268 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 887061007269 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 887061007270 active site 887061007271 dimer interface [polypeptide binding]; other site 887061007272 effector binding site; other site 887061007273 TSCPD domain; Region: TSCPD; cl14834 887061007274 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 887061007275 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 887061007276 putative substrate translocation pore; other site 887061007277 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 887061007278 Sodium / potassium ATPase beta chain; Region: Na_K-ATPase; cl08255 887061007279 Pilin (bacterial filament); Region: Pilin; pfam00114 887061007280 Protein of unknown function (DUF3604); Region: DUF3604; pfam12228 887061007281 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061007282 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...; Region: TM_PBP2; cd06261 887061007283 dimer interface [polypeptide binding]; other site 887061007284 conserved gate region; other site 887061007285 putative PBP binding loops; other site 887061007286 ABC-ATPase subunit interface; other site 887061007287 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 887061007288 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 887061007289 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061007290 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 887061007291 Walker A/P-loop; other site 887061007292 ATP binding site [chemical binding]; other site 887061007293 Q-loop/lid; other site 887061007294 ABC transporter signature motif; other site 887061007295 Walker B; other site 887061007296 D-loop; other site 887061007297 H-loop/switch region; other site 887061007298 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 887061007299 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061007300 DNA-binding site [nucleotide binding]; DNA binding site 887061007301 UTRA domain; Region: UTRA; cl06649 887061007302 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 887061007303 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 887061007304 DGQHR domain; Region: DGQHR; cl14002 887061007305 Cupin domain; Region: Cupin_2; cl09118 887061007306 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007307 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 887061007308 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007309 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 887061007310 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 887061007311 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 887061007312 Acyl transferase domain; Region: Acyl_transf_1; cl08282 887061007313 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061007314 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061007315 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061007316 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007317 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_2; cd08471 887061007318 putative effector binding pocket; other site 887061007319 putative dimerization interface [polypeptide binding]; other site 887061007320 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 887061007321 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 887061007322 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 887061007323 DNA-binding site [nucleotide binding]; DNA binding site 887061007324 RNA-binding motif; other site 887061007325 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 887061007326 BON domain; Region: BON; cl02771 887061007327 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 887061007328 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061007329 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 887061007330 ligand binding site [chemical binding]; other site 887061007331 flexible hinge region; other site 887061007332 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007333 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 887061007334 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 887061007335 active site 887061007336 phosphorylation site [posttranslational modification] 887061007337 intermolecular recognition site; other site 887061007338 dimerization interface [polypeptide binding]; other site 887061007339 PAS domain S-box; Region: sensory_box; TIGR00229 887061007340 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 887061007341 putative active site [active] 887061007342 heme pocket [chemical binding]; other site 887061007343 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007344 metal binding site [ion binding]; metal-binding site 887061007345 active site 887061007346 I-site; other site 887061007347 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061007348 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 887061007349 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007350 Uncharacterized protein conserved in bacteria (DUF2329); Region: DUF2329; pfam10091 887061007351 Putative carbohydrate binding domain; Region: CBM_X; pfam06204 887061007352 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 887061007353 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 887061007354 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 887061007355 Putative carbohydrate binding domain; Region: CBM_X; pfam06204 887061007356 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 887061007357 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 887061007358 Transcriptional regulators [Transcription]; Region: MarR; COG1846 887061007359 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007360 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 887061007361 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 887061007362 FAD binding pocket [chemical binding]; other site 887061007363 FAD binding motif [chemical binding]; other site 887061007364 phosphate binding motif [ion binding]; other site 887061007365 NAD binding pocket [chemical binding]; other site 887061007366 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 887061007367 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061007368 putative active site [active] 887061007369 heme pocket [chemical binding]; other site 887061007370 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 887061007371 putative active site [active] 887061007372 heme pocket [chemical binding]; other site 887061007373 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 887061007374 PAS fold; Region: PAS_4; pfam08448 887061007375 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 887061007376 putative active site [active] 887061007377 heme pocket [chemical binding]; other site 887061007378 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007379 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007380 PAS fold; Region: PAS_4; pfam08448 887061007381 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 887061007382 putative active site [active] 887061007383 heme pocket [chemical binding]; other site 887061007384 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 887061007385 putative active site [active] 887061007386 heme pocket [chemical binding]; other site 887061007387 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 887061007388 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 887061007389 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061007390 DNA-binding site [nucleotide binding]; DNA binding site 887061007391 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 887061007392 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061007393 homodimer interface [polypeptide binding]; other site 887061007394 catalytic residue [active] 887061007395 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 887061007396 Outer membrane efflux protein; Region: OEP; pfam02321 887061007397 Outer membrane efflux protein; Region: OEP; pfam02321 887061007398 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 887061007399 Protein export membrane protein; Region: SecD_SecF; cl14618 887061007400 Protein export membrane protein; Region: SecD_SecF; cl14618 887061007401 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 887061007402 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061007403 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007404 metal binding site [ion binding]; metal-binding site 887061007405 active site 887061007406 I-site; other site 887061007407 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 887061007408 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 887061007409 putative heme binding pocket [chemical binding]; other site 887061007410 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007411 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007412 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 887061007413 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007414 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061007415 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007416 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 887061007417 dimerization interface [polypeptide binding]; other site 887061007418 Pirin-related protein [General function prediction only]; Region: COG1741 887061007419 Cupin domain; Region: Cupin_2; cl09118 887061007420 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 887061007421 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 887061007422 NADP binding site [chemical binding]; other site 887061007423 Isochorismatase family; Region: Isochorismatase; pfam00857 887061007424 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 887061007425 catalytic triad [active] 887061007426 dimer interface [polypeptide binding]; other site 887061007427 conserved cis-peptide bond; other site 887061007428 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 887061007429 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 887061007430 active site 887061007431 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 887061007432 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 887061007433 putative substrate translocation pore; other site 887061007434 Protein of unknown function (DUF1427); Region: DUF1427; cl01771 887061007435 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...; Region: Peptidase_M17; cl08294 887061007436 LysR family transcriptional regulator; Provisional; Region: PRK14997 887061007437 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007438 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 887061007439 putative effector binding pocket; other site 887061007440 dimerization interface [polypeptide binding]; other site 887061007441 C-term; Region: GreA_GreB; pfam01272 887061007442 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061007443 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 887061007444 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061007445 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061007446 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 887061007447 metal ion-dependent adhesion site (MIDAS); other site 887061007448 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 887061007449 metal ion-dependent adhesion site (MIDAS); other site 887061007450 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 887061007451 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 887061007452 putative NAD(P) binding site [chemical binding]; other site 887061007453 dimer interface [polypeptide binding]; other site 887061007454 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061007455 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007456 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 887061007457 putative effector binding pocket; other site 887061007458 dimerization interface [polypeptide binding]; other site 887061007459 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl01961 887061007460 PAS fold; Region: PAS_3; pfam08447 887061007461 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 887061007462 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007463 metal binding site [ion binding]; metal-binding site 887061007464 active site 887061007465 I-site; other site 887061007466 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 887061007467 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 887061007468 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 887061007469 active site 887061007470 phosphorylation site [posttranslational modification] 887061007471 intermolecular recognition site; other site 887061007472 dimerization interface [polypeptide binding]; other site 887061007473 CheB methylesterase; Region: CheB_methylest; pfam01339 887061007474 CheD chemotactic sensory transduction; Region: CheD; cl00810 887061007475 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 887061007476 Methyltransferase, chemotaxis proteins; Region: MeTrc; smart00138 887061007477 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; cl12011 887061007478 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 887061007479 putative CheA interaction surface; other site 887061007480 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007481 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061007482 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007483 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 887061007484 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 887061007485 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061007486 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 connected by an extended linker. The...; Region: HAMP; cl01054 887061007487 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007488 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061007489 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007490 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 887061007491 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 887061007492 putative CheA interaction surface; other site 887061007493 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061007494 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007495 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_2; pfam12729 887061007496 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007497 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 887061007498 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 887061007499 putative binding surface; other site 887061007500 active site 887061007501 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 887061007502 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 887061007503 ATP binding site [chemical binding]; other site 887061007504 Mg2+ binding site [ion binding]; other site 887061007505 G-X-G motif; other site 887061007506 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 887061007507 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 887061007508 anti sigma factor interaction site; other site 887061007509 regulatory phosphorylation site [posttranslational modification]; other site 887061007510 Response regulator receiver domain; Region: Response_reg; pfam00072 887061007511 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 887061007512 active site 887061007513 phosphorylation site [posttranslational modification] 887061007514 intermolecular recognition site; other site 887061007515 dimerization interface [polypeptide binding]; other site 887061007516 Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These...; Region: TarH; cl00144 887061007517 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 887061007518 DNA-binding transcriptional regulator EnvR; Provisional; Region: PRK09975 887061007519 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061007520 PAS domain S-box; Region: sensory_box; TIGR00229 887061007521 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 887061007522 putative active site [active] 887061007523 heme pocket [chemical binding]; other site 887061007524 PAS fold; Region: PAS_4; pfam08448 887061007525 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 887061007526 putative active site [active] 887061007527 heme pocket [chemical binding]; other site 887061007528 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007529 metal binding site [ion binding]; metal-binding site 887061007530 active site 887061007531 I-site; other site 887061007532 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 887061007533 Protein of unknown function, DUF399; Region: DUF399; cl01139 887061007534 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 887061007535 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 887061007536 classical (c) SDRs; Region: SDR_c; cd05233 887061007537 NAD(P) binding site [chemical binding]; other site 887061007538 active site 887061007539 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 887061007540 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 887061007541 conserved cys residue [active] 887061007542 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007543 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 887061007544 PAS fold; Region: PAS_3; pfam08447 887061007545 putative active site [active] 887061007546 heme pocket [chemical binding]; other site 887061007547 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007548 metal binding site [ion binding]; metal-binding site 887061007549 active site 887061007550 I-site; other site 887061007551 Protein of unknown function DUF45; Region: DUF45; cl00636 887061007552 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 887061007553 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...; Region: PBPb; cd00134 887061007554 substrate binding pocket [chemical binding]; other site 887061007555 membrane-bound complex binding site; other site 887061007556 hinge residues; other site 887061007557 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 887061007558 PAS fold; Region: PAS_3; pfam08447 887061007559 putative active site [active] 887061007560 heme pocket [chemical binding]; other site 887061007561 PAS fold; Region: PAS_4; pfam08448 887061007562 PAS domain S-box; Region: sensory_box; TIGR00229 887061007563 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 887061007564 putative active site [active] 887061007565 heme pocket [chemical binding]; other site 887061007566 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007567 metal binding site [ion binding]; metal-binding site 887061007568 active site 887061007569 I-site; other site 887061007570 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 887061007571 transcriptional regulator; Provisional; Region: PRK10632 887061007572 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 887061007573 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 887061007574 putative effector binding pocket; other site 887061007575 putative dimerization interface [polypeptide binding]; other site 887061007576 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 887061007577 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061007578 NAD(P) binding site [chemical binding]; other site 887061007579 active site 887061007580 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 887061007581 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 887061007582 active site residue [active] 887061007583 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 887061007584 MgtC family; Region: MgtC; cl12207 887061007585 putative chaperone; Provisional; Region: PRK11678 887061007586 Putative exonuclease, RdgC; Region: RdgC; cl01122 887061007587 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061007588 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 887061007589 Uncharacterized conserved protein [Function unknown]; Region: COG0397; cl00428 887061007590 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; pfam02696 887061007591 Sel1 repeat; Region: Sel1; cl02723 887061007592 Sel1 repeat; Region: Sel1; cl02723 887061007593 Sel1 repeat; Region: Sel1; cl02723 887061007594 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 887061007595 Domain of unknown function DUF21; Region: DUF21; pfam01595 887061007596 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 887061007597 Transporter associated domain; Region: CorC_HlyC; pfam03471 887061007598 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 887061007599 DNA-binding site [nucleotide binding]; DNA binding site 887061007600 RNA-binding motif; other site 887061007601 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 887061007602 rRNA binding site [nucleotide binding]; other site 887061007603 predicted 30S ribosome binding site; other site 887061007604 Cupin domain; Region: Cupin_2; cl09118 887061007605 Helix-turn-helix domain; Region: HTH_18; pfam12833 887061007606 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061007607 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 887061007608 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 887061007609 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 887061007610 binding surface 887061007611 TPR motif; other site 887061007612 AsmA family; Region: AsmA; pfam05170 887061007613 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 887061007614 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 887061007615 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 887061007616 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061007617 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061007618 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...; Region: Sigma70_r4; cl01055 887061007619 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061007620 FecR protein; Region: FecR; pfam04773 887061007621 Secretin and TonB N terminus short domain; Region: STN; pfam07660 887061007622 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 887061007623 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 887061007624 N-terminal plug; other site 887061007625 ligand-binding site [chemical binding]; other site 887061007626 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061007627 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 887061007628 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 higher-...; Region: HU_IHF; cd00591 887061007629 IHF dimer interface [polypeptide binding]; other site 887061007630 IHF - DNA interface [nucleotide binding]; other site 887061007631 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061007632 putative cation:proton antiport protein; Provisional; Region: PRK10669 887061007633 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 887061007634 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061007635 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 887061007636 putative substrate binding site [chemical binding]; other site 887061007637 putative ATP binding site [chemical binding]; other site 887061007638 sucrose-phosphate synthase, putative, glycosyltransferase domain; Region: sucr_P_syn_N; TIGR02472 887061007639 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 887061007640 putative ADP-binding pocket [chemical binding]; other site 887061007641 sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial; Region: sucr_syn_bact_C; TIGR02471 887061007642 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; cl11391 887061007643 active site 887061007644 motif I; other site 887061007645 motif II; other site 887061007646 trehalose synthase; Region: treS_nterm; TIGR02456 887061007647 Alpha amylase, catalytic domain; Region: Alpha-amylase; cl07893 887061007648 Mechanosensitive ion channel; Region: MS_channel; pfam00924 887061007649 H+ Antiporter protein; Region: 2A0121; TIGR00900 887061007650 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 887061007651 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007652 metal binding site [ion binding]; metal-binding site 887061007653 active site 887061007654 I-site; other site 887061007655 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 887061007656 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007657 metal binding site [ion binding]; metal-binding site 887061007658 active site 887061007659 I-site; other site 887061007660 Uncharacterized protein conserved in bacteria (DUF2257); Region: DUF2257; cl01794 887061007661 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 887061007662 dimerization interface [polypeptide binding]; other site 887061007663 putative DNA binding site [nucleotide binding]; other site 887061007664 putative Zn2+ binding site [ion binding]; other site 887061007665 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 887061007666 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 887061007667 putative acyl-acceptor binding pocket; other site 887061007668 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 887061007669 lysophospholipid transporter LplT; Provisional; Region: PRK11195 887061007670 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 887061007671 putative substrate translocation pore; other site 887061007672 Entericidin EcnA/B family; Region: Entericidin; cl02322 887061007673 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061007674 DoxX; Region: DoxX; cl00976 887061007675 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 887061007676 putative active site [active] 887061007677 metal binding site [ion binding]; metal-binding site 887061007678 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 887061007679 MltA specific insert domain; Region: MltA; pfam03562 887061007680 3D domain; Region: 3D; cl01439 887061007681 Protein of unknown function (DUF525); Region: DUF525; cl01119 887061007682 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 887061007683 ThiS interaction site; other site 887061007684 putative active site [active] 887061007685 tetramer interface [polypeptide binding]; other site 887061007686 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 887061007687 thiS-thiF/thiG interaction site; other site 887061007688 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 887061007689 binding surface 887061007690 TPR motif; other site 887061007691 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 887061007692 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 887061007693 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061007694 catalytic residue [active] 887061007695 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 887061007696 dimer interface [polypeptide binding]; other site 887061007697 active site 887061007698 CoA binding pocket [chemical binding]; other site 887061007699 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 887061007700 classical (c) SDRs; Region: SDR_c; cd05233 887061007701 NAD(P) binding site [chemical binding]; other site 887061007702 active site 887061007703 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 887061007704 classical (c) SDRs; Region: SDR_c; cd05233 887061007705 NAD(P) binding site [chemical binding]; other site 887061007706 active site 887061007707 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 887061007708 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 887061007709 putative trimer interface [polypeptide binding]; other site 887061007710 putative CoA binding site [chemical binding]; other site 887061007711 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; cl12011 887061007712 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 887061007713 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 887061007714 [2Fe-2S] cluster binding site [ion binding]; other site 887061007715 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 887061007716 alpha subunit interface [polypeptide binding]; other site 887061007717 active site 887061007718 substrate binding site [chemical binding]; other site 887061007719 Fe binding site [ion binding]; other site 887061007720 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 887061007721 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 887061007722 putative trimer interface [polypeptide binding]; other site 887061007723 putative CoA binding site [chemical binding]; other site 887061007724 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 887061007725 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 887061007726 [2Fe-2S] cluster binding site [ion binding]; other site 887061007727 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 887061007728 alpha subunit interface [polypeptide binding]; other site 887061007729 active site 887061007730 substrate binding site [chemical binding]; other site 887061007731 Fe binding site [ion binding]; other site 887061007732 CsbD-like; Region: CsbD; cl01272 887061007733 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 887061007734 active site 887061007735 substrate binding site [chemical binding]; other site 887061007736 catalytic site [active] 887061007737 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 887061007738 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 887061007739 Rubredoxin [Energy production and conversion]; Region: COG1773 887061007740 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They...; Region: rubredoxin; cd00730 887061007741 iron binding site [ion binding]; other site 887061007742 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed; Region: PRK06427 887061007743 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 887061007744 dimer interface [polypeptide binding]; other site 887061007745 substrate binding site [chemical binding]; other site 887061007746 ATP binding site [chemical binding]; other site 887061007747 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- (beta-...; Region: TMP_TenI; cd00564 887061007748 thiamine phosphate binding site [chemical binding]; other site 887061007749 active site 887061007750 pyrophosphate binding site [ion binding]; other site 887061007751 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 887061007752 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 887061007753 inhibitor-cofactor binding pocket; inhibition site 887061007754 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061007755 catalytic residue [active] 887061007756 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 887061007757 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 N-...; Region: GltS; cd00713 887061007758 active site 887061007759 dimer interface [polypeptide binding]; other site 887061007760 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 887061007761 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...; Region: GltS_FMN; cd02808 887061007762 active site 887061007763 FMN binding site [chemical binding]; other site 887061007764 substrate binding site [chemical binding]; other site 887061007765 3Fe-4S cluster binding site [ion binding]; other site 887061007766 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 887061007767 domain interface; other site 887061007768 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 887061007769 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 887061007770 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 887061007771 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...; Region: URO-D; cd00717 887061007772 substrate binding site [chemical binding]; other site 887061007773 active site 887061007774 primosome assembly protein PriA; Validated; Region: PRK05580 887061007775 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 887061007776 ATP binding site [chemical binding]; other site 887061007777 putative Mg++ binding site [ion binding]; other site 887061007778 Hydrogenase expression/synthesis hypA family; Region: HypA; cl00418 887061007779 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; cl14882 887061007780 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 887061007781 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 887061007782 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 887061007783 active site 887061007784 HIGH motif; other site 887061007785 KMSK motif region; other site 887061007786 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 887061007787 tRNA binding surface [nucleotide binding]; other site 887061007788 anticodon binding site; other site 887061007789 Sporulation related domain; Region: SPOR; cl10051 887061007790 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 887061007791 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 887061007792 catalytic residues [active] 887061007793 hinge region; other site 887061007794 alpha helical domain; other site 887061007795 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 887061007796 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061007797 NAD(P) binding site [chemical binding]; other site 887061007798 active site 887061007799 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 887061007800 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061007801 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 887061007802 putative active site [active] 887061007803 heme pocket [chemical binding]; other site 887061007804 PAS fold; Region: PAS_4; pfam08448 887061007805 PAS fold; Region: PAS_4; pfam08448 887061007806 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007807 metal binding site [ion binding]; metal-binding site 887061007808 active site 887061007809 I-site; other site 887061007810 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 887061007811 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 887061007812 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...; Region: GFAT; cd00714 887061007813 glutaminase active site [active] 887061007814 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 887061007815 dimer interface [polypeptide binding]; other site 887061007816 active site 887061007817 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 887061007818 dimer interface [polypeptide binding]; other site 887061007819 active site 887061007820 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 887061007821 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 887061007822 Substrate binding site [chemical binding]; other site 887061007823 Mg++ binding site [ion binding]; other site 887061007824 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 887061007825 active site 887061007826 substrate binding site [chemical binding]; other site 887061007827 CoA binding site [chemical binding]; other site 887061007828 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 887061007829 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 887061007830 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 887061007831 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 887061007832 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 887061007833 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 887061007834 alpha subunit interaction interface [polypeptide binding]; other site 887061007835 Walker A motif; other site 887061007836 ATP binding site [chemical binding]; other site 887061007837 Walker B motif; other site 887061007838 inhibitor binding site; inhibition site 887061007839 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 887061007840 ATP synthase; Region: ATP-synt; cl00365 887061007841 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 887061007842 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 887061007843 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 887061007844 beta subunit interaction interface [polypeptide binding]; other site 887061007845 Walker A motif; other site 887061007846 ATP binding site [chemical binding]; other site 887061007847 Walker B motif; other site 887061007848 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 887061007849 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 887061007850 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 887061007851 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 887061007852 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 887061007853 ATP synthase A chain; Region: ATP-synt_A; cl00413 887061007854 ParB-like partition proteins; Region: parB_part; TIGR00180 887061007855 ParB-like nuclease domain; Region: ParBc; cl02129 887061007856 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 887061007857 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...; Region: ParA; cd02042 887061007858 P-loop; other site 887061007859 Magnesium ion binding site [ion binding]; other site 887061007860 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...; Region: ParA; cd02042 887061007861 Magnesium ion binding site [ion binding]; other site 887061007862 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 887061007863 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; cl12011 887061007864 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 887061007865 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 887061007866 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 887061007867 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 887061007868 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 887061007869 G1 box; other site 887061007870 GTP/Mg2+ binding site [chemical binding]; other site 887061007871 Switch I region; other site 887061007872 G2 box; other site 887061007873 Switch II region; other site 887061007874 G3 box; other site 887061007875 G4 box; other site 887061007876 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 887061007877 membrane protein insertase; Provisional; Region: PRK01318 887061007878 60Kd inner membrane protein; Region: 60KD_IMP; cl00489