-- dump date 20140619_145445 -- class Genbank::misc_feature -- table misc_feature_note -- id note 887061000001 DnaA N-terminal domain; Region: DnaA_N; pfam11638 887061000002 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 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 ABC; 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 trimeric...; 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; cd00075 887061000018 Mg2+ binding site [ion binding]; other site 887061000019 G-X-G motif; other site 887061000020 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 887061000021 anchoring element; other site 887061000022 dimer interface [polypeptide binding]; other site 887061000023 ATP binding site [chemical binding]; other site 887061000024 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 887061000025 active site 887061000026 putative metal-binding site [ion binding]; other site 887061000027 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 887061000028 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 887061000029 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 887061000030 HflX GTPase family; Region: HflX; cd01878 887061000031 G1 box; other site 887061000032 GTP/Mg2+ binding site [chemical binding]; other site 887061000033 Switch I region; other site 887061000034 G2 box; other site 887061000035 G3 box; other site 887061000036 Switch II region; other site 887061000037 G4 box; other site 887061000038 G5 box; other site 887061000039 Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms / Cell division and chromosome partitioning]; Region: RIO1; COG1718 887061000040 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 887061000041 ATP binding site [chemical binding]; other site 887061000042 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 887061000043 chromosome condensation membrane protein; Provisional; Region: PRK14196 887061000044 Glycine-zipper containing OmpA-like membrane domain; Region: Gly-zipper_OmpA; pfam13436 887061000045 malate:quinone oxidoreductase; Validated; Region: PRK05257 887061000046 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 887061000047 Glycosyl hydrolases family 2, sugar binding domain; Region: Glyco_hydro_2_N; pfam02837 887061000048 Glycosyl hydrolases family 2; Region: Glyco_hydro_2; pfam00703 887061000049 Glycosyl hydrolases family 2, TIM barrel domain; Region: Glyco_hydro_2_C; pfam02836 887061000050 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 887061000051 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 887061000052 putative substrate translocation pore; other site 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; cd00130 887061000055 putative active site [active] 887061000056 heme pocket [chemical binding]; other site 887061000057 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061000058 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 887061000059 putative active site [active] 887061000060 heme pocket [chemical binding]; other site 887061000061 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 887061000062 putative active site [active] 887061000063 heme pocket [chemical binding]; other site 887061000064 PAS fold; Region: PAS_4; pfam08448 887061000065 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 887061000066 putative active site [active] 887061000067 heme pocket [chemical binding]; other site 887061000068 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 887061000069 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 887061000070 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 887061000071 PAS domain; Region: PAS_9; pfam13426 887061000072 putative active site [active] 887061000073 heme pocket [chemical binding]; other site 887061000074 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061000075 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061000076 metal binding site [ion binding]; metal-binding site 887061000077 active site 887061000078 I-site; other site 887061000079 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 887061000080 Cytochrome c; Region: Cytochrom_C; cl11414 887061000081 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061000082 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 887061000083 Trp docking motif [polypeptide binding]; other site 887061000084 dimer interface [polypeptide binding]; other site 887061000085 active site 887061000086 small subunit binding site [polypeptide binding]; other site 887061000087 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 887061000088 GAF domain; Region: GAF; pfam01590 887061000089 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061000090 Walker A motif; other site 887061000091 ATP binding site [chemical binding]; other site 887061000092 Walker B motif; other site 887061000093 arginine finger; other site 887061000094 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061000095 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 887061000096 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061000097 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 887061000098 dimerization interface [polypeptide binding]; other site 887061000099 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061000100 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 887061000101 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 887061000102 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 887061000103 S-adenosylmethionine binding site [chemical binding]; other site 887061000104 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 887061000105 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061000106 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 887061000107 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 887061000108 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 887061000109 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 887061000110 carboxyltransferase (CT) interaction site; other site 887061000111 biotinylation site [posttranslational modification]; other site 887061000112 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 887061000113 Dehydroquinase class II; Region: DHquinase_II; pfam01220 887061000114 trimer interface [polypeptide binding]; other site 887061000115 active site 887061000116 dimer interface [polypeptide binding]; other site 887061000117 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 887061000118 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 887061000119 catalytic residues [active] 887061000120 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 887061000121 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 887061000122 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 887061000123 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 887061000124 DsbD alpha interface [polypeptide binding]; other site 887061000125 catalytic residues [active] 887061000126 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 887061000127 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 887061000128 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 887061000129 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 887061000130 catalytic loop [active] 887061000131 iron binding site [ion binding]; other site 887061000132 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 887061000133 FAD binding pocket [chemical binding]; other site 887061000134 FAD binding motif [chemical binding]; other site 887061000135 phosphate binding motif [ion binding]; other site 887061000136 beta-alpha-beta structure motif; other site 887061000137 NAD binding pocket [chemical binding]; other site 887061000138 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 887061000139 HemY protein N-terminus; Region: HemY_N; pfam07219 887061000140 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 887061000141 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 887061000142 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 887061000143 active site 887061000144 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 887061000145 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 887061000146 domain interfaces; other site 887061000147 active site 887061000148 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 887061000149 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061000150 active site 887061000151 phosphorylation site [posttranslational modification] 887061000152 intermolecular recognition site; other site 887061000153 dimerization interface [polypeptide binding]; other site 887061000154 LytTr DNA-binding domain; Region: LytTR; smart00850 887061000155 Histidine kinase; Region: His_kinase; pfam06580 887061000156 argininosuccinate lyase; Provisional; Region: PRK00855 887061000157 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 887061000158 active sites [active] 887061000159 tetramer interface [polypeptide binding]; other site 887061000160 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 887061000161 cellulose synthase catalytic subunit (UDP-forming); Region: CelA; TIGR03030 887061000162 CESA_CelA_like are involved in the elongation of the glucan chain of cellulose; Region: CESA_CelA_like; cd06421 887061000163 DXD motif; other site 887061000164 PilZ domain; Region: PilZ; pfam07238 887061000165 Bacterial cellulose synthase subunit; Region: BcsB; pfam03170 887061000166 cyclase homology domain; Region: CHD; cd07302 887061000167 metal binding site [ion binding]; metal-binding site 887061000168 Glycosyl hydrolases family 8; Region: Glyco_hydro_8; cl01351 887061000169 Cellulose synthase operon protein C C-terminus (BCSC_C); Region: BCSC_C; pfam05420 887061000170 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 887061000171 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 887061000172 FeS/SAM binding site; other site 887061000173 HemN C-terminal domain; Region: HemN_C; pfam06969 887061000174 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 887061000175 active site 887061000176 dimerization interface [polypeptide binding]; other site 887061000177 ribonuclease PH; Reviewed; Region: rph; PRK00173 887061000178 Ribonuclease PH; Region: RNase_PH_bact; cd11362 887061000179 hexamer interface [polypeptide binding]; other site 887061000180 active site 887061000181 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 887061000182 active site 887061000183 Protein kinase domain; Region: Pkinase; pfam00069 887061000184 Catalytic domain of Protein Kinases; Region: PKc; cd00180 887061000185 active site 887061000186 ATP binding site [chemical binding]; other site 887061000187 substrate binding site [chemical binding]; other site 887061000188 activation loop (A-loop); other site 887061000189 hypothetical protein; Provisional; Region: PRK11820 887061000190 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 887061000191 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 887061000192 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 887061000193 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 887061000194 catalytic site [active] 887061000195 G-X2-G-X-G-K; other site 887061000196 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 887061000197 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 887061000198 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061000199 Zn2+ binding site [ion binding]; other site 887061000200 Mg2+ binding site [ion binding]; other site 887061000201 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 887061000202 synthetase active site [active] 887061000203 NTP binding site [chemical binding]; other site 887061000204 metal binding site [ion binding]; metal-binding site 887061000205 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 887061000206 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 887061000207 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 887061000208 homotrimer interaction site [polypeptide binding]; other site 887061000209 putative active site [active] 887061000210 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 887061000211 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 887061000212 generic binding surface II; other site 887061000213 ssDNA binding site; other site 887061000214 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 887061000215 ATP binding site [chemical binding]; other site 887061000216 putative Mg++ binding site [ion binding]; other site 887061000217 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 887061000218 nucleotide binding region [chemical binding]; other site 887061000219 ATP-binding site [chemical binding]; other site 887061000220 Chorismate lyase; Region: Chor_lyase; cl01230 887061000221 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 887061000222 UbiA prenyltransferase family; Region: UbiA; pfam01040 887061000223 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 887061000224 23S rRNA interface [nucleotide binding]; other site 887061000225 L3 interface [polypeptide binding]; other site 887061000226 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 887061000227 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 887061000228 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 887061000229 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 887061000230 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 887061000231 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 887061000232 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 887061000233 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 887061000234 dimer interface [polypeptide binding]; other site 887061000235 active site 887061000236 citrylCoA binding site [chemical binding]; other site 887061000237 NADH binding [chemical binding]; other site 887061000238 cationic pore residues; other site 887061000239 oxalacetate/citrate binding site [chemical binding]; other site 887061000240 coenzyme A binding site [chemical binding]; other site 887061000241 catalytic triad [active] 887061000242 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 887061000243 putative peptidase; Provisional; Region: PRK11649 887061000244 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061000245 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 887061000246 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 887061000247 active site 887061000248 HIGH motif; other site 887061000249 dimer interface [polypeptide binding]; other site 887061000250 KMSKS motif; other site 887061000251 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 887061000252 RNA binding surface [nucleotide binding]; other site 887061000253 ribosome maturation protein RimP; Reviewed; Region: PRK00092 887061000254 Sm and related proteins; Region: Sm_like; cl00259 887061000255 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 887061000256 putative oligomer interface [polypeptide binding]; other site 887061000257 putative RNA binding site [nucleotide binding]; other site 887061000258 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 887061000259 NusA N-terminal domain; Region: NusA_N; pfam08529 887061000260 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 887061000261 RNA binding site [nucleotide binding]; other site 887061000262 homodimer interface [polypeptide binding]; other site 887061000263 NusA-like KH domain; Region: KH_5; pfam13184 887061000264 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 887061000265 G-X-X-G motif; other site 887061000266 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 887061000267 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 887061000268 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 887061000269 translation initiation factor IF-2; Region: IF-2; TIGR00487 887061000270 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 887061000271 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 887061000272 G1 box; other site 887061000273 putative GEF interaction site [polypeptide binding]; other site 887061000274 GTP/Mg2+ binding site [chemical binding]; other site 887061000275 Switch I region; other site 887061000276 G2 box; other site 887061000277 G3 box; other site 887061000278 Switch II region; other site 887061000279 G4 box; other site 887061000280 G5 box; other site 887061000281 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 887061000282 Translation-initiation factor 2; Region: IF-2; pfam11987 887061000283 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 887061000284 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 887061000285 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 887061000286 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 887061000287 RNA binding site [nucleotide binding]; other site 887061000288 active site 887061000289 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 887061000290 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 887061000291 16S/18S rRNA binding site [nucleotide binding]; other site 887061000292 25S rRNA binding site [nucleotide binding]; other site 887061000293 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 887061000294 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 887061000295 RNase E interface [polypeptide binding]; other site 887061000296 trimer interface [polypeptide binding]; other site 887061000297 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 887061000298 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 887061000299 RNase E interface [polypeptide binding]; other site 887061000300 trimer interface [polypeptide binding]; other site 887061000301 active site 887061000302 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 887061000303 putative nucleic acid binding region [nucleotide binding]; other site 887061000304 G-X-X-G motif; other site 887061000305 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 887061000306 RNA binding site [nucleotide binding]; other site 887061000307 domain interface; other site 887061000308 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 887061000309 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 887061000310 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 887061000311 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 887061000312 homodimer interface [polypeptide binding]; other site 887061000313 NADP binding site [chemical binding]; other site 887061000314 substrate binding site [chemical binding]; other site 887061000315 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061000316 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061000317 active site 887061000318 phosphorylation site [posttranslational modification] 887061000319 intermolecular recognition site; other site 887061000320 dimerization interface [polypeptide binding]; other site 887061000321 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061000322 Walker A motif; other site 887061000323 ATP binding site [chemical binding]; other site 887061000324 Walker B motif; other site 887061000325 arginine finger; other site 887061000326 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061000327 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 887061000328 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DamX; COG3266 887061000329 Sporulation related domain; Region: SPOR; pfam05036 887061000330 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 887061000331 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 887061000332 Tetratricopeptide repeat; Region: TPR_16; pfam13432 887061000333 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 887061000334 TPR motif; other site 887061000335 binding surface 887061000336 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 887061000337 binding surface 887061000338 TPR motif; other site 887061000339 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 887061000340 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061000341 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 887061000342 Walker A motif; other site 887061000343 ATP binding site [chemical binding]; other site 887061000344 Walker B motif; other site 887061000345 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061000346 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061000347 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061000348 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 887061000349 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 887061000350 ATP binding site [chemical binding]; other site 887061000351 substrate interface [chemical binding]; other site 887061000352 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 887061000353 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 887061000354 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 887061000355 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 887061000356 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 887061000357 HIGH motif; other site 887061000358 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 887061000359 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 887061000360 active site 887061000361 KMSKS motif; other site 887061000362 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 887061000363 tRNA binding surface [nucleotide binding]; other site 887061000364 anticodon binding site; other site 887061000365 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 887061000366 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 887061000367 CPxP motif; other site 887061000368 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 887061000369 active site residue [active] 887061000370 Bacterial sugar transferase; Region: Bac_transf; pfam02397 887061000371 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 887061000372 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 887061000373 putative NAD(P) binding site [chemical binding]; other site 887061000374 active site 887061000375 putative substrate binding site [chemical binding]; other site 887061000376 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 887061000377 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 887061000378 active site 887061000379 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 887061000380 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 887061000381 Glycosyl hydrolase family 99-like domain of WbsX-like glycosyltransferases; Region: Glyco_tran_WbsX; cd11579 887061000382 putative ligand binding site [chemical binding]; other site 887061000383 putative catalytic site [active] 887061000384 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 887061000385 Methyltransferase domain; Region: Methyltransf_23; pfam13489 887061000386 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 887061000387 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 887061000388 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 887061000389 NADP-binding site; other site 887061000390 homotetramer interface [polypeptide binding]; other site 887061000391 substrate binding site [chemical binding]; other site 887061000392 homodimer interface [polypeptide binding]; other site 887061000393 active site 887061000394 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 887061000395 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 887061000396 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 887061000397 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 887061000398 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 887061000399 NADP-binding site; other site 887061000400 homotetramer interface [polypeptide binding]; other site 887061000401 substrate binding site [chemical binding]; other site 887061000402 homodimer interface [polypeptide binding]; other site 887061000403 active site 887061000404 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 887061000405 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061000406 Walker A motif; other site 887061000407 ATP binding site [chemical binding]; other site 887061000408 Walker B motif; other site 887061000409 arginine finger; other site 887061000410 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 887061000411 active site 887061000412 Class II Aldolase and Adducin N-terminal domain; Region: Aldolase_II; smart01007 887061000413 intersubunit interface [polypeptide binding]; other site 887061000414 Zn2+ binding site [ion binding]; other site 887061000415 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000416 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061000417 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000418 substrate binding pocket [chemical binding]; other site 887061000419 membrane-bound complex binding site; other site 887061000420 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061000421 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 887061000422 Walker A/P-loop; other site 887061000423 ATP binding site [chemical binding]; other site 887061000424 Q-loop/lid; other site 887061000425 ABC transporter signature motif; other site 887061000426 Walker B; other site 887061000427 D-loop; other site 887061000428 H-loop/switch region; other site 887061000429 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 887061000430 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 887061000431 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061000432 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 887061000433 TolR protein; Region: tolR; TIGR02801 887061000434 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061000435 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061000436 dimer interface [polypeptide binding]; other site 887061000437 conserved gate region; other site 887061000438 putative PBP binding loops; other site 887061000439 ABC-ATPase subunit interface; other site 887061000440 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061000441 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061000442 dimer interface [polypeptide binding]; other site 887061000443 conserved gate region; other site 887061000444 putative PBP binding loops; other site 887061000445 ABC-ATPase subunit interface; other site 887061000446 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000447 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 887061000448 Winged helix-turn helix; Region: HTH_29; pfam13551 887061000449 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061000450 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 887061000451 N-terminal plug; other site 887061000452 ligand-binding site [chemical binding]; other site 887061000453 choline dehydrogenase; Validated; Region: PRK02106 887061000454 lycopene cyclase; Region: lycopene_cycl; TIGR01789 887061000455 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 887061000456 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 887061000457 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 887061000458 NAD(P) binding site [chemical binding]; other site 887061000459 catalytic residues [active] 887061000460 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 887061000461 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061000462 putative substrate translocation pore; other site 887061000463 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 887061000464 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 887061000465 dimer interface [polypeptide binding]; other site 887061000466 decamer (pentamer of dimers) interface [polypeptide binding]; other site 887061000467 catalytic triad [active] 887061000468 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061000469 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 887061000470 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 887061000471 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 887061000472 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 887061000473 Walker A/P-loop; other site 887061000474 ATP binding site [chemical binding]; other site 887061000475 Q-loop/lid; other site 887061000476 ABC transporter signature motif; other site 887061000477 Walker B; other site 887061000478 D-loop; other site 887061000479 H-loop/switch region; other site 887061000480 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 887061000481 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 887061000482 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061000483 Walker A/P-loop; other site 887061000484 ATP binding site [chemical binding]; other site 887061000485 Q-loop/lid; other site 887061000486 ABC transporter signature motif; other site 887061000487 Walker B; other site 887061000488 D-loop; other site 887061000489 H-loop/switch region; other site 887061000490 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061000491 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 887061000492 N-terminal plug; other site 887061000493 ligand-binding site [chemical binding]; other site 887061000494 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 887061000495 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 887061000496 putative FMN binding site [chemical binding]; other site 887061000497 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 887061000498 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 887061000499 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 887061000500 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 887061000501 dimer interface [polypeptide binding]; other site 887061000502 active site 887061000503 non-prolyl cis peptide bond; other site 887061000504 insertion regions; other site 887061000505 PAS domain S-box; Region: sensory_box; TIGR00229 887061000506 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 887061000507 putative active site [active] 887061000508 heme pocket [chemical binding]; other site 887061000509 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 887061000510 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 887061000511 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061000512 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061000513 metal binding site [ion binding]; metal-binding site 887061000514 active site 887061000515 I-site; other site 887061000516 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 887061000517 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 887061000518 active site pocket [active] 887061000519 putative dimer interface [polypeptide binding]; other site 887061000520 putative cataytic base [active] 887061000521 cobalamin synthase; Reviewed; Region: cobS; PRK00235 887061000522 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 887061000523 catalytic core [active] 887061000524 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 887061000525 TPR motif; other site 887061000526 binding surface 887061000527 TPR repeat; Region: TPR_11; pfam13414 887061000528 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 887061000529 binding surface 887061000530 TPR motif; other site 887061000531 TPR repeat; Region: TPR_11; pfam13414 887061000532 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 887061000533 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 887061000534 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 887061000535 TPR motif; other site 887061000536 Tetratricopeptide repeat; Region: TPR_12; pfam13424 887061000537 binding surface 887061000538 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 887061000539 TPR motif; other site 887061000540 binding surface 887061000541 TPR repeat; Region: TPR_11; pfam13414 887061000542 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 887061000543 binding surface 887061000544 TPR motif; other site 887061000545 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 887061000546 TPR repeat; Region: TPR_11; pfam13414 887061000547 binding surface 887061000548 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 887061000549 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 887061000550 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 887061000551 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061000552 homodimer interface [polypeptide binding]; other site 887061000553 catalytic residue [active] 887061000554 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 887061000555 cobyric acid synthase; Provisional; Region: PRK00784 887061000556 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 887061000557 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 887061000558 catalytic triad [active] 887061000559 S4 domain; Region: S4_2; pfam13275 887061000560 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 887061000561 homotrimer interface [polypeptide binding]; other site 887061000562 Walker A motif; other site 887061000563 GTP binding site [chemical binding]; other site 887061000564 Walker B motif; other site 887061000565 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 887061000566 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 887061000567 cobalamin binding residues [chemical binding]; other site 887061000568 putative BtuC binding residues; other site 887061000569 dimer interface [polypeptide binding]; other site 887061000570 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)...; Region: BluB; cd02145 887061000571 putative FMN binding site [chemical binding]; other site 887061000572 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 887061000573 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 887061000574 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 887061000575 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 887061000576 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 887061000577 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 887061000578 catalytic triad [active] 887061000579 Cob(I)alamin adenosyltransferase N terminal; Region: Co_AT_N; pfam12557 887061000580 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 887061000581 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 887061000582 homodimer interface [polypeptide binding]; other site 887061000583 Walker A motif; other site 887061000584 ATP binding site [chemical binding]; other site 887061000585 hydroxycobalamin binding site [chemical binding]; other site 887061000586 Walker B motif; other site 887061000587 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 887061000588 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 887061000589 N-terminal plug; other site 887061000590 ligand-binding site [chemical binding]; other site 887061000591 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 887061000592 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 887061000593 N-terminal plug; other site 887061000594 ligand-binding site [chemical binding]; other site 887061000595 TIGR02449 family protein; Region: TIGR02449 887061000596 Cell division protein ZapA; Region: ZapA; pfam05164 887061000597 Uncharacterized protein conserved in bacteria (DUF2237); Region: DUF2237; pfam09996 887061000598 EVE domain; Region: EVE; cl00728 887061000599 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 887061000600 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 887061000601 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 887061000602 structural tetrad; other site 887061000603 threonine dehydratase; Reviewed; Region: PRK09224 887061000604 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 887061000605 tetramer interface [polypeptide binding]; other site 887061000606 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061000607 catalytic residue [active] 887061000608 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 887061000609 putative Ile/Val binding site [chemical binding]; other site 887061000610 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 887061000611 putative Ile/Val binding site [chemical binding]; other site 887061000612 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 887061000613 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061000614 active site 887061000615 dimer interface [polypeptide binding]; other site 887061000616 transcriptional regulator PhoU; Provisional; Region: PRK11115 887061000617 PhoU domain; Region: PhoU; pfam01895 887061000618 PhoU domain; Region: PhoU; pfam01895 887061000619 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 887061000620 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 887061000621 polyphosphate kinase; Provisional; Region: PRK05443 887061000622 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 887061000623 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 887061000624 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 887061000625 putative domain interface [polypeptide binding]; other site 887061000626 putative active site [active] 887061000627 catalytic site [active] 887061000628 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 887061000629 putative domain interface [polypeptide binding]; other site 887061000630 putative active site [active] 887061000631 catalytic site [active] 887061000632 oxidative damage protection protein; Provisional; Region: PRK05408 887061000633 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 887061000634 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 887061000635 N-terminal plug; other site 887061000636 ligand-binding site [chemical binding]; other site 887061000637 superoxide dismutase; Provisional; Region: PRK10543 887061000638 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 887061000639 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 887061000640 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 887061000641 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 887061000642 active site 887061000643 Int/Topo IB signature motif; other site 887061000644 Protein of unknown function, DUF484; Region: DUF484; cl17449 887061000645 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 887061000646 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 887061000647 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 887061000648 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 887061000649 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 887061000650 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 887061000651 putative acyl-acceptor binding pocket; other site 887061000652 S-adenosylmethionine synthetase; Validated; Region: PRK05250 887061000653 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 887061000654 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 887061000655 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 887061000656 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 887061000657 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 887061000658 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061000659 Zn2+ binding site [ion binding]; other site 887061000660 Mg2+ binding site [ion binding]; other site 887061000661 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 887061000662 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 887061000663 homotetramer interface [polypeptide binding]; other site 887061000664 ligand binding site [chemical binding]; other site 887061000665 catalytic site [active] 887061000666 NAD binding site [chemical binding]; other site 887061000667 Membrane protein of unknown function; Region: DUF360; cl00850 887061000668 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 887061000669 FAD binding site [chemical binding]; other site 887061000670 Protein of unknown function (DUF494); Region: DUF494; pfam04361 887061000671 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 887061000672 DNA protecting protein DprA; Region: dprA; TIGR00732 887061000673 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 887061000674 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 887061000675 active site 887061000676 catalytic residues [active] 887061000677 metal binding site [ion binding]; metal-binding site 887061000678 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 887061000679 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 887061000680 putative active site [active] 887061000681 substrate binding site [chemical binding]; other site 887061000682 putative cosubstrate binding site; other site 887061000683 catalytic site [active] 887061000684 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 887061000685 substrate binding site [chemical binding]; other site 887061000686 M48 family peptidase; Provisional; Region: PRK03001 887061000687 16S rRNA methyltransferase B; Provisional; Region: PRK10901 887061000688 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 887061000689 putative RNA binding site [nucleotide binding]; other site 887061000690 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 887061000691 S-adenosylmethionine binding site [chemical binding]; other site 887061000692 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 887061000693 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 887061000694 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061000695 dimerization interface [polypeptide binding]; other site 887061000696 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061000697 dimer interface [polypeptide binding]; other site 887061000698 phosphorylation site [posttranslational modification] 887061000699 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 887061000700 ATP binding site [chemical binding]; other site 887061000701 Mg2+ binding site [ion binding]; other site 887061000702 G-X-G motif; other site 887061000703 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061000704 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061000705 active site 887061000706 phosphorylation site [posttranslational modification] 887061000707 intermolecular recognition site; other site 887061000708 dimerization interface [polypeptide binding]; other site 887061000709 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 887061000710 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 887061000711 TfoX N-terminal domain; Region: TfoX_N; pfam04993 887061000712 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 887061000713 putative catalytic site [active] 887061000714 putative phosphate binding site [ion binding]; other site 887061000715 active site 887061000716 metal binding site A [ion binding]; metal-binding site 887061000717 DNA binding site [nucleotide binding] 887061000718 putative AP binding site [nucleotide binding]; other site 887061000719 putative metal binding site B [ion binding]; other site 887061000720 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 887061000721 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 887061000722 catalytic residues [active] 887061000723 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 887061000724 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 887061000725 active site 887061000726 Zn binding site [ion binding]; other site 887061000727 Tic20-like protein; Region: Tic20; pfam09685 887061000728 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 887061000729 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 887061000730 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 887061000731 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 887061000732 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 887061000733 dimerization domain swap beta strand [polypeptide binding]; other site 887061000734 regulatory protein interface [polypeptide binding]; other site 887061000735 active site 887061000736 regulatory phosphorylation site [posttranslational modification]; other site 887061000737 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 family...; Region: PTS_IIA_man; cd00006 887061000738 active pocket/dimerization site; other site 887061000739 active site 887061000740 phosphorylation site [posttranslational modification] 887061000741 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 887061000742 AAA domain; Region: AAA_18; pfam13238 887061000743 HPr kinase/phosphorylase; Provisional; Region: PRK05428 887061000744 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 887061000745 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-dependent...; Region: HprK_C; cd01918 887061000746 Hpr binding site; other site 887061000747 active site 887061000748 homohexamer subunit interaction site [polypeptide binding]; other site 887061000749 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...; Region: RaiA; cd00552 887061000750 30S subunit binding site; other site 887061000751 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 887061000752 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 887061000753 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 887061000754 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 887061000755 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 887061000756 Walker A/P-loop; other site 887061000757 ATP binding site [chemical binding]; other site 887061000758 Q-loop/lid; other site 887061000759 ABC transporter signature motif; other site 887061000760 Walker B; other site 887061000761 D-loop; other site 887061000762 H-loop/switch region; other site 887061000763 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 887061000764 OstA-like protein; Region: OstA; pfam03968 887061000765 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 887061000766 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 887061000767 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 887061000768 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 887061000769 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 887061000770 putative active site [active] 887061000771 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 887061000772 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 887061000773 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 887061000774 TrkA-N domain; Region: TrkA_N; pfam02254 887061000775 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 887061000776 periplasmic chaperone; Provisional; Region: PRK10780 887061000777 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 887061000778 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 887061000779 trimer interface [polypeptide binding]; other site 887061000780 dimer interface [polypeptide binding]; other site 887061000781 putative active site [active] 887061000782 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 887061000783 Peptidase family M48; Region: Peptidase_M48; pfam01435 887061000784 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 887061000785 TPR motif; other site 887061000786 binding surface 887061000787 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 887061000788 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 887061000789 peroxiredoxin; Region: AhpC; TIGR03137 887061000790 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 887061000791 dimer interface [polypeptide binding]; other site 887061000792 decamer (pentamer of dimers) interface [polypeptide binding]; other site 887061000793 catalytic triad [active] 887061000794 peroxidatic and resolving cysteines [active] 887061000795 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 887061000796 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 887061000797 catalytic residue [active] 887061000798 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 887061000799 catalytic residues [active] 887061000800 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 887061000801 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 887061000802 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 887061000803 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 887061000804 Walker A motif; other site 887061000805 ATP binding site [chemical binding]; other site 887061000806 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 887061000807 Domain of unknown function DUF20; Region: UPF0118; pfam01594 887061000808 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 887061000809 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 887061000810 dimerization interface [polypeptide binding]; other site 887061000811 putative ATP binding site [chemical binding]; other site 887061000812 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 887061000813 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 887061000814 16S rRNA methyltransferase B; Provisional; Region: PRK14902 887061000815 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 887061000816 S-adenosylmethionine binding site [chemical binding]; other site 887061000817 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 887061000818 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 887061000819 azurin; Region: azurin; TIGR02695 887061000820 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 887061000821 EamA-like transporter family; Region: EamA; pfam00892 887061000822 EamA-like transporter family; Region: EamA; pfam00892 887061000823 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 887061000824 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 887061000825 amidase catalytic site [active] 887061000826 Zn binding residues [ion binding]; other site 887061000827 substrate binding site [chemical binding]; other site 887061000828 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 887061000829 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 887061000830 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061000831 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061000832 active site 887061000833 phosphorylation site [posttranslational modification] 887061000834 intermolecular recognition site; other site 887061000835 dimerization interface [polypeptide binding]; other site 887061000836 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061000837 Walker A motif; other site 887061000838 ATP binding site [chemical binding]; other site 887061000839 Walker B motif; other site 887061000840 arginine finger; other site 887061000841 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061000842 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 887061000843 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061000844 dimer interface [polypeptide binding]; other site 887061000845 phosphorylation site [posttranslational modification] 887061000846 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 887061000847 ATP binding site [chemical binding]; other site 887061000848 Mg2+ binding site [ion binding]; other site 887061000849 G-X-G motif; other site 887061000850 RNA polymerase factor sigma-70; Validated; Region: PRK09047 887061000851 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061000852 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061000853 DNA binding residues [nucleotide binding] 887061000854 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 887061000855 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 887061000856 RDD family; Region: RDD; pfam06271 887061000857 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 887061000858 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 887061000859 Predicted permeases [General function prediction only]; Region: COG0795 887061000860 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 887061000861 multifunctional aminopeptidase A; Provisional; Region: PRK00913 887061000862 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 887061000863 interface (dimer of trimers) [polypeptide binding]; other site 887061000864 Substrate-binding/catalytic site; other site 887061000865 Zn-binding sites [ion binding]; other site 887061000866 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 887061000867 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 887061000868 lipoyl attachment site [posttranslational modification]; other site 887061000869 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 887061000870 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 887061000871 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 887061000872 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 887061000873 active site 887061000874 interdomain interaction site; other site 887061000875 putative metal-binding site [ion binding]; other site 887061000876 nucleotide binding site [chemical binding]; other site 887061000877 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 887061000878 domain I; other site 887061000879 DNA binding groove [nucleotide binding] 887061000880 phosphate binding site [ion binding]; other site 887061000881 domain II; other site 887061000882 domain III; other site 887061000883 nucleotide binding site [chemical binding]; other site 887061000884 catalytic site [active] 887061000885 domain IV; other site 887061000886 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 887061000887 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 887061000888 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 887061000889 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 887061000890 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 887061000891 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 887061000892 Ligand Binding Site [chemical binding]; other site 887061000893 pteridine reductase; Provisional; Region: PRK09135 887061000894 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 887061000895 NADP binding site [chemical binding]; other site 887061000896 substrate binding pocket [chemical binding]; other site 887061000897 active site 887061000898 Uncharacterized conserved protein [Function unknown]; Region: COG1565 887061000899 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 887061000900 S-adenosylmethionine binding site [chemical binding]; other site 887061000901 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 887061000902 G1 box; other site 887061000903 GTP/Mg2+ binding site [chemical binding]; other site 887061000904 Switch I region; other site 887061000905 G2 box; other site 887061000906 G3 box; other site 887061000907 Switch II region; other site 887061000908 G4 box; other site 887061000909 G5 box; other site 887061000910 Cytochrome c553 [Energy production and conversion]; Region: COG2863 887061000911 Cytochrome c; Region: Cytochrom_C; cl11414 887061000912 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 887061000913 ResB-like family; Region: ResB; pfam05140 887061000914 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 887061000915 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061000916 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 887061000917 ATP binding site [chemical binding]; other site 887061000918 Mg2+ binding site [ion binding]; other site 887061000919 G-X-G motif; other site 887061000920 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 887061000921 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 887061000922 Walker A/P-loop; other site 887061000923 ATP binding site [chemical binding]; other site 887061000924 Q-loop/lid; other site 887061000925 ABC transporter signature motif; other site 887061000926 Walker B; other site 887061000927 D-loop; other site 887061000928 H-loop/switch region; other site 887061000929 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 887061000930 Permease; Region: Permease; pfam02405 887061000931 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 887061000932 mce related protein; Region: MCE; pfam02470 887061000933 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 887061000934 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 887061000935 anti sigma factor interaction site; other site 887061000936 regulatory phosphorylation site [posttranslational modification]; other site 887061000937 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 887061000938 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 887061000939 Walker A/P-loop; other site 887061000940 ATP binding site [chemical binding]; other site 887061000941 Q-loop/lid; other site 887061000942 ABC transporter signature motif; other site 887061000943 Walker B; other site 887061000944 D-loop; other site 887061000945 H-loop/switch region; other site 887061000946 ABC-2 type transporter; Region: ABC2_membrane; cl17235 887061000947 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 887061000948 BolA-like protein; Region: BolA; pfam01722 887061000949 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 887061000950 putative GSH binding site [chemical binding]; other site 887061000951 catalytic residues [active] 887061000952 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 887061000953 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 887061000954 hinge; other site 887061000955 active site 887061000956 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 887061000957 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 887061000958 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 887061000959 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 887061000960 NAD binding site [chemical binding]; other site 887061000961 dimerization interface [polypeptide binding]; other site 887061000962 product binding site; other site 887061000963 substrate binding site [chemical binding]; other site 887061000964 zinc binding site [ion binding]; other site 887061000965 catalytic residues [active] 887061000966 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 887061000967 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 887061000968 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061000969 homodimer interface [polypeptide binding]; other site 887061000970 catalytic residue [active] 887061000971 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 887061000972 active site 887061000973 dimer interface [polypeptide binding]; other site 887061000974 magnesium binding site [ion binding]; other site 887061000975 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 887061000976 putative active site pocket [active] 887061000977 4-fold oligomerization interface [polypeptide binding]; other site 887061000978 metal binding residues [ion binding]; metal-binding site 887061000979 3-fold/trimer interface [polypeptide binding]; other site 887061000980 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 887061000981 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 887061000982 putative active site [active] 887061000983 oxyanion strand; other site 887061000984 catalytic triad [active] 887061000985 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 887061000986 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 887061000987 catalytic residues [active] 887061000988 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 887061000989 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 887061000990 substrate binding site [chemical binding]; other site 887061000991 glutamase interaction surface [polypeptide binding]; other site 887061000992 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 887061000993 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 887061000994 metal binding site [ion binding]; metal-binding site 887061000995 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 887061000996 nucleotide binding site/active site [active] 887061000997 HIT family signature motif; other site 887061000998 catalytic residue [active] 887061000999 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 887061001000 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 887061001001 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 887061001002 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 887061001003 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 887061001004 protein binding site [polypeptide binding]; other site 887061001005 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 887061001006 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 887061001007 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 887061001008 [2Fe-2S] cluster binding site [ion binding]; other site 887061001009 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 887061001010 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 887061001011 Qi binding site; other site 887061001012 intrachain domain interface; other site 887061001013 interchain domain interface [polypeptide binding]; other site 887061001014 heme bH binding site [chemical binding]; other site 887061001015 heme bL binding site [chemical binding]; other site 887061001016 Qo binding site; other site 887061001017 interchain domain interface [polypeptide binding]; other site 887061001018 intrachain domain interface; other site 887061001019 Qi binding site; other site 887061001020 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 887061001021 Qo binding site; other site 887061001022 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 887061001023 stringent starvation protein A; Provisional; Region: sspA; PRK09481 887061001024 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 887061001025 C-terminal domain interface [polypeptide binding]; other site 887061001026 putative GSH binding site (G-site) [chemical binding]; other site 887061001027 dimer interface [polypeptide binding]; other site 887061001028 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 887061001029 dimer interface [polypeptide binding]; other site 887061001030 N-terminal domain interface [polypeptide binding]; other site 887061001031 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 887061001032 elongation factor Tu; Reviewed; Region: PRK00049 887061001033 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 887061001034 G1 box; other site 887061001035 GEF interaction site [polypeptide binding]; other site 887061001036 GTP/Mg2+ binding site [chemical binding]; other site 887061001037 Switch I region; other site 887061001038 G2 box; other site 887061001039 G3 box; other site 887061001040 Switch II region; other site 887061001041 G4 box; other site 887061001042 G5 box; other site 887061001043 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 887061001044 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 887061001045 Antibiotic Binding Site [chemical binding]; other site 887061001046 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 887061001047 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 887061001048 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 887061001049 putative homodimer interface [polypeptide binding]; other site 887061001050 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 887061001051 heterodimer interface [polypeptide binding]; other site 887061001052 homodimer interface [polypeptide binding]; other site 887061001053 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 887061001054 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 887061001055 23S rRNA interface [nucleotide binding]; other site 887061001056 L7/L12 interface [polypeptide binding]; other site 887061001057 putative thiostrepton binding site; other site 887061001058 L25 interface [polypeptide binding]; other site 887061001059 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 887061001060 mRNA/rRNA interface [nucleotide binding]; other site 887061001061 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 887061001062 23S rRNA interface [nucleotide binding]; other site 887061001063 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 887061001064 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 887061001065 core dimer interface [polypeptide binding]; other site 887061001066 peripheral dimer interface [polypeptide binding]; other site 887061001067 L10 interface [polypeptide binding]; other site 887061001068 L11 interface [polypeptide binding]; other site 887061001069 putative EF-Tu interaction site [polypeptide binding]; other site 887061001070 putative EF-G interaction site [polypeptide binding]; other site 887061001071 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 887061001072 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; cl17585 887061001073 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 887061001074 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 887061001075 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 887061001076 RPB3 interaction site [polypeptide binding]; other site 887061001077 RPB1 interaction site [polypeptide binding]; other site 887061001078 RPB11 interaction site [polypeptide binding]; other site 887061001079 RPB10 interaction site [polypeptide binding]; other site 887061001080 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 887061001081 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 887061001082 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 887061001083 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 887061001084 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 887061001085 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 887061001086 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 887061001087 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 887061001088 DNA binding site [nucleotide binding] 887061001089 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 887061001090 30S ribosomal protein S12; Validated; Region: rpsL; PRK05163 887061001091 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 887061001092 30S ribosomal protein S7; Validated; Region: PRK05302 887061001093 elongation factor G; Reviewed; Region: PRK00007 887061001094 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 887061001095 G1 box; other site 887061001096 putative GEF interaction site [polypeptide binding]; other site 887061001097 GTP/Mg2+ binding site [chemical binding]; other site 887061001098 Switch I region; other site 887061001099 G2 box; other site 887061001100 G3 box; other site 887061001101 Switch II region; other site 887061001102 G4 box; other site 887061001103 G5 box; other site 887061001104 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 887061001105 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 887061001106 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 887061001107 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 887061001108 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 887061001109 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 887061001110 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 887061001111 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 887061001112 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 887061001113 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 887061001114 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 887061001115 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 887061001116 protein-rRNA interface [nucleotide binding]; other site 887061001117 putative translocon binding site; other site 887061001118 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 887061001119 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 887061001120 G-X-X-G motif; other site 887061001121 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 887061001122 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 887061001123 23S rRNA interface [nucleotide binding]; other site 887061001124 5S rRNA interface [nucleotide binding]; other site 887061001125 putative antibiotic binding site [chemical binding]; other site 887061001126 L25 interface [polypeptide binding]; other site 887061001127 L27 interface [polypeptide binding]; other site 887061001128 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 887061001129 23S rRNA interface [nucleotide binding]; other site 887061001130 putative translocon interaction site; other site 887061001131 signal recognition particle (SRP54) interaction site; other site 887061001132 L23 interface [polypeptide binding]; other site 887061001133 trigger factor interaction site; other site 887061001134 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 887061001135 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 887061001136 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 887061001137 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 887061001138 RNA binding site [nucleotide binding]; other site 887061001139 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 887061001140 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 887061001141 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 887061001142 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 887061001143 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 887061001144 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 887061001145 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 887061001146 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 887061001147 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 887061001148 5S rRNA interface [nucleotide binding]; other site 887061001149 23S rRNA interface [nucleotide binding]; other site 887061001150 L5 interface [polypeptide binding]; other site 887061001151 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 887061001152 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 887061001153 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 887061001154 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 887061001155 23S rRNA binding site [nucleotide binding]; other site 887061001156 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 887061001157 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 887061001158 SecY translocase; Region: SecY; pfam00344 887061001159 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 887061001160 rRNA binding site [nucleotide binding]; other site 887061001161 predicted 30S ribosome binding site; other site 887061001162 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 887061001163 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 887061001164 30S ribosomal protein S11; Validated; Region: PRK05309 887061001165 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 887061001166 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 887061001167 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 887061001168 RNA binding surface [nucleotide binding]; other site 887061001169 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 887061001170 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 887061001171 alphaNTD homodimer interface [polypeptide binding]; other site 887061001172 alphaNTD - beta interaction site [polypeptide binding]; other site 887061001173 alphaNTD - beta' interaction site [polypeptide binding]; other site 887061001174 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 887061001175 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 887061001176 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 887061001177 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 887061001178 MgtE intracellular N domain; Region: MgtE_N; smart00924 887061001179 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 887061001180 Divalent cation transporter; Region: MgtE; pfam01769 887061001181 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 887061001182 Mechanosensitive ion channel; Region: MS_channel; pfam00924 887061001183 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 887061001184 Fatty acid desaturase; Region: FA_desaturase; pfam00487 887061001185 Di-iron ligands [ion binding]; other site 887061001186 Transposase; Region: DDE_Tnp_ISL3; pfam01610 887061001187 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 887061001188 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 887061001189 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 887061001190 trimer interface [polypeptide binding]; other site 887061001191 active site 887061001192 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 887061001193 Flavoprotein; Region: Flavoprotein; pfam02441 887061001194 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 887061001195 hypothetical protein; Reviewed; Region: PRK00024 887061001196 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 887061001197 MPN+ (JAMM) motif; other site 887061001198 Zinc-binding site [ion binding]; other site 887061001199 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061001200 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 887061001201 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 887061001202 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 887061001203 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 887061001204 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 887061001205 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061001206 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 887061001207 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 887061001208 Putative amidoligase enzyme (DUF2126); Region: DUF2126; pfam09899 887061001209 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4196 887061001210 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 887061001211 [4Fe-4S] binding site [ion binding]; other site 887061001212 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 887061001213 molybdopterin cofactor binding site; other site 887061001214 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 887061001215 molybdopterin cofactor binding site; other site 887061001216 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 887061001217 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 887061001218 [2Fe-2S] cluster binding site [ion binding]; other site 887061001219 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 887061001220 active site 887061001221 Catalytic domain of Protein Kinases; Region: PKc; cd00180 887061001222 active site 887061001223 ATP binding site [chemical binding]; other site 887061001224 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 887061001225 substrate binding site [chemical binding]; other site 887061001226 activation loop (A-loop); other site 887061001227 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 887061001228 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 887061001229 putative substrate translocation pore; other site 887061001230 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 887061001231 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 887061001232 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 887061001233 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 887061001234 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 887061001235 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 887061001236 active site 887061001237 SAM binding site [chemical binding]; other site 887061001238 homodimer interface [polypeptide binding]; other site 887061001239 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 887061001240 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061001241 putative CheW interface [polypeptide binding]; other site 887061001242 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 887061001243 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061001244 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 887061001245 Walker A/P-loop; other site 887061001246 ATP binding site [chemical binding]; other site 887061001247 Q-loop/lid; other site 887061001248 ABC transporter signature motif; other site 887061001249 Walker B; other site 887061001250 D-loop; other site 887061001251 H-loop/switch region; other site 887061001252 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061001253 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061001254 dimer interface [polypeptide binding]; other site 887061001255 conserved gate region; other site 887061001256 putative PBP binding loops; other site 887061001257 ABC-ATPase subunit interface; other site 887061001258 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061001259 NMT1-like family; Region: NMT1_2; pfam13379 887061001260 Nitrate and nitrite sensing; Region: NIT; pfam08376 887061001261 ANTAR domain; Region: ANTAR; pfam03861 887061001262 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 887061001263 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 887061001264 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 887061001265 Walker A/P-loop; other site 887061001266 ATP binding site [chemical binding]; other site 887061001267 Q-loop/lid; other site 887061001268 ABC transporter signature motif; other site 887061001269 Walker B; other site 887061001270 D-loop; other site 887061001271 H-loop/switch region; other site 887061001272 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 887061001273 lipoprotein; Provisional; Region: PRK10540 887061001274 carbon starvation protein A; Provisional; Region: PRK15015 887061001275 Carbon starvation protein CstA; Region: CstA; pfam02554 887061001276 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 887061001277 Protein of unknown function (DUF466); Region: DUF466; cl01082 887061001278 Protein of unknown function (DUF2805); Region: DUF2805; pfam10985 887061001279 proteobacterial dedicated sortase system histidine kinase; Region: marine_sort_HK; TIGR03785 887061001280 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 887061001281 PAS fold; Region: PAS_4; pfam08448 887061001282 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 887061001283 putative active site [active] 887061001284 heme pocket [chemical binding]; other site 887061001285 PAS fold; Region: PAS_4; pfam08448 887061001286 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061001287 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001288 metal binding site [ion binding]; metal-binding site 887061001289 active site 887061001290 I-site; other site 887061001291 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 887061001292 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 887061001293 D-hexose-6-phosphate epimerase-like; Region: D-hex-6-P-epi_like; cd09020 887061001294 active site 887061001295 phosphate binding residues; other site 887061001296 catalytic residues [active] 887061001297 Cytochrome c; Region: Cytochrom_C; cl11414 887061001298 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 887061001299 homotrimer interaction site [polypeptide binding]; other site 887061001300 putative active site [active] 887061001301 amino acid transporter; Region: 2A0306; TIGR00909 887061001302 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 887061001303 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 887061001304 amino acid carrier protein; Region: agcS; TIGR00835 887061001305 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 887061001306 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 887061001307 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 887061001308 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 887061001309 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 887061001310 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 887061001311 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 887061001312 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 887061001313 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 887061001314 purine monophosphate binding site [chemical binding]; other site 887061001315 dimer interface [polypeptide binding]; other site 887061001316 putative catalytic residues [active] 887061001317 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 887061001318 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 887061001319 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 887061001320 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 887061001321 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 887061001322 FMN binding site [chemical binding]; other site 887061001323 active site 887061001324 catalytic residues [active] 887061001325 substrate binding site [chemical binding]; other site 887061001326 metabolite-proton symporter; Region: 2A0106; TIGR00883 887061001327 Flagellin N-methylase; Region: FliB; cl00497 887061001328 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 887061001329 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 887061001330 putative MPT binding site; other site 887061001331 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 887061001332 DNA polymerase I; Provisional; Region: PRK05755 887061001333 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 887061001334 active site 887061001335 metal binding site 1 [ion binding]; metal-binding site 887061001336 putative 5' ssDNA interaction site; other site 887061001337 metal binding site 3; metal-binding site 887061001338 metal binding site 2 [ion binding]; metal-binding site 887061001339 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 887061001340 putative DNA binding site [nucleotide binding]; other site 887061001341 putative metal binding site [ion binding]; other site 887061001342 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 887061001343 active site 887061001344 catalytic site [active] 887061001345 substrate binding site [chemical binding]; other site 887061001346 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 887061001347 active site 887061001348 DNA binding site [nucleotide binding] 887061001349 catalytic site [active] 887061001350 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 887061001351 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 887061001352 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 887061001353 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 887061001354 putative active site [active] 887061001355 putative substrate binding site [chemical binding]; other site 887061001356 ATP binding site [chemical binding]; other site 887061001357 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 887061001358 Part of AAA domain; Region: AAA_19; pfam13245 887061001359 Family description; Region: UvrD_C_2; pfam13538 887061001360 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061001361 ligand binding site [chemical binding]; other site 887061001362 putative inner membrane diguanylate cyclase; Provisional; Region: PRK09966 887061001363 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 887061001364 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001365 metal binding site [ion binding]; metal-binding site 887061001366 active site 887061001367 I-site; other site 887061001368 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 887061001369 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 887061001370 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061001371 dimerization interface [polypeptide binding]; other site 887061001372 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061001373 dimer interface [polypeptide binding]; other site 887061001374 phosphorylation site [posttranslational modification] 887061001375 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 887061001376 ATP binding site [chemical binding]; other site 887061001377 Mg2+ binding site [ion binding]; other site 887061001378 G-X-G motif; other site 887061001379 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 887061001380 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061001381 active site 887061001382 phosphorylation site [posttranslational modification] 887061001383 intermolecular recognition site; other site 887061001384 dimerization interface [polypeptide binding]; other site 887061001385 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061001386 DNA binding site [nucleotide binding] 887061001387 Outer membrane efflux protein; Region: OEP; pfam02321 887061001388 Outer membrane efflux protein; Region: OEP; pfam02321 887061001389 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 887061001390 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 887061001391 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 887061001392 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 887061001393 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 887061001394 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 887061001395 ring oligomerisation interface [polypeptide binding]; other site 887061001396 ATP/Mg binding site [chemical binding]; other site 887061001397 stacking interactions; other site 887061001398 hinge regions; other site 887061001399 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 887061001400 oligomerisation interface [polypeptide binding]; other site 887061001401 mobile loop; other site 887061001402 roof hairpin; other site 887061001403 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 887061001404 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 887061001405 putative deacylase active site [active] 887061001406 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 887061001407 DEAD_2; Region: DEAD_2; pfam06733 887061001408 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 887061001409 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 887061001410 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 887061001411 active site 887061001412 DNA binding site [nucleotide binding] 887061001413 Int/Topo IB signature motif; other site 887061001414 catalytic residues [active] 887061001415 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 887061001416 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061001417 DNA-binding site [nucleotide binding]; DNA binding site 887061001418 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 887061001419 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061001420 homodimer interface [polypeptide binding]; other site 887061001421 catalytic residue [active] 887061001422 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 887061001423 4Fe-4S binding domain; Region: Fer4; pfam00037 887061001424 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 887061001425 Response regulator receiver domain; Region: Response_reg; pfam00072 887061001426 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061001427 active site 887061001428 phosphorylation site [posttranslational modification] 887061001429 intermolecular recognition site; other site 887061001430 dimerization interface [polypeptide binding]; other site 887061001431 PAS domain S-box; Region: sensory_box; TIGR00229 887061001432 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 887061001433 putative active site [active] 887061001434 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061001435 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001436 metal binding site [ion binding]; metal-binding site 887061001437 active site 887061001438 I-site; other site 887061001439 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 887061001440 HDOD domain; Region: HDOD; pfam08668 887061001441 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061001442 Zn2+ binding site [ion binding]; other site 887061001443 Mg2+ binding site [ion binding]; other site 887061001444 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061001445 dimer interface [polypeptide binding]; other site 887061001446 phosphorylation site [posttranslational modification] 887061001447 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 887061001448 ATP binding site [chemical binding]; other site 887061001449 Mg2+ binding site [ion binding]; other site 887061001450 G-X-G motif; other site 887061001451 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061001452 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061001453 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 887061001454 N-terminal plug; other site 887061001455 ligand-binding site [chemical binding]; other site 887061001456 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061001457 FecR protein; Region: FecR; pfam04773 887061001458 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061001459 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061001460 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061001461 DNA binding residues [nucleotide binding] 887061001462 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061001463 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 887061001464 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 887061001465 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061001466 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061001467 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 887061001468 DNA binding residues [nucleotide binding] 887061001469 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061001470 FecR protein; Region: FecR; pfam04773 887061001471 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061001472 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 887061001473 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 887061001474 N-terminal plug; other site 887061001475 ligand-binding site [chemical binding]; other site 887061001476 Protein of unknown function (DUF3649); Region: DUF3649; pfam12365 887061001477 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061001478 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 887061001479 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 887061001480 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 887061001481 macrolide transporter subunit MacA; Provisional; Region: PRK11578 887061001482 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061001483 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061001484 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 887061001485 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 887061001486 Walker A/P-loop; other site 887061001487 ATP binding site [chemical binding]; other site 887061001488 Q-loop/lid; other site 887061001489 ABC transporter signature motif; other site 887061001490 Walker B; other site 887061001491 D-loop; other site 887061001492 H-loop/switch region; other site 887061001493 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 887061001494 FtsX-like permease family; Region: FtsX; pfam02687 887061001495 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 887061001496 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 887061001497 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 887061001498 inhibitor-cofactor binding pocket; inhibition site 887061001499 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061001500 catalytic residue [active] 887061001501 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 887061001502 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 887061001503 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 887061001504 OsmC-like protein; Region: OsmC; cl00767 887061001505 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 887061001506 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 887061001507 active site 887061001508 metal binding site [ion binding]; metal-binding site 887061001509 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 887061001510 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 887061001511 N-terminal plug; other site 887061001512 ligand-binding site [chemical binding]; other site 887061001513 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 887061001514 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 887061001515 diiron binding motif [ion binding]; other site 887061001516 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 887061001517 C-terminal peptidase (prc); Region: prc; TIGR00225 887061001518 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 887061001519 protein binding site [polypeptide binding]; other site 887061001520 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 887061001521 Catalytic dyad [active] 887061001522 Rdx family; Region: Rdx; cl01407 887061001523 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 887061001524 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 887061001525 NlpC/P60 family; Region: NLPC_P60; pfam00877 887061001526 ABC1 family; Region: ABC1; cl17513 887061001527 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 887061001528 Uncharacterized conserved protein [Function unknown]; Region: COG2308 887061001529 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 887061001530 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 887061001531 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061001532 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 887061001533 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 887061001534 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 887061001535 Peptidase family U32; Region: Peptidase_U32; pfam01136 887061001536 Collagenase; Region: DUF3656; pfam12392 887061001537 cell division protein MraZ; Reviewed; Region: PRK00326 887061001538 MraZ protein; Region: MraZ; pfam02381 887061001539 MraZ protein; Region: MraZ; pfam02381 887061001540 MraW methylase family; Region: Methyltransf_5; cl17771 887061001541 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 887061001542 Cell division protein FtsL; Region: FtsL; pfam04999 887061001543 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 887061001544 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 887061001545 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 887061001546 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 887061001547 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 887061001548 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061001549 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 887061001550 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 887061001551 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 887061001552 Mg++ binding site [ion binding]; other site 887061001553 putative catalytic motif [active] 887061001554 putative substrate binding site [chemical binding]; other site 887061001555 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 887061001556 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061001557 cell division protein FtsW; Region: ftsW; TIGR02614 887061001558 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 887061001559 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 887061001560 active site 887061001561 homodimer interface [polypeptide binding]; other site 887061001562 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 887061001563 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 887061001564 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061001565 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 887061001566 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 887061001567 FAD binding domain; Region: FAD_binding_4; pfam01565 887061001568 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 887061001569 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 887061001570 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 887061001571 D-ala D-ala ligase C-terminus; Region: Dala_Dala_lig_C; pfam07478 887061001572 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 887061001573 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 887061001574 Cell division protein FtsQ; Region: FtsQ; pfam03799 887061001575 cell division protein FtsA; Region: ftsA; TIGR01174 887061001576 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 887061001577 nucleotide binding site [chemical binding]; other site 887061001578 Cell division protein FtsA; Region: FtsA; pfam14450 887061001579 cell division protein FtsZ; Validated; Region: PRK09330 887061001580 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 887061001581 nucleotide binding site [chemical binding]; other site 887061001582 SulA interaction site; other site 887061001583 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 887061001584 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 887061001585 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 887061001586 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...; Region: LT_GEWL; cd00254 887061001587 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061001588 catalytic residue [active] 887061001589 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 887061001590 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 887061001591 putative NAD(P) binding site [chemical binding]; other site 887061001592 active site 887061001593 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 887061001594 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 887061001595 active site 887061001596 NTP binding site [chemical binding]; other site 887061001597 metal binding triad [ion binding]; metal-binding site 887061001598 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 887061001599 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 887061001600 division inhibitor protein; Provisional; Region: slmA; PRK09480 887061001601 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061001602 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 887061001603 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 887061001604 motif II; other site 887061001605 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 887061001606 feedback inhibition sensing region; other site 887061001607 homohexameric interface [polypeptide binding]; other site 887061001608 nucleotide binding site [chemical binding]; other site 887061001609 N-acetyl-L-glutamate binding site [chemical binding]; other site 887061001610 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 887061001611 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 887061001612 Potassium binding sites [ion binding]; other site 887061001613 Cesium cation binding sites [ion binding]; other site 887061001614 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 887061001615 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 887061001616 putative dimer interface [polypeptide binding]; other site 887061001617 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 887061001618 non-specific DNA binding site [nucleotide binding]; other site 887061001619 salt bridge; other site 887061001620 sequence-specific DNA binding site [nucleotide binding]; other site 887061001621 N-acetylglutamate synthase; Validated; Region: PRK05279 887061001622 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 887061001623 putative feedback inhibition sensing region; other site 887061001624 putative nucleotide binding site [chemical binding]; other site 887061001625 putative substrate binding site [chemical binding]; other site 887061001626 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061001627 Coenzyme A binding pocket [chemical binding]; other site 887061001628 manganese transport protein MntH; Reviewed; Region: PRK00701 887061001629 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 887061001630 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 887061001631 RNA methyltransferase, RsmE family; Region: TIGR00046 887061001632 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 887061001633 putative catalytic residue [active] 887061001634 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061001635 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001636 metal binding site [ion binding]; metal-binding site 887061001637 active site 887061001638 I-site; other site 887061001639 transketolase; Reviewed; Region: PRK12753 887061001640 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 887061001641 TPP-binding site [chemical binding]; other site 887061001642 dimer interface [polypeptide binding]; other site 887061001643 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 887061001644 PYR/PP interface [polypeptide binding]; other site 887061001645 dimer interface [polypeptide binding]; other site 887061001646 TPP binding site [chemical binding]; other site 887061001647 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 887061001648 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 887061001649 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 887061001650 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 887061001651 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 887061001652 Phosphoglycerate kinase; Region: PGK; pfam00162 887061001653 substrate binding site [chemical binding]; other site 887061001654 hinge regions; other site 887061001655 ADP binding site [chemical binding]; other site 887061001656 catalytic site [active] 887061001657 pyruvate kinase; Provisional; Region: PRK05826 887061001658 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; cl17342 887061001659 domain interfaces; other site 887061001660 active site 887061001661 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 887061001662 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 887061001663 intersubunit interface [polypeptide binding]; other site 887061001664 active site 887061001665 zinc binding site [ion binding]; other site 887061001666 Na+ binding site [ion binding]; other site 887061001667 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 887061001668 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 887061001669 ATP binding site [chemical binding]; other site 887061001670 active site 887061001671 substrate binding site [chemical binding]; other site 887061001672 Uncharacterized conserved protein [Function unknown]; Region: COG3339 887061001673 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 887061001674 active site clefts [active] 887061001675 zinc binding site [ion binding]; other site 887061001676 dimer interface [polypeptide binding]; other site 887061001677 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 887061001678 dimer interface [polypeptide binding]; other site 887061001679 substrate binding site [chemical binding]; other site 887061001680 metal binding sites [ion binding]; metal-binding site 887061001681 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 887061001682 ligand binding site [chemical binding]; other site 887061001683 active site 887061001684 UGI interface [polypeptide binding]; other site 887061001685 catalytic site [active] 887061001686 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 887061001687 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 887061001688 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 887061001689 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 887061001690 Walker A/P-loop; other site 887061001691 ATP binding site [chemical binding]; other site 887061001692 Q-loop/lid; other site 887061001693 ABC transporter signature motif; other site 887061001694 Walker B; other site 887061001695 D-loop; other site 887061001696 H-loop/switch region; other site 887061001697 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 887061001698 Protein of unknown function (DUF721); Region: DUF721; pfam05258 887061001699 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 887061001700 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061001701 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 887061001702 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 887061001703 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; cl17351 887061001704 nucleotide binding region [chemical binding]; other site 887061001705 SEC-C motif; Region: SEC-C; pfam02810 887061001706 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 887061001707 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 887061001708 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 887061001709 heterotetramer interface [polypeptide binding]; other site 887061001710 active site pocket [active] 887061001711 cleavage site 887061001712 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 887061001713 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061001714 Walker A motif; other site 887061001715 ATP binding site [chemical binding]; other site 887061001716 Walker B motif; other site 887061001717 hypothetical protein; Provisional; Region: PRK08999 887061001718 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 887061001719 active site 887061001720 8-oxo-dGMP binding site [chemical binding]; other site 887061001721 nudix motif; other site 887061001722 metal binding site [ion binding]; metal-binding site 887061001723 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 887061001724 thiamine phosphate binding site [chemical binding]; other site 887061001725 active site 887061001726 pyrophosphate binding site [ion binding]; other site 887061001727 Protein of unknown function (DUF461); Region: DUF461; pfam04314 887061001728 Domain of unknown function (DUF329); Region: DUF329; pfam03884 887061001729 hypothetical protein; Provisional; Region: PRK05287 887061001730 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 887061001731 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 887061001732 CoA-binding site [chemical binding]; other site 887061001733 ATP-binding [chemical binding]; other site 887061001734 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 887061001735 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 887061001736 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 887061001737 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 887061001738 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 887061001739 substrate binding pocket [chemical binding]; other site 887061001740 chain length determination region; other site 887061001741 substrate-Mg2+ binding site; other site 887061001742 catalytic residues [active] 887061001743 aspartate-rich region 1; other site 887061001744 active site lid residues [active] 887061001745 aspartate-rich region 2; other site 887061001746 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 887061001747 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 887061001748 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 887061001749 GTPase CgtA; Reviewed; Region: obgE; PRK12299 887061001750 GTP1/OBG; Region: GTP1_OBG; pfam01018 887061001751 Obg GTPase; Region: Obg; cd01898 887061001752 G1 box; other site 887061001753 GTP/Mg2+ binding site [chemical binding]; other site 887061001754 Switch I region; other site 887061001755 G2 box; other site 887061001756 G3 box; other site 887061001757 Switch II region; other site 887061001758 G4 box; other site 887061001759 G5 box; other site 887061001760 gamma-glutamyl kinase; Provisional; Region: PRK05429 887061001761 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 887061001762 nucleotide binding site [chemical binding]; other site 887061001763 homotetrameric interface [polypeptide binding]; other site 887061001764 putative phosphate binding site [ion binding]; other site 887061001765 putative allosteric binding site; other site 887061001766 PUA domain; Region: PUA; pfam01472 887061001767 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 887061001768 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 887061001769 ATP-grasp domain; Region: ATP-grasp; pfam02222 887061001770 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 887061001771 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 887061001772 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 887061001773 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 887061001774 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 887061001775 active site 887061001776 Riboflavin kinase; Region: Flavokinase; smart00904 887061001777 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 887061001778 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061001779 active site 887061001780 HIGH motif; other site 887061001781 nucleotide binding site [chemical binding]; other site 887061001782 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 887061001783 active site 887061001784 KMSKS motif; other site 887061001785 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 887061001786 tRNA binding surface [nucleotide binding]; other site 887061001787 anticodon binding site; other site 887061001788 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 887061001789 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 887061001790 lipoprotein signal peptidase; Provisional; Region: PRK14787 887061001791 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 887061001792 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 887061001793 Moco binding site; other site 887061001794 metal coordination site [ion binding]; other site 887061001795 methionine sulfoxide reductase B; Provisional; Region: PRK00222 887061001796 SelR domain; Region: SelR; pfam01641 887061001797 Protein of unknown function (DUF808); Region: DUF808; pfam05661 887061001798 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 887061001799 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 887061001800 putative NAD(P) binding site [chemical binding]; other site 887061001801 putative substrate binding site [chemical binding]; other site 887061001802 catalytic Zn binding site [ion binding]; other site 887061001803 structural Zn binding site [ion binding]; other site 887061001804 dimer interface [polypeptide binding]; other site 887061001805 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 887061001806 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 887061001807 tetramer interface [polypeptide binding]; other site 887061001808 heme binding pocket [chemical binding]; other site 887061001809 NADPH binding site [chemical binding]; other site 887061001810 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 887061001811 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 887061001812 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 887061001813 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 887061001814 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 887061001815 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061001816 active site 887061001817 phosphorylation site [posttranslational modification] 887061001818 intermolecular recognition site; other site 887061001819 dimerization interface [polypeptide binding]; other site 887061001820 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061001821 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061001822 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061001823 phosphorylation site [posttranslational modification] 887061001824 dimer interface [polypeptide binding]; other site 887061001825 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 887061001826 ATP binding site [chemical binding]; other site 887061001827 Mg2+ binding site [ion binding]; other site 887061001828 G-X-G motif; other site 887061001829 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 887061001830 N-terminal plug; other site 887061001831 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061001832 ligand-binding site [chemical binding]; other site 887061001833 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061001834 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 887061001835 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061001836 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 887061001837 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 887061001838 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061001839 Zn2+ binding site [ion binding]; other site 887061001840 Mg2+ binding site [ion binding]; other site 887061001841 PAS fold; Region: PAS_4; pfam08448 887061001842 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 887061001843 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 887061001844 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 887061001845 PAS domain; Region: PAS_9; pfam13426 887061001846 putative active site [active] 887061001847 heme pocket [chemical binding]; other site 887061001848 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061001849 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061001850 metal binding site [ion binding]; metal-binding site 887061001851 active site 887061001852 I-site; other site 887061001853 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 887061001854 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 887061001855 Clp amino terminal domain; Region: Clp_N; pfam02861 887061001856 Clp amino terminal domain; Region: Clp_N; pfam02861 887061001857 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061001858 Walker A motif; other site 887061001859 ATP binding site [chemical binding]; other site 887061001860 Walker B motif; other site 887061001861 arginine finger; other site 887061001862 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061001863 Walker A motif; other site 887061001864 ATP binding site [chemical binding]; other site 887061001865 Walker B motif; other site 887061001866 arginine finger; other site 887061001867 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 887061001868 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 887061001869 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 887061001870 NADP binding site [chemical binding]; other site 887061001871 Predicted transcriptional regulators [Transcription]; Region: COG1733 887061001872 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 887061001873 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 887061001874 Sel1-like repeats; Region: SEL1; smart00671 887061001875 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 887061001876 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...; Region: LT_GEWL; cd00254 887061001877 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061001878 catalytic residue [active] 887061001879 Uncharacterized protein family UPF0047; Region: UPF0047; pfam01894 887061001880 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH2; cd08183 887061001881 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 887061001882 putative active site [active] 887061001883 metal binding site [ion binding]; metal-binding site 887061001884 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061001885 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 887061001886 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 887061001887 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061001888 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 887061001889 phosphoglyceromutase; Provisional; Region: PRK05434 887061001890 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 887061001891 active site residue [active] 887061001892 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061001893 preprotein translocase subunit SecB; Validated; Region: PRK05751 887061001894 SecA binding site; other site 887061001895 Preprotein binding site; other site 887061001896 Src Homology 3 domain superfamily; Region: SH3; cl17036 887061001897 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 887061001898 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 887061001899 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 887061001900 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 887061001901 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 887061001902 active site clefts [active] 887061001903 zinc binding site [ion binding]; other site 887061001904 dimer interface [polypeptide binding]; other site 887061001905 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 887061001906 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 887061001907 Sulfate transporter family; Region: Sulfate_transp; pfam00916 887061001908 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 887061001909 anti sigma factor interaction site; other site 887061001910 regulatory phosphorylation site [posttranslational modification]; other site 887061001911 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 887061001912 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061001913 active site 887061001914 biotin synthase; Region: bioB; TIGR00433 887061001915 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 887061001916 FeS/SAM binding site; other site 887061001917 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 887061001918 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 887061001919 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 887061001920 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061001921 catalytic residue [active] 887061001922 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 887061001923 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 887061001924 TAP-like protein; Region: Abhydrolase_4; pfam08386 887061001925 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 887061001926 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 887061001927 S-adenosylmethionine binding site [chemical binding]; other site 887061001928 AAA domain; Region: AAA_26; pfam13500 887061001929 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 887061001930 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 887061001931 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 887061001932 active site 887061001933 (T/H)XGH motif; other site 887061001934 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 887061001935 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 887061001936 putative catalytic cysteine [active] 887061001937 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 887061001938 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 887061001939 Lipopolysaccharide-assembly; Region: LptE; cl01125 887061001940 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 887061001941 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 887061001942 HIGH motif; other site 887061001943 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 887061001944 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 887061001945 active site 887061001946 KMSKS motif; other site 887061001947 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 887061001948 tRNA binding surface [nucleotide binding]; other site 887061001949 adenylate kinase; Reviewed; Region: adk; PRK00279 887061001950 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 887061001951 AMP-binding site [chemical binding]; other site 887061001952 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 887061001953 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 887061001954 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 887061001955 S-adenosylmethionine binding site [chemical binding]; other site 887061001956 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 887061001957 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 887061001958 SurA N-terminal domain; Region: SurA_N; pfam09312 887061001959 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 887061001960 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 887061001961 OstA-like protein; Region: OstA; cl00844 887061001962 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 887061001963 Organic solvent tolerance protein; Region: OstA_C; pfam04453 887061001964 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 887061001965 Phosphotransferase enzyme family; Region: APH; pfam01636 887061001966 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 887061001967 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 887061001968 Substrate binding site; other site 887061001969 metal-binding site 887061001970 proline aminopeptidase P II; Provisional; Region: PRK10879 887061001971 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 887061001972 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 887061001973 active site 887061001974 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 887061001975 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 887061001976 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 887061001977 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 887061001978 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 887061001979 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 887061001980 dimerization domain [polypeptide binding]; other site 887061001981 dimer interface [polypeptide binding]; other site 887061001982 catalytic residues [active] 887061001983 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061001984 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061001985 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061001986 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 887061001987 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 887061001988 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 887061001989 Walker A motif; other site 887061001990 ATP binding site [chemical binding]; other site 887061001991 Walker B motif; other site 887061001992 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...; Region: CSP_CDS; cd04458 887061001993 DNA-binding site [nucleotide binding]; DNA binding site 887061001994 RNA-binding motif; other site 887061001995 isocitrate dehydrogenase; Validated; Region: PRK07362 887061001996 isocitrate dehydrogenase; Reviewed; Region: PRK07006 887061001997 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 887061001998 pseudouridine synthase; Region: TIGR00093 887061001999 active site 887061002000 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 887061002001 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 887061002002 catalytic triad [active] 887061002003 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 887061002004 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 887061002005 active site 887061002006 Tetramer interface [polypeptide binding]; other site 887061002007 FMN-binding site [chemical binding]; other site 887061002008 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 887061002009 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 887061002010 putative substrate translocation pore; other site 887061002011 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 887061002012 catalytic motif [active] 887061002013 Catalytic residue [active] 887061002014 putative GTP cyclohydrolase; Provisional; Region: PRK13674 887061002015 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 887061002016 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 887061002017 TPP-binding site; other site 887061002018 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 887061002019 PYR/PP interface [polypeptide binding]; other site 887061002020 dimer interface [polypeptide binding]; other site 887061002021 TPP binding site [chemical binding]; other site 887061002022 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 887061002023 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 887061002024 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 887061002025 substrate binding pocket [chemical binding]; other site 887061002026 chain length determination region; other site 887061002027 substrate-Mg2+ binding site; other site 887061002028 catalytic residues [active] 887061002029 aspartate-rich region 1; other site 887061002030 active site lid residues [active] 887061002031 aspartate-rich region 2; other site 887061002032 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 887061002033 putative hydrolase; Provisional; Region: PRK11460 887061002034 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 887061002035 cAMP phosphodiesterases class-II; Region: PDEase_II; cl17776 887061002036 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061002037 putative hydrophobic ligand binding site [chemical binding]; other site 887061002038 protein interface [polypeptide binding]; other site 887061002039 gate; other site 887061002040 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061002041 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 887061002042 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061002043 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061002044 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061002045 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061002046 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 887061002047 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 887061002048 putative active site [active] 887061002049 Ap4A binding site [chemical binding]; other site 887061002050 nudix motif; other site 887061002051 putative metal binding site [ion binding]; other site 887061002052 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 887061002053 ketol-acid reductoisomerase; Provisional; Region: PRK05479 887061002054 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 887061002055 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 887061002056 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 887061002057 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 887061002058 putative valine binding site [chemical binding]; other site 887061002059 dimer interface [polypeptide binding]; other site 887061002060 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 887061002061 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 887061002062 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 887061002063 PYR/PP interface [polypeptide binding]; other site 887061002064 dimer interface [polypeptide binding]; other site 887061002065 TPP binding site [chemical binding]; other site 887061002066 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 887061002067 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 887061002068 TPP-binding site [chemical binding]; other site 887061002069 dimer interface [polypeptide binding]; other site 887061002070 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 887061002071 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061002072 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 887061002073 Walker A motif; other site 887061002074 ATP binding site [chemical binding]; other site 887061002075 Walker B motif; other site 887061002076 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 887061002077 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 887061002078 dimerization interface [polypeptide binding]; other site 887061002079 active site 887061002080 putative glutathione S-transferase; Provisional; Region: PRK10357 887061002081 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 887061002082 putative C-terminal domain interface [polypeptide binding]; other site 887061002083 putative GSH binding site (G-site) [chemical binding]; other site 887061002084 putative dimer interface [polypeptide binding]; other site 887061002085 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 887061002086 dimer interface [polypeptide binding]; other site 887061002087 N-terminal domain interface [polypeptide binding]; other site 887061002088 putative substrate binding pocket (H-site) [chemical binding]; other site 887061002089 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 887061002090 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 887061002091 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 887061002092 nudix motif; other site 887061002093 MarC family integral membrane protein; Region: MarC; cl00919 887061002094 DJ-1 family protein; Region: not_thiJ; TIGR01383 887061002095 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 887061002096 conserved cys residue [active] 887061002097 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 887061002098 active site 887061002099 dimer interface [polypeptide binding]; other site 887061002100 ribonuclease G; Provisional; Region: PRK11712 887061002101 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 887061002102 homodimer interface [polypeptide binding]; other site 887061002103 oligonucleotide binding site [chemical binding]; other site 887061002104 YGGT family; Region: YGGT; pfam02325 887061002105 YGGT family; Region: YGGT; pfam02325 887061002106 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 887061002107 pyrroline-5-carboxylate reductase; Region: PLN02688 887061002108 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 887061002109 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 887061002110 catalytic residue [active] 887061002111 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 887061002112 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 887061002113 Walker A motif; other site 887061002114 ATP binding site [chemical binding]; other site 887061002115 Walker B motif; other site 887061002116 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 887061002117 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061002118 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 887061002119 Walker A motif; other site 887061002120 Walker A/P-loop; other site 887061002121 ATP binding site [chemical binding]; other site 887061002122 ATP binding site [chemical binding]; other site 887061002123 Walker B motif; other site 887061002124 Protein of unknown function DUF72; Region: DUF72; pfam01904 887061002125 dihydroorotase; Provisional; Region: PRK07627 887061002126 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 887061002127 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 887061002128 active site 887061002129 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 887061002130 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 887061002131 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 887061002132 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061002133 active site 887061002134 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 887061002135 hypothetical protein; Validated; Region: PRK00228 887061002136 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 887061002137 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 887061002138 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 887061002139 dimerization interface [polypeptide binding]; other site 887061002140 active site 887061002141 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 887061002142 Lumazine binding domain; Region: Lum_binding; pfam00677 887061002143 Lumazine binding domain; Region: Lum_binding; pfam00677 887061002144 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 887061002145 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 887061002146 FtsX-like permease family; Region: FtsX; pfam02687 887061002147 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 887061002148 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 887061002149 Walker A/P-loop; other site 887061002150 ATP binding site [chemical binding]; other site 887061002151 Q-loop/lid; other site 887061002152 ABC transporter signature motif; other site 887061002153 Walker B; other site 887061002154 D-loop; other site 887061002155 H-loop/switch region; other site 887061002156 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 887061002157 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 887061002158 Competence protein; Region: Competence; pfam03772 887061002159 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 887061002160 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 887061002161 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 887061002162 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 887061002163 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061002164 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 887061002165 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 887061002166 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 887061002167 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 887061002168 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 887061002169 Walker A/P-loop; other site 887061002170 ATP binding site [chemical binding]; other site 887061002171 Q-loop/lid; other site 887061002172 ABC transporter signature motif; other site 887061002173 Walker B; other site 887061002174 D-loop; other site 887061002175 H-loop/switch region; other site 887061002176 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 887061002177 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 887061002178 Uncharacterized conserved protein [Function unknown]; Region: COG2835 887061002179 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 887061002180 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 887061002181 Ligand binding site; other site 887061002182 oligomer interface; other site 887061002183 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 887061002184 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 887061002185 active site 887061002186 catalytic site [active] 887061002187 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 887061002188 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 887061002189 P-loop; other site 887061002190 Magnesium ion binding site [ion binding]; other site 887061002191 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 887061002192 Magnesium ion binding site [ion binding]; other site 887061002193 methionine sulfoxide reductase A; Provisional; Region: PRK14054 887061002194 Thermotoga maritima CorA_like subfamily; Region: TmCorA-like_1; cd12828 887061002195 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 887061002196 oligomer interface [polypeptide binding]; other site 887061002197 metal binding site [ion binding]; metal-binding site 887061002198 metal binding site [ion binding]; metal-binding site 887061002199 Cl binding site [ion binding]; other site 887061002200 aspartate ring; other site 887061002201 basic sphincter; other site 887061002202 putative hydrophobic gate; other site 887061002203 periplasmic entrance; other site 887061002204 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 887061002205 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 887061002206 dimer interface [polypeptide binding]; other site 887061002207 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002208 catalytic residue [active] 887061002209 FimV N-terminal domain; Region: FimV_core; TIGR03505 887061002210 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 887061002211 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 887061002212 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061002213 active site 887061002214 HIGH motif; other site 887061002215 nucleotide binding site [chemical binding]; other site 887061002216 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061002217 active site 887061002218 KMSKS motif; other site 887061002219 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 887061002220 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 887061002221 Biotin operon repressor [Transcription]; Region: BirA; COG1654 887061002222 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 887061002223 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 887061002224 Type III pantothenate kinase; Region: Pan_kinase; cl17198 887061002225 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 887061002226 E3 interaction surface; other site 887061002227 lipoyl attachment site [posttranslational modification]; other site 887061002228 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 887061002229 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 887061002230 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 887061002231 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 887061002232 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 887061002233 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 887061002234 E3 interaction surface; other site 887061002235 lipoyl attachment site [posttranslational modification]; other site 887061002236 e3 binding domain; Region: E3_binding; pfam02817 887061002237 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 887061002238 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 887061002239 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 887061002240 dimer interface [polypeptide binding]; other site 887061002241 TPP-binding site [chemical binding]; other site 887061002242 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 887061002243 interface (dimer of trimers) [polypeptide binding]; other site 887061002244 Substrate-binding/catalytic site; other site 887061002245 Zn-binding sites [ion binding]; other site 887061002246 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061002247 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 887061002248 ligand binding site [chemical binding]; other site 887061002249 flexible hinge region; other site 887061002250 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 887061002251 non-specific DNA interactions [nucleotide binding]; other site 887061002252 DNA binding site [nucleotide binding] 887061002253 sequence specific DNA binding site [nucleotide binding]; other site 887061002254 putative cAMP binding site [chemical binding]; other site 887061002255 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 887061002256 TrkA-N domain; Region: TrkA_N; pfam02254 887061002257 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 887061002258 TrkA-N domain; Region: TrkA_N; pfam02254 887061002259 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 887061002260 putative active site [active] 887061002261 putative metal binding residues [ion binding]; other site 887061002262 signature motif; other site 887061002263 putative triphosphate binding site [ion binding]; other site 887061002264 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 887061002265 ParA-like protein; Provisional; Region: PHA02518 887061002266 P-loop; other site 887061002267 Magnesium ion binding site [ion binding]; other site 887061002268 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 887061002269 catalytic core [active] 887061002270 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 887061002271 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 887061002272 DHH family; Region: DHH; pfam01368 887061002273 DHHA1 domain; Region: DHHA1; pfam02272 887061002274 triosephosphate isomerase; Provisional; Region: PRK14567 887061002275 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 887061002276 substrate binding site [chemical binding]; other site 887061002277 dimer interface [polypeptide binding]; other site 887061002278 catalytic triad [active] 887061002279 preprotein translocase subunit SecG; Reviewed; Region: secG; PRK06870 887061002280 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 887061002281 NADH dehydrogenase subunit B; Validated; Region: PRK06411 887061002282 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 887061002283 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 887061002284 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 887061002285 NADH dehydrogenase subunit D; Validated; Region: PRK06075 887061002286 NADH dehydrogenase subunit E; Validated; Region: PRK07539 887061002287 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 887061002288 putative dimer interface [polypeptide binding]; other site 887061002289 [2Fe-2S] cluster binding site [ion binding]; other site 887061002290 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 887061002291 SLBB domain; Region: SLBB; pfam10531 887061002292 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 887061002293 NADH dehydrogenase subunit G; Validated; Region: PRK09129 887061002294 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 887061002295 catalytic loop [active] 887061002296 iron binding site [ion binding]; other site 887061002297 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 887061002298 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 as...; Region: MopB_NDH-1_NuoG2; cd02772 887061002299 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 887061002300 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 887061002301 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 887061002302 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 887061002303 4Fe-4S binding domain; Region: Fer4; pfam00037 887061002304 4Fe-4S binding domain; Region: Fer4; pfam00037 887061002305 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 887061002306 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 887061002307 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 887061002308 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 887061002309 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 887061002310 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 887061002311 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 887061002312 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 887061002313 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 887061002314 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 887061002315 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 887061002316 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 887061002317 dimer interface [polypeptide binding]; other site 887061002318 ADP-ribose binding site [chemical binding]; other site 887061002319 active site 887061002320 nudix motif; other site 887061002321 metal binding site [ion binding]; metal-binding site 887061002322 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 887061002323 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 887061002324 putative NAD(P) binding site [chemical binding]; other site 887061002325 tyrosine decarboxylase; Region: PLN02880 887061002326 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 887061002327 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061002328 catalytic residue [active] 887061002329 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 887061002330 Acetamidase/Formamidase family; Region: FmdA_AmdA; pfam03069 887061002331 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 887061002332 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 887061002333 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 887061002334 putative ligand binding site [chemical binding]; other site 887061002335 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 887061002336 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 887061002337 TM-ABC transporter signature motif; other site 887061002338 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 887061002339 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 887061002340 TM-ABC transporter signature motif; other site 887061002341 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 887061002342 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 887061002343 Walker A/P-loop; other site 887061002344 ATP binding site [chemical binding]; other site 887061002345 Q-loop/lid; other site 887061002346 ABC transporter signature motif; other site 887061002347 Walker B; other site 887061002348 D-loop; other site 887061002349 H-loop/switch region; other site 887061002350 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 887061002351 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 887061002352 Walker A/P-loop; other site 887061002353 ATP binding site [chemical binding]; other site 887061002354 Q-loop/lid; other site 887061002355 ABC transporter signature motif; other site 887061002356 Walker B; other site 887061002357 D-loop; other site 887061002358 H-loop/switch region; other site 887061002359 UreD urease accessory protein; Region: UreD; pfam01774 887061002360 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 887061002361 alpha-gamma subunit interface [polypeptide binding]; other site 887061002362 beta-gamma subunit interface [polypeptide binding]; other site 887061002363 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 887061002364 gamma-beta subunit interface [polypeptide binding]; other site 887061002365 alpha-beta subunit interface [polypeptide binding]; other site 887061002366 urease subunit alpha; Reviewed; Region: ureC; PRK13207 887061002367 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 887061002368 subunit interactions [polypeptide binding]; other site 887061002369 active site 887061002370 flap region; other site 887061002371 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 887061002372 dimer interface [polypeptide binding]; other site 887061002373 catalytic residues [active] 887061002374 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 887061002375 UreF; Region: UreF; pfam01730 887061002376 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 887061002377 HupE / UreJ protein; Region: HupE_UreJ; pfam04955 887061002378 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 887061002379 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061002380 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061002381 dimer interface [polypeptide binding]; other site 887061002382 phosphorylation site [posttranslational modification] 887061002383 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 887061002384 ATP binding site [chemical binding]; other site 887061002385 Mg2+ binding site [ion binding]; other site 887061002386 G-X-G motif; other site 887061002387 Response regulator receiver domain; Region: Response_reg; pfam00072 887061002388 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002389 active site 887061002390 phosphorylation site [posttranslational modification] 887061002391 intermolecular recognition site; other site 887061002392 dimerization interface [polypeptide binding]; other site 887061002393 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002394 active site 887061002395 phosphorylation site [posttranslational modification] 887061002396 intermolecular recognition site; other site 887061002397 dimerization interface [polypeptide binding]; other site 887061002398 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061002399 DNA binding residues [nucleotide binding] 887061002400 dimerization interface [polypeptide binding]; other site 887061002401 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 887061002402 Catalytic domain of Protein Kinases; Region: PKc; cd00180 887061002403 active site 887061002404 ATP binding site [chemical binding]; other site 887061002405 substrate binding site [chemical binding]; other site 887061002406 activation loop (A-loop); other site 887061002407 HDOD domain; Region: HDOD; pfam08668 887061002408 Protein of unknown function (DUF2789); Region: DUF2789; pfam10982 887061002409 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 887061002410 endonuclease III; Region: ENDO3c; smart00478 887061002411 minor groove reading motif; other site 887061002412 helix-hairpin-helix signature motif; other site 887061002413 substrate binding pocket [chemical binding]; other site 887061002414 active site 887061002415 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 887061002416 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 887061002417 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 887061002418 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 887061002419 active site 887061002420 dimer interface [polypeptide binding]; other site 887061002421 motif 1; other site 887061002422 motif 2; other site 887061002423 motif 3; other site 887061002424 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 887061002425 anticodon binding site; other site 887061002426 translation initiation factor IF-3; Region: infC; TIGR00168 887061002427 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 887061002428 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 887061002429 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 887061002430 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 887061002431 23S rRNA binding site [nucleotide binding]; other site 887061002432 L21 binding site [polypeptide binding]; other site 887061002433 L13 binding site [polypeptide binding]; other site 887061002434 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 887061002435 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 887061002436 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 887061002437 dimer interface [polypeptide binding]; other site 887061002438 motif 1; other site 887061002439 active site 887061002440 motif 2; other site 887061002441 motif 3; other site 887061002442 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 887061002443 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 887061002444 putative tRNA-binding site [nucleotide binding]; other site 887061002445 B3/4 domain; Region: B3_4; pfam03483 887061002446 tRNA synthetase B5 domain; Region: B5; smart00874 887061002447 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 887061002448 dimer interface [polypeptide binding]; other site 887061002449 motif 1; other site 887061002450 motif 3; other site 887061002451 motif 2; other site 887061002452 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 887061002453 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 887061002454 IHF - DNA interface [nucleotide binding]; other site 887061002455 IHF dimer interface [polypeptide binding]; other site 887061002456 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 887061002457 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 887061002458 DNA binding residues [nucleotide binding] 887061002459 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061002460 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 887061002461 N-terminal plug; other site 887061002462 ligand-binding site [chemical binding]; other site 887061002463 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061002464 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 887061002465 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 887061002466 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 887061002467 N-terminal plug; other site 887061002468 ligand-binding site [chemical binding]; other site 887061002469 DEAD-like helicases superfamily; Region: DEXDc; smart00487 887061002470 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; cl17251 887061002471 ATP binding site [chemical binding]; other site 887061002472 putative Mg++ binding site [ion binding]; other site 887061002473 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 887061002474 nucleotide binding region [chemical binding]; other site 887061002475 ATP-binding site [chemical binding]; other site 887061002476 Mitochondrial degradasome RNA helicase subunit C terminal; Region: SUV3_C; pfam12513 887061002477 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 887061002478 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 887061002479 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 887061002480 Walker A motif; other site 887061002481 ATP binding site [chemical binding]; other site 887061002482 Walker B motif; other site 887061002483 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 887061002484 HAMP domain; Region: HAMP; pfam00672 887061002485 dimerization interface [polypeptide binding]; other site 887061002486 Histidine kinase; Region: HisKA_3; pfam07730 887061002487 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 887061002488 ATP binding site [chemical binding]; other site 887061002489 Mg2+ binding site [ion binding]; other site 887061002490 G-X-G motif; other site 887061002491 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061002492 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002493 active site 887061002494 phosphorylation site [posttranslational modification] 887061002495 intermolecular recognition site; other site 887061002496 dimerization interface [polypeptide binding]; other site 887061002497 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061002498 DNA binding residues [nucleotide binding] 887061002499 dimerization interface [polypeptide binding]; other site 887061002500 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061002501 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002502 active site 887061002503 phosphorylation site [posttranslational modification] 887061002504 intermolecular recognition site; other site 887061002505 dimerization interface [polypeptide binding]; other site 887061002506 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061002507 DNA binding residues [nucleotide binding] 887061002508 dimerization interface [polypeptide binding]; other site 887061002509 PAS domain; Region: PAS_9; pfam13426 887061002510 Histidine kinase; Region: HisKA_3; pfam07730 887061002511 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 887061002512 ATP binding site [chemical binding]; other site 887061002513 Mg2+ binding site [ion binding]; other site 887061002514 G-X-G motif; other site 887061002515 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061002516 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 887061002517 Trp docking motif [polypeptide binding]; other site 887061002518 dimer interface [polypeptide binding]; other site 887061002519 active site 887061002520 small subunit binding site [polypeptide binding]; other site 887061002521 methanol oxidation system protein MoxJ; Region: ABC_MoxJ; TIGR03870 887061002522 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061002523 substrate binding pocket [chemical binding]; other site 887061002524 membrane-bound complex binding site; other site 887061002525 hinge residues; other site 887061002526 cytochrome c(L), periplasmic; Region: cytochrome_MoxG; TIGR03872 887061002527 Methanol dehydrogenase beta subunit; Region: MDH; pfam02315 887061002528 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061002529 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 887061002530 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061002531 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061002532 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 887061002533 metal ion-dependent adhesion site (MIDAS); other site 887061002534 von Willebrand factor type A domain; Region: VWA_2; pfam13519 887061002535 metal ion-dependent adhesion site (MIDAS); other site 887061002536 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061002537 putative hydrophobic ligand binding site [chemical binding]; other site 887061002538 protein interface [polypeptide binding]; other site 887061002539 gate; other site 887061002540 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 887061002541 PAS fold; Region: PAS_3; pfam08447 887061002542 putative active site [active] 887061002543 heme pocket [chemical binding]; other site 887061002544 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 887061002545 Histidine kinase; Region: HisKA_3; pfam07730 887061002546 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 887061002547 ATP binding site [chemical binding]; other site 887061002548 Mg2+ binding site [ion binding]; other site 887061002549 G-X-G motif; other site 887061002550 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061002551 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002552 active site 887061002553 phosphorylation site [posttranslational modification] 887061002554 intermolecular recognition site; other site 887061002555 dimerization interface [polypeptide binding]; other site 887061002556 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061002557 DNA binding residues [nucleotide binding] 887061002558 dimerization interface [polypeptide binding]; other site 887061002559 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 887061002560 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 887061002561 FlaG protein; Region: FlaG; pfam03646 887061002562 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 887061002563 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 887061002564 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 887061002565 flagellar protein FliS; Validated; Region: fliS; PRK05685 887061002566 Flagellar protein FliT; Region: FliT; pfam05400 887061002567 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 887061002568 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 887061002569 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 887061002570 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 887061002571 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 887061002572 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 887061002573 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 887061002574 FliG C-terminal domain; Region: FliG_C; pfam01706 887061002575 flagellar assembly protein H; Validated; Region: fliH; PRK05687 887061002576 Flagellar assembly protein FliH; Region: FliH; pfam02108 887061002577 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 887061002578 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 887061002579 Walker A motif/ATP binding site; other site 887061002580 Walker B motif; other site 887061002581 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 887061002582 Flagellar FliJ protein; Region: FliJ; pfam02050 887061002583 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 887061002584 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07021 887061002585 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 887061002586 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 887061002587 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 887061002588 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 887061002589 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 887061002590 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 887061002591 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 887061002592 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 887061002593 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 887061002594 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 887061002595 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 887061002596 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 887061002597 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 887061002598 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 887061002599 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 887061002600 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 887061002601 Flagellar L-ring protein; Region: FlgH; pfam02107 887061002602 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 887061002603 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 887061002604 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 887061002605 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 887061002606 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 887061002607 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 887061002608 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 887061002609 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 887061002610 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 887061002611 Flagellar hook capping protein [Cell motility and secretion]; Region: FlgD; COG1843 887061002612 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 887061002613 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 887061002614 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 887061002615 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 887061002616 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 887061002617 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 887061002618 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK07018 887061002619 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 887061002620 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 887061002621 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 887061002622 FlgN protein; Region: FlgN; pfam05130 887061002623 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 887061002624 VRR-NUC domain; Region: VRR_NUC; cl17748 887061002625 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 887061002626 This model contains proteins with the VRR-NUC domain; Region: VRR_NUC; smart00990 887061002627 VRR-NUC domain; Region: VRR_NUC; cl17748 887061002628 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 887061002629 MgtC family; Region: MgtC; pfam02308 887061002630 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 887061002631 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 887061002632 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 887061002633 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 887061002634 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 887061002635 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061002636 ligand binding site [chemical binding]; other site 887061002637 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 887061002638 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 887061002639 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 887061002640 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061002641 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 887061002642 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061002643 DNA binding residues [nucleotide binding] 887061002644 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 887061002645 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 887061002646 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 887061002647 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 887061002648 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 887061002649 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 887061002650 FHIPEP family; Region: FHIPEP; pfam00771 887061002651 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 887061002652 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 887061002653 transcriptional activator FlhD; Provisional; Region: PRK02909 887061002654 transcriptional activator FlhC; Provisional; Region: PRK12722 887061002655 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 887061002656 S-adenosylmethionine binding site [chemical binding]; other site 887061002657 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061002658 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061002659 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 887061002660 N-terminal plug; other site 887061002661 ligand-binding site [chemical binding]; other site 887061002662 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061002663 FecR protein; Region: FecR; pfam04773 887061002664 RNA polymerase sigma factor FecI; Provisional; Region: PRK09651 887061002665 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061002666 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 887061002667 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 887061002668 flagellar motor protein MotA; Validated; Region: PRK09110 887061002669 flagellar motor protein MotB; Validated; Region: motB; PRK09041 887061002670 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 887061002671 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061002672 ligand binding site [chemical binding]; other site 887061002673 Response regulator receiver domain; Region: Response_reg; pfam00072 887061002674 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002675 active site 887061002676 phosphorylation site [posttranslational modification] 887061002677 intermolecular recognition site; other site 887061002678 dimerization interface [polypeptide binding]; other site 887061002679 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 887061002680 putative binding surface; other site 887061002681 active site 887061002682 CheY binding; Region: CheY-binding; pfam09078 887061002683 CheY binding; Region: CheY-binding; pfam09078 887061002684 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 887061002685 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 887061002686 ATP binding site [chemical binding]; other site 887061002687 Mg2+ binding site [ion binding]; other site 887061002688 G-X-G motif; other site 887061002689 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 887061002690 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 887061002691 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 887061002692 PAS domain; Region: PAS_9; pfam13426 887061002693 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061002694 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061002695 dimer interface [polypeptide binding]; other site 887061002696 putative CheW interface [polypeptide binding]; other site 887061002697 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 887061002698 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 887061002699 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 887061002700 chemoreceptor glutamine deamidase CheD; Provisional; Region: PRK13487 887061002701 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 887061002702 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002703 active site 887061002704 phosphorylation site [posttranslational modification] 887061002705 intermolecular recognition site; other site 887061002706 dimerization interface [polypeptide binding]; other site 887061002707 CheB methylesterase; Region: CheB_methylest; pfam01339 887061002708 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 887061002709 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002710 active site 887061002711 phosphorylation site [posttranslational modification] 887061002712 intermolecular recognition site; other site 887061002713 dimerization interface [polypeptide binding]; other site 887061002714 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 887061002715 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 887061002716 metal-binding site [ion binding] 887061002717 phosphoglucomutase; Region: PLN02307 887061002718 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 direction; Region: PGM1; cd03085 887061002719 substrate binding site [chemical binding]; other site 887061002720 dimer interface [polypeptide binding]; other site 887061002721 active site 887061002722 metal binding site [ion binding]; metal-binding site 887061002723 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 887061002724 catalytic motif [active] 887061002725 Catalytic residue [active] 887061002726 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 887061002727 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 887061002728 active site 887061002729 substrate binding site [chemical binding]; other site 887061002730 metal binding site [ion binding]; metal-binding site 887061002731 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 887061002732 HemN C-terminal domain; Region: HemN_C; pfam06969 887061002733 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 887061002734 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 887061002735 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 887061002736 active site 887061002737 FMN binding site [chemical binding]; other site 887061002738 substrate binding site [chemical binding]; other site 887061002739 homotetramer interface [polypeptide binding]; other site 887061002740 catalytic residue [active] 887061002741 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 887061002742 Fumarase C-terminus; Region: Fumerase_C; pfam05683 887061002743 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 887061002744 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 887061002745 dimer interface [polypeptide binding]; other site 887061002746 active site 887061002747 glycine-pyridoxal phosphate binding site [chemical binding]; other site 887061002748 folate binding site [chemical binding]; other site 887061002749 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 887061002750 ATP cone domain; Region: ATP-cone; pfam03477 887061002751 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 887061002752 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 887061002753 catalytic motif [active] 887061002754 Zn binding site [ion binding]; other site 887061002755 RibD C-terminal domain; Region: RibD_C; cl17279 887061002756 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 887061002757 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 887061002758 active site 887061002759 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 887061002760 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 887061002761 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 887061002762 Tetratricopeptide repeat; Region: TPR_16; pfam13432 887061002763 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 887061002764 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061002765 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 887061002766 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 887061002767 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 887061002768 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061002769 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 887061002770 Walker A motif; other site 887061002771 ATP binding site [chemical binding]; other site 887061002772 Walker B motif; other site 887061002773 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061002774 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061002775 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061002776 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 887061002777 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 887061002778 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 887061002779 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 887061002780 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061002781 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061002782 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 887061002783 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182 887061002784 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 887061002785 intersubunit interface [polypeptide binding]; other site 887061002786 active site 887061002787 Zn2+ binding site [ion binding]; other site 887061002788 Uncharacterized conserved protein [Function unknown]; Region: COG0062 887061002789 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 887061002790 putative substrate binding site [chemical binding]; other site 887061002791 putative ATP binding site [chemical binding]; other site 887061002792 CTP synthetase; Validated; Region: pyrG; PRK05380 887061002793 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 887061002794 Catalytic site [active] 887061002795 active site 887061002796 UTP binding site [chemical binding]; other site 887061002797 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 887061002798 active site 887061002799 putative oxyanion hole; other site 887061002800 catalytic triad [active] 887061002801 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 887061002802 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 887061002803 enolase; Provisional; Region: eno; PRK00077 887061002804 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 887061002805 dimer interface [polypeptide binding]; other site 887061002806 metal binding site [ion binding]; metal-binding site 887061002807 substrate binding pocket [chemical binding]; other site 887061002808 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 887061002809 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 887061002810 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061002811 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061002812 metal binding site [ion binding]; metal-binding site 887061002813 active site 887061002814 I-site; other site 887061002815 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 887061002816 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 887061002817 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 887061002818 von Willebrand factor type A domain; Region: VWA_2; pfam13519 887061002819 metal ion-dependent adhesion site (MIDAS); other site 887061002820 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 887061002821 metal ion-dependent adhesion site (MIDAS); other site 887061002822 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061002823 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061002824 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061002825 Walker A motif; other site 887061002826 ATP binding site [chemical binding]; other site 887061002827 Walker B motif; other site 887061002828 arginine finger; other site 887061002829 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 887061002830 active site 1 [active] 887061002831 dimer interface [polypeptide binding]; other site 887061002832 active site 2 [active] 887061002833 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 887061002834 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 887061002835 dimer interface [polypeptide binding]; other site 887061002836 active site 887061002837 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 887061002838 aminotransferase AlaT; Validated; Region: PRK09265 887061002839 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 887061002840 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002841 homodimer interface [polypeptide binding]; other site 887061002842 catalytic residue [active] 887061002843 homoserine dehydrogenase; Provisional; Region: PRK06349 887061002844 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 887061002845 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 887061002846 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 887061002847 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 887061002848 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 887061002849 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061002850 catalytic residue [active] 887061002851 thymidylate synthase; Reviewed; Region: thyA; PRK01827 887061002852 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 887061002853 dimerization interface [polypeptide binding]; other site 887061002854 active site 887061002855 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 887061002856 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 887061002857 BON domain; Region: BON; pfam04972 887061002858 response regulator GlrR; Provisional; Region: PRK15115 887061002859 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061002860 active site 887061002861 phosphorylation site [posttranslational modification] 887061002862 intermolecular recognition site; other site 887061002863 dimerization interface [polypeptide binding]; other site 887061002864 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061002865 Walker A motif; other site 887061002866 ATP binding site [chemical binding]; other site 887061002867 Walker B motif; other site 887061002868 arginine finger; other site 887061002869 CHASE3 domain; Region: CHASE3; cl05000 887061002870 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061002871 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 887061002872 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061002873 dimer interface [polypeptide binding]; other site 887061002874 phosphorylation site [posttranslational modification] 887061002875 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 887061002876 ATP binding site [chemical binding]; other site 887061002877 Mg2+ binding site [ion binding]; other site 887061002878 G-X-G motif; other site 887061002879 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 887061002880 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 887061002881 folate binding site [chemical binding]; other site 887061002882 NADP+ binding site [chemical binding]; other site 887061002883 TPR repeat; Region: TPR_11; pfam13414 887061002884 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 887061002885 binding surface 887061002886 TPR motif; other site 887061002887 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 887061002888 TPR motif; other site 887061002889 binding surface 887061002890 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 887061002891 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 887061002892 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 887061002893 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 887061002894 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061002895 catalytic residue [active] 887061002896 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 887061002897 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 887061002898 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 887061002899 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 887061002900 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 887061002901 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 887061002902 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 887061002903 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 887061002904 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 887061002905 metal binding site 2 [ion binding]; metal-binding site 887061002906 putative DNA binding helix; other site 887061002907 metal binding site 1 [ion binding]; metal-binding site 887061002908 dimer interface [polypeptide binding]; other site 887061002909 structural Zn2+ binding site [ion binding]; other site 887061002910 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 887061002911 RNB domain; Region: RNB; pfam00773 887061002912 spermidine synthase; Provisional; Region: PRK04457 887061002913 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 887061002914 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 887061002915 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; cl17173 887061002916 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs; Region: NTP-PPase_RS21-C6_like; cd11537 887061002917 homodimer interface [polypeptide binding]; other site 887061002918 chemical substrate binding site [chemical binding]; other site 887061002919 oligomer interface [polypeptide binding]; other site 887061002920 metal binding site [ion binding]; metal-binding site 887061002921 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 887061002922 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 887061002923 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 887061002924 dimerization interface [polypeptide binding]; other site 887061002925 ATP binding site [chemical binding]; other site 887061002926 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 887061002927 dimerization interface [polypeptide binding]; other site 887061002928 ATP binding site [chemical binding]; other site 887061002929 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 887061002930 putative active site [active] 887061002931 catalytic triad [active] 887061002932 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 887061002933 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002934 Cytochrome c553 [Energy production and conversion]; Region: COG2863 887061002935 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 887061002936 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 887061002937 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 887061002938 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 887061002939 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 887061002940 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 887061002941 phosphoserine phosphatase SerB; Region: serB; TIGR00338 887061002942 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 887061002943 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 887061002944 motif II; other site 887061002945 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 887061002946 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 887061002947 CoA-ligase; Region: Ligase_CoA; pfam00549 887061002948 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 887061002949 CoA binding domain; Region: CoA_binding; pfam02629 887061002950 CoA-ligase; Region: Ligase_CoA; pfam00549 887061002951 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002952 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 887061002953 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 887061002954 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 887061002955 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002956 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 887061002957 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 887061002958 NAD synthetase; Provisional; Region: PRK13981 887061002959 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 887061002960 multimer interface [polypeptide binding]; other site 887061002961 active site 887061002962 catalytic triad [active] 887061002963 protein interface 1 [polypeptide binding]; other site 887061002964 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 887061002965 homodimer interface [polypeptide binding]; other site 887061002966 NAD binding pocket [chemical binding]; other site 887061002967 ATP binding pocket [chemical binding]; other site 887061002968 Mg binding site [ion binding]; other site 887061002969 active-site loop [active] 887061002970 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 887061002971 Nitrogen regulatory protein P-II; Region: P-II; smart00938 887061002972 Protein of unknown function, DUF486; Region: DUF486; cl01236 887061002973 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 887061002974 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 887061002975 G1 box; other site 887061002976 GTP/Mg2+ binding site [chemical binding]; other site 887061002977 Switch I region; other site 887061002978 G2 box; other site 887061002979 G3 box; other site 887061002980 Switch II region; other site 887061002981 G4 box; other site 887061002982 G5 box; other site 887061002983 Nucleoside recognition; Region: Gate; pfam07670 887061002984 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 887061002985 Nucleoside recognition; Region: Gate; pfam07670 887061002986 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 887061002987 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 887061002988 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 887061002989 SurA N-terminal domain; Region: SurA_N_3; cl07813 887061002990 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 887061002991 BolA-like protein; Region: BolA; pfam01722 887061002992 YciI-like protein; Reviewed; Region: PRK11370 887061002993 intracellular septation protein A; Reviewed; Region: PRK00259 887061002994 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 887061002995 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 887061002996 active site 887061002997 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 887061002998 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 887061002999 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 887061003000 Peptidase family M50; Region: Peptidase_M50; pfam02163 887061003001 active site 887061003002 putative substrate binding region [chemical binding]; other site 887061003003 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 887061003004 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 887061003005 active site 887061003006 HIGH motif; other site 887061003007 dimer interface [polypeptide binding]; other site 887061003008 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 887061003009 active site 887061003010 KMSKS motif; other site 887061003011 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 887061003012 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 887061003013 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 887061003014 23S rRNA pseudouridylate synthase B; Provisional; Region: PRK10700 887061003015 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 887061003016 RNA binding surface [nucleotide binding]; other site 887061003017 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 887061003018 probable active site [active] 887061003019 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 887061003020 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 887061003021 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 887061003022 N-terminal plug; other site 887061003023 ligand-binding site [chemical binding]; other site 887061003024 HemK family putative methylases; Region: hemK_fam; TIGR00536 887061003025 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 887061003026 S-adenosylmethionine binding site [chemical binding]; other site 887061003027 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 887061003028 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 887061003029 metal binding site [ion binding]; metal-binding site 887061003030 dimer interface [polypeptide binding]; other site 887061003031 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 887061003032 ArsC family; Region: ArsC; pfam03960 887061003033 putative catalytic residues [active] 887061003034 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 887061003035 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 887061003036 trimer interface [polypeptide binding]; other site 887061003037 active site 887061003038 substrate binding site [chemical binding]; other site 887061003039 CoA binding site [chemical binding]; other site 887061003040 Peptidase family M48; Region: Peptidase_M48; pfam01435 887061003041 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 887061003042 potassium uptake protein; Region: kup; TIGR00794 887061003043 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 887061003044 PEP-CTERM motif; Region: VPEP; pfam07589 887061003045 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 887061003046 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 887061003047 generic binding surface II; other site 887061003048 generic binding surface I; other site 887061003049 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 887061003050 cysteine synthase B; Region: cysM; TIGR01138 887061003051 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 887061003052 dimer interface [polypeptide binding]; other site 887061003053 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061003054 catalytic residue [active] 887061003055 Protein of unknown function (DUF1318); Region: DUF1318; cl01547 887061003056 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 887061003057 active site 887061003058 catalytic site [active] 887061003059 substrate binding site [chemical binding]; other site 887061003060 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 887061003061 Protein of unknown function (DUF1236); Region: DUF1236; pfam06823 887061003062 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 887061003063 ABC transporter periplasmic binding protein, urea carboxylase region; Region: ABC_peri_uca; TIGR03427 887061003064 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061003065 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061003066 dimer interface [polypeptide binding]; other site 887061003067 conserved gate region; other site 887061003068 putative PBP binding loops; other site 887061003069 ABC-ATPase subunit interface; other site 887061003070 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061003071 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 887061003072 Walker A/P-loop; other site 887061003073 ATP binding site [chemical binding]; other site 887061003074 Q-loop/lid; other site 887061003075 ABC transporter signature motif; other site 887061003076 Walker B; other site 887061003077 D-loop; other site 887061003078 H-loop/switch region; other site 887061003079 Creatinine amidohydrolase; Region: Creatininase; pfam02633 887061003080 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 887061003081 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 887061003082 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain [Transcription]; Region: NikR; COG0864 887061003083 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 887061003084 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 887061003085 urea carboxylase-associated protein 2; Region: urea_degr_2; TIGR03425 887061003086 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 887061003087 urea carboxylase-associated protein 1; Region: urea_degr_1; TIGR03424 887061003088 Domain of unknown function (DUF1989); Region: DUF1989; pfam09347 887061003089 urea carboxylase; Region: urea_carbox; TIGR02712 887061003090 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061003091 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061003092 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 887061003093 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 887061003094 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 887061003095 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 887061003096 carboxyltransferase (CT) interaction site; other site 887061003097 biotinylation site [posttranslational modification]; other site 887061003098 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 887061003099 Amidase; Region: Amidase; cl11426 887061003100 allophanate hydrolase; Provisional; Region: PRK08186 887061003101 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 887061003102 ethanolamine permease; Region: 2A0305; TIGR00908 887061003103 hypothetical protein; Provisional; Region: PHA02764 887061003104 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 887061003105 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 887061003106 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 887061003107 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 887061003108 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 887061003109 HSP70 interaction site [polypeptide binding]; other site 887061003110 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 887061003111 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 887061003112 Helix-turn-helix domain; Region: HTH_18; pfam12833 887061003113 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 887061003114 TRAM domain; Region: TRAM; cl01282 887061003115 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 887061003116 S-adenosylmethionine binding site [chemical binding]; other site 887061003117 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 887061003118 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061003119 Coenzyme A binding pocket [chemical binding]; other site 887061003120 Isochorismatase family; Region: Isochorismatase; pfam00857 887061003121 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 887061003122 catalytic triad [active] 887061003123 conserved cis-peptide bond; other site 887061003124 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 887061003125 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 887061003126 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 887061003127 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 887061003128 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 887061003129 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 887061003130 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 887061003131 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061003132 putative PBP binding loops; other site 887061003133 dimer interface [polypeptide binding]; other site 887061003134 ABC-ATPase subunit interface; other site 887061003135 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 887061003136 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061003137 dimer interface [polypeptide binding]; other site 887061003138 conserved gate region; other site 887061003139 putative PBP binding loops; other site 887061003140 ABC-ATPase subunit interface; other site 887061003141 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 887061003142 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 887061003143 beta-hexosaminidase; Provisional; Region: PRK05337 887061003144 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 887061003145 YccA-like proteins; Region: YccA_like; cd10433 887061003146 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 887061003147 nucleoside/Zn binding site; other site 887061003148 dimer interface [polypeptide binding]; other site 887061003149 catalytic motif [active] 887061003150 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 887061003151 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061003152 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 887061003153 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 887061003154 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061003155 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061003156 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061003157 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061003158 Walker A motif; other site 887061003159 ATP binding site [chemical binding]; other site 887061003160 Walker B motif; other site 887061003161 arginine finger; other site 887061003162 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061003163 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 887061003164 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 887061003165 dimerization interface [polypeptide binding]; other site 887061003166 Pirin-related protein [General function prediction only]; Region: COG1741 887061003167 Pirin; Region: Pirin; pfam02678 887061003168 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 887061003169 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 887061003170 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 887061003171 YceI-like domain; Region: YceI; cl01001 887061003172 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 887061003173 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 887061003174 FMN binding site [chemical binding]; other site 887061003175 active site 887061003176 substrate binding site [chemical binding]; other site 887061003177 catalytic residue [active] 887061003178 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 887061003179 putative FMN binding site [chemical binding]; other site 887061003180 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 887061003181 catalytic residues [active] 887061003182 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 887061003183 Peptidase family M23; Region: Peptidase_M23; pfam01551 887061003184 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 887061003185 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 887061003186 S-adenosylmethionine binding site [chemical binding]; other site 887061003187 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 887061003188 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 887061003189 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 887061003190 Pyridoxamine 5'-phosphate oxidase; Region: Pyrid_oxidase_2; pfam13883 887061003191 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 887061003192 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 887061003193 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 887061003194 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 887061003195 putative metal binding site [ion binding]; other site 887061003196 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 887061003197 adenylosuccinate lyase; Provisional; Region: PRK09285 887061003198 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 887061003199 tetramer interface [polypeptide binding]; other site 887061003200 active site 887061003201 EF-hand domain pair; Region: EF_hand_5; pfam13499 887061003202 PAS domain; Region: PAS_9; pfam13426 887061003203 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 887061003204 putative active site [active] 887061003205 heme pocket [chemical binding]; other site 887061003206 PAS fold; Region: PAS_4; pfam08448 887061003207 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 887061003208 putative active site [active] 887061003209 heme pocket [chemical binding]; other site 887061003210 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003211 metal binding site [ion binding]; metal-binding site 887061003212 active site 887061003213 I-site; other site 887061003214 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 887061003215 Predicted transcriptional regulator [Transcription]; Region: COG2932 887061003216 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 887061003217 Catalytic site [active] 887061003218 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 887061003219 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 887061003220 substrate binding site [chemical binding]; other site 887061003221 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 887061003222 substrate binding site [chemical binding]; other site 887061003223 ligand binding site [chemical binding]; other site 887061003224 Protein of unknown function (DUF3016); Region: DUF3016; pfam11454 887061003225 hypothetical protein; Provisional; Region: PRK05208 887061003226 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 887061003227 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 887061003228 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 887061003229 E-class dimer interface [polypeptide binding]; other site 887061003230 P-class dimer interface [polypeptide binding]; other site 887061003231 active site 887061003232 Cu2+ binding site [ion binding]; other site 887061003233 Zn2+ binding site [ion binding]; other site 887061003234 EF-hand domain pair; Region: EF_hand_5; pfam13499 887061003235 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 to...; Region: EFh; cl17302 887061003236 Ca2+ binding site [ion binding]; other site 887061003237 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 887061003238 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 887061003239 active site 1 [active] 887061003240 dimer interface [polypeptide binding]; other site 887061003241 hexamer interface [polypeptide binding]; other site 887061003242 active site 2 [active] 887061003243 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 887061003244 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 887061003245 GIY-YIG motif/motif A; other site 887061003246 active site 887061003247 catalytic site [active] 887061003248 putative DNA binding site [nucleotide binding]; other site 887061003249 metal binding site [ion binding]; metal-binding site 887061003250 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 887061003251 Helix-hairpin-helix motif; Region: HHH; pfam00633 887061003252 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 887061003253 psiF repeat; Region: PsiF_repeat; pfam07769 887061003254 psiF repeat; Region: PsiF_repeat; pfam07769 887061003255 psiF repeat; Region: PsiF_repeat; pfam07769 887061003256 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 887061003257 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 887061003258 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 887061003259 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 887061003260 Walker A/P-loop; other site 887061003261 ATP binding site [chemical binding]; other site 887061003262 Q-loop/lid; other site 887061003263 ABC transporter signature motif; other site 887061003264 Walker B; other site 887061003265 D-loop; other site 887061003266 H-loop/switch region; other site 887061003267 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 887061003268 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061003269 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061003270 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061003271 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061003272 DNA binding residues [nucleotide binding] 887061003273 dimerization interface [polypeptide binding]; other site 887061003274 VCBS repeat; Region: VCBS_repeat; TIGR01965 887061003275 VCBS repeat; Region: VCBS_repeat; TIGR01965 887061003276 VCBS repeat; Region: VCBS_repeat; TIGR01965 887061003277 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 887061003278 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 887061003279 metal ion-dependent adhesion site (MIDAS); other site 887061003280 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 887061003281 biofilm formation regulator HmsP; Provisional; Region: PRK11829 887061003282 HAMP domain; Region: HAMP; pfam00672 887061003283 dimerization interface [polypeptide binding]; other site 887061003284 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003285 metal binding site [ion binding]; metal-binding site 887061003286 active site 887061003287 I-site; other site 887061003288 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 887061003289 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 887061003290 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061003291 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 887061003292 SnoaL-like domain; Region: SnoaL_3; pfam13474 887061003293 cryptochrome, DASH family; Region: crypto_DASH; TIGR02765 887061003294 DNA photolyase; Region: DNA_photolyase; pfam00875 887061003295 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 887061003296 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 887061003297 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 887061003298 GIY-YIG motif/motif A; other site 887061003299 putative active site [active] 887061003300 putative metal binding site [ion binding]; other site 887061003301 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 887061003302 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 887061003303 dimer interface [polypeptide binding]; other site 887061003304 active site 887061003305 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; cl15837 887061003306 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 887061003307 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 887061003308 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 887061003309 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 887061003310 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061003311 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 887061003312 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 887061003313 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 887061003314 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 887061003315 Walker A motif; other site 887061003316 ATP binding site [chemical binding]; other site 887061003317 Walker B motif; other site 887061003318 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 887061003319 ICE2; Region: ICE2; pfam08426 887061003320 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 887061003321 binding surface 887061003322 Tetratricopeptide repeat; Region: TPR_16; pfam13432 887061003323 TPR motif; other site 887061003324 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 887061003325 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 887061003326 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 887061003327 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 887061003328 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 887061003329 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 887061003330 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 887061003331 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 887061003332 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...; Region: LT_GEWL; cd00254 887061003333 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061003334 catalytic residue [active] 887061003335 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 887061003336 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 887061003337 catalytic triad [active] 887061003338 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 887061003339 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 887061003340 active site 887061003341 Int/Topo IB signature motif; other site 887061003342 DNA binding site [nucleotide binding] 887061003343 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 887061003344 Catalytic site [active] 887061003345 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 887061003346 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 887061003347 active site 887061003348 DNA binding site [nucleotide binding] 887061003349 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 887061003350 Transposase, Mutator family; Region: Transposase_mut; pfam00872 887061003351 MULE transposase domain; Region: MULE; pfam10551 887061003352 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 887061003353 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 887061003354 active site 887061003355 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 887061003356 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 887061003357 Chromate transporter; Region: Chromate_transp; pfam02417 887061003358 Protein of unknown function (DUF2380); Region: DUF3280; pfam11684 887061003359 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 887061003360 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 887061003361 binding surface 887061003362 TPR motif; other site 887061003363 TPR repeat; Region: TPR_11; pfam13414 887061003364 TPR repeat; Region: TPR_11; pfam13414 887061003365 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 887061003366 binding surface 887061003367 TPR motif; other site 887061003368 TPR repeat; Region: TPR_11; pfam13414 887061003369 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 887061003370 binding surface 887061003371 TPR motif; other site 887061003372 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 887061003373 binding surface 887061003374 TPR motif; other site 887061003375 Putative 2OG-Fe(II) oxygenase; Region: 2OG-FeII_Oxy_5; pfam13759 887061003376 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 887061003377 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 887061003378 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 887061003379 N-terminal plug; other site 887061003380 ligand-binding site [chemical binding]; other site 887061003381 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 887061003382 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 887061003383 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 887061003384 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 887061003385 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 887061003386 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 887061003387 N-terminal plug; other site 887061003388 ligand-binding site [chemical binding]; other site 887061003389 ABC transporter ATPase component; Reviewed; Region: PRK11147 887061003390 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061003391 Walker A/P-loop; other site 887061003392 ATP binding site [chemical binding]; other site 887061003393 Q-loop/lid; other site 887061003394 ABC transporter signature motif; other site 887061003395 Walker B; other site 887061003396 D-loop; other site 887061003397 H-loop/switch region; other site 887061003398 ABC transporter; Region: ABC_tran_2; pfam12848 887061003399 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 887061003400 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 887061003401 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 887061003402 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 887061003403 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 887061003404 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061003405 active site 887061003406 phosphorylation site [posttranslational modification] 887061003407 intermolecular recognition site; other site 887061003408 dimerization interface [polypeptide binding]; other site 887061003409 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061003410 DNA binding site [nucleotide binding] 887061003411 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 887061003412 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 887061003413 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 887061003414 Ligand Binding Site [chemical binding]; other site 887061003415 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 887061003416 GAF domain; Region: GAF_3; pfam13492 887061003417 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061003418 dimer interface [polypeptide binding]; other site 887061003419 phosphorylation site [posttranslational modification] 887061003420 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 887061003421 ATP binding site [chemical binding]; other site 887061003422 Mg2+ binding site [ion binding]; other site 887061003423 G-X-G motif; other site 887061003424 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 887061003425 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 887061003426 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 887061003427 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 887061003428 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 887061003429 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061003430 putative substrate translocation pore; other site 887061003431 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 887061003432 Part of AAA domain; Region: AAA_19; pfam13245 887061003433 Family description; Region: UvrD_C_2; pfam13538 887061003434 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061003435 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003436 metal binding site [ion binding]; metal-binding site 887061003437 active site 887061003438 I-site; other site 887061003439 MEKHLA domain; Region: MEKHLA; pfam08670 887061003440 CHASE3 domain; Region: CHASE3; pfam05227 887061003441 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061003442 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003443 metal binding site [ion binding]; metal-binding site 887061003444 active site 887061003445 I-site; other site 887061003446 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 887061003447 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 887061003448 GTP/Mg2+ binding site [chemical binding]; other site 887061003449 G4 box; other site 887061003450 G5 box; other site 887061003451 G1 box; other site 887061003452 Switch I region; other site 887061003453 G2 box; other site 887061003454 G3 box; other site 887061003455 Switch II region; other site 887061003456 ApbE family; Region: ApbE; pfam02424 887061003457 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 887061003458 FMN-binding domain; Region: FMN_bind; pfam04205 887061003459 Methyltransferase domain; Region: Methyltransf_32; pfam13679 887061003460 Methyltransferase domain; Region: Methyltransf_31; pfam13847 887061003461 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 887061003462 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 887061003463 MG2 domain; Region: A2M_N; pfam01835 887061003464 Alpha-2-macroglobulin family; Region: A2M; pfam00207 887061003465 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 887061003466 penicillin-binding protein 1C; Region: PBP_1c; TIGR02073 887061003467 Transglycosylase; Region: Transgly; pfam00912 887061003468 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 887061003469 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 887061003470 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 887061003471 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 887061003472 ATP binding site [chemical binding]; other site 887061003473 putative Mg++ binding site [ion binding]; other site 887061003474 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 887061003475 nucleotide binding region [chemical binding]; other site 887061003476 Helicase associated domain (HA2); Region: HA2; pfam04408 887061003477 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 887061003478 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 887061003479 MarR family; Region: MarR_2; cl17246 887061003480 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 887061003481 Fusaric acid resistance protein family; Region: FUSC; pfam04632 887061003482 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 887061003483 Protein of unknown function (DUF1656); Region: DUF1656; pfam07869 887061003484 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 887061003485 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061003486 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061003487 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 887061003488 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061003489 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 887061003490 dimerization interface [polypeptide binding]; other site 887061003491 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 887061003492 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 887061003493 THF binding site; other site 887061003494 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 887061003495 substrate binding site [chemical binding]; other site 887061003496 THF binding site; other site 887061003497 zinc-binding site [ion binding]; other site 887061003498 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 887061003499 EamA-like transporter family; Region: EamA; cl17759 887061003500 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 887061003501 ATP cone domain; Region: ATP-cone; pfam03477 887061003502 ATP cone domain; Region: ATP-cone; pfam03477 887061003503 Class I ribonucleotide reductase; Region: RNR_I; cd01679 887061003504 active site 887061003505 dimer interface [polypeptide binding]; other site 887061003506 catalytic residues [active] 887061003507 effector binding site; other site 887061003508 R2 peptide binding site; other site 887061003509 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 887061003510 dimer interface [polypeptide binding]; other site 887061003511 putative radical transfer pathway; other site 887061003512 diiron center [ion binding]; other site 887061003513 tyrosyl radical; other site 887061003514 AAA domain; Region: AAA_21; pfam13304 887061003515 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 887061003516 putative active site [active] 887061003517 putative metal-binding site [ion binding]; other site 887061003518 Part of AAA domain; Region: AAA_19; pfam13245 887061003519 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 887061003520 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 887061003521 trimer interface [polypeptide binding]; other site 887061003522 active site 887061003523 glucose-6-phosphate 1-dehydrogenase; Provisional; Region: PRK12853 887061003524 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 887061003525 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 887061003526 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 887061003527 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK12490 887061003528 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 887061003529 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 887061003530 putative active site [active] 887061003531 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; cl17173 887061003532 Methyltransferase domain; Region: Methyltransf_23; pfam13489 887061003533 Domain of unknown function DUF59; Region: DUF59; pfam01883 887061003534 antiporter inner membrane protein; Provisional; Region: PRK11670 887061003535 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 887061003536 Walker A motif; other site 887061003537 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 887061003538 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 887061003539 active site 887061003540 HIGH motif; other site 887061003541 KMSKS motif; other site 887061003542 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 887061003543 tRNA binding surface [nucleotide binding]; other site 887061003544 anticodon binding site; other site 887061003545 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 887061003546 dimer interface [polypeptide binding]; other site 887061003547 putative tRNA-binding site [nucleotide binding]; other site 887061003548 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 887061003549 Helix-hairpin-helix motif; Region: HHH; pfam00633 887061003550 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...; Region: OMP_decarboxylase_like; cd04725 887061003551 active site 887061003552 dimer interface [polypeptide binding]; other site 887061003553 tetratricopeptide repeat protein; Provisional; Region: PRK11788 887061003554 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 887061003555 binding surface 887061003556 TPR motif; other site 887061003557 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 887061003558 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 887061003559 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 887061003560 IHF dimer interface [polypeptide binding]; other site 887061003561 IHF - DNA interface [nucleotide binding]; other site 887061003562 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 887061003563 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 887061003564 RNA binding site [nucleotide binding]; other site 887061003565 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 887061003566 RNA binding site [nucleotide binding]; other site 887061003567 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...; Region: S1_RPS1_repeat_ec3; cd05688 887061003568 RNA binding site [nucleotide binding]; other site 887061003569 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...; Region: S1_RPS1_repeat_ec4; cd05689 887061003570 RNA binding site [nucleotide binding]; other site 887061003571 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...; Region: S1_RPS1_repeat_ec5; cd05690 887061003572 RNA binding site [nucleotide binding]; other site 887061003573 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...; Region: S1_RPS1_repeat_ec6; cd05691 887061003574 RNA binding site [nucleotide binding]; other site 887061003575 cytidylate kinase; Provisional; Region: cmk; PRK00023 887061003576 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 887061003577 CMP-binding site; other site 887061003578 The sites determining sugar specificity; other site 887061003579 Predicted membrane protein [Function unknown]; Region: COG3205 887061003580 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 887061003581 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 887061003582 hinge; other site 887061003583 active site 887061003584 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 887061003585 prephenate dehydrogenase; Validated; Region: PRK08507 887061003586 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 887061003587 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 887061003588 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 887061003589 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 887061003590 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 887061003591 PAS domain; Region: PAS_9; pfam13426 887061003592 putative active site [active] 887061003593 heme pocket [chemical binding]; other site 887061003594 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061003595 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003596 metal binding site [ion binding]; metal-binding site 887061003597 active site 887061003598 I-site; other site 887061003599 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 887061003600 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061003601 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003602 metal binding site [ion binding]; metal-binding site 887061003603 active site 887061003604 I-site; other site 887061003605 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061003606 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061003607 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 887061003608 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 887061003609 TAP-like protein; Region: Abhydrolase_4; pfam08386 887061003610 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 887061003611 hypothetical protein; Provisional; Region: PRK01254 887061003612 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 887061003613 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 887061003614 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 887061003615 TraB family; Region: TraB; pfam01963 887061003616 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 887061003617 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 887061003618 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061003619 active site 887061003620 phosphorylation site [posttranslational modification] 887061003621 intermolecular recognition site; other site 887061003622 dimerization interface [polypeptide binding]; other site 887061003623 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061003624 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061003625 active site 887061003626 phosphorylation site [posttranslational modification] 887061003627 intermolecular recognition site; other site 887061003628 dimerization interface [polypeptide binding]; other site 887061003629 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061003630 DNA binding residues [nucleotide binding] 887061003631 dimerization interface [polypeptide binding]; other site 887061003632 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 887061003633 Ferritin-like domain; Region: Ferritin; pfam00210 887061003634 dinuclear metal binding motif [ion binding]; other site 887061003635 CHASE3 domain; Region: CHASE3; pfam05227 887061003636 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 887061003637 Histidine kinase; Region: HisKA_3; pfam07730 887061003638 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 887061003639 ATP binding site [chemical binding]; other site 887061003640 Mg2+ binding site [ion binding]; other site 887061003641 G-X-G motif; other site 887061003642 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 to...; Region: EFh; cl17302 887061003643 Ca2+ binding site [ion binding]; other site 887061003644 BON domain; Region: BON; pfam04972 887061003645 BON domain; Region: BON; pfam04972 887061003646 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 887061003647 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 887061003648 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 887061003649 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 887061003650 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061003651 active site 887061003652 phosphorylation site [posttranslational modification] 887061003653 intermolecular recognition site; other site 887061003654 dimerization interface [polypeptide binding]; other site 887061003655 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061003656 DNA binding site [nucleotide binding] 887061003657 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061003658 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061003659 dimer interface [polypeptide binding]; other site 887061003660 phosphorylation site [posttranslational modification] 887061003661 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 887061003662 ATP binding site [chemical binding]; other site 887061003663 Mg2+ binding site [ion binding]; other site 887061003664 G-X-G motif; other site 887061003665 BON domain; Region: BON; pfam04972 887061003666 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 to...; Region: EFh; cl17302 887061003667 Ca2+ binding site [ion binding]; other site 887061003668 BON domain; Region: BON; pfam04972 887061003669 outer membrane lipoprotein Blc; Provisional; Region: PRK10477 887061003670 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 887061003671 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 887061003672 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 887061003673 DEAD-like helicases superfamily; Region: DEXDc; smart00487 887061003674 ATP binding site [chemical binding]; other site 887061003675 Mg++ binding site [ion binding]; other site 887061003676 motif III; other site 887061003677 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 887061003678 nucleotide binding region [chemical binding]; other site 887061003679 ATP-binding site [chemical binding]; other site 887061003680 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 887061003681 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 887061003682 RNA binding surface [nucleotide binding]; other site 887061003683 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 887061003684 active site 887061003685 uracil binding [chemical binding]; other site 887061003686 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 887061003687 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 887061003688 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061003689 active site 887061003690 dimer interface [polypeptide binding]; other site 887061003691 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481 887061003692 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 887061003693 DAK2 domain; Region: Dak2; cl03685 887061003694 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 887061003695 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 887061003696 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 887061003697 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 887061003698 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 887061003699 dimerization interface [polypeptide binding]; other site 887061003700 domain crossover interface; other site 887061003701 redox-dependent activation switch; other site 887061003702 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 887061003703 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 887061003704 active site 887061003705 HIGH motif; other site 887061003706 nucleotide binding site [chemical binding]; other site 887061003707 active site 887061003708 KMSKS motif; other site 887061003709 Protein of unknown function (DUF3301); Region: DUF3301; pfam11743 887061003710 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 887061003711 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 887061003712 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 887061003713 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 887061003714 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 887061003715 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061003716 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061003717 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 887061003718 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 887061003719 DNA binding site [nucleotide binding] 887061003720 active site 887061003721 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 887061003722 dimerization interface [polypeptide binding]; other site 887061003723 putative DNA binding site [nucleotide binding]; other site 887061003724 putative Zn2+ binding site [ion binding]; other site 887061003725 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 887061003726 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 887061003727 putative metal binding site [ion binding]; other site 887061003728 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 887061003729 Low molecular weight phosphatase family; Region: LMWPc; cd00115 887061003730 active site 887061003731 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 887061003732 Sodium Bile acid symporter family; Region: SBF; cl17470 887061003733 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 887061003734 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 887061003735 dimer interface [polypeptide binding]; other site 887061003736 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 887061003737 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061003738 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061003739 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 887061003740 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 887061003741 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 887061003742 Domain of unknown function (DUF4186); Region: DUF4186; pfam13811 887061003743 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 887061003744 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 887061003745 active site 887061003746 DNA binding site [nucleotide binding] 887061003747 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 887061003748 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 887061003749 Catalytic site [active] 887061003750 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 887061003751 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 887061003752 HAMP domain; Region: HAMP; pfam00672 887061003753 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061003754 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061003755 dimer interface [polypeptide binding]; other site 887061003756 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 887061003757 putative CheW interface [polypeptide binding]; other site 887061003758 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 887061003759 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061003760 ligand binding site [chemical binding]; other site 887061003761 ImcF-related N-terminal domain; Region: ImcF-related_N; pfam14331 887061003762 Type VI secretion lipoprotein; Region: T6SS-SciN; pfam12790 887061003763 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522 887061003764 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 887061003765 PAAR motif; Region: PAAR_motif; pfam05488 887061003766 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 887061003767 catalytic residue [active] 887061003768 Domain of unknown function (DUF1870); Region: DUF1870; pfam08965 887061003769 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 887061003770 PAS domain S-box; Region: sensory_box; TIGR00229 887061003771 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 887061003772 putative active site [active] 887061003773 heme pocket [chemical binding]; other site 887061003774 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061003775 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003776 metal binding site [ion binding]; metal-binding site 887061003777 active site 887061003778 I-site; other site 887061003779 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 887061003780 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 887061003781 cyclopropane fatty acyl phospholipid synthase; Provisional; Region: PRK11705 887061003782 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; cl17173 887061003783 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 887061003784 S-adenosylmethionine binding site [chemical binding]; other site 887061003785 cyclic-di-GMP phosphodiesterase; Provisional; Region: PRK11359 887061003786 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 887061003787 putative active site [active] 887061003788 heme pocket [chemical binding]; other site 887061003789 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 887061003790 putative active site [active] 887061003791 heme pocket [chemical binding]; other site 887061003792 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061003793 metal binding site [ion binding]; metal-binding site 887061003794 active site 887061003795 I-site; other site 887061003796 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 887061003797 Protein of unknown function (DUF779); Region: DUF779; pfam05610 887061003798 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 887061003799 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 887061003800 NAD(P) binding site [chemical binding]; other site 887061003801 catalytic residues [active] 887061003802 formate dehydrogenase subunit gamma; Validated; Region: PRK05988 887061003803 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 887061003804 putative dimer interface [polypeptide binding]; other site 887061003805 [2Fe-2S] cluster binding site [ion binding]; other site 887061003806 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 887061003807 putative dimer interface [polypeptide binding]; other site 887061003808 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 887061003809 SLBB domain; Region: SLBB; pfam10531 887061003810 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 887061003811 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 887061003812 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 887061003813 catalytic loop [active] 887061003814 iron binding site [ion binding]; other site 887061003815 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 887061003816 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 887061003817 [4Fe-4S] binding site [ion binding]; other site 887061003818 molybdopterin cofactor binding site; other site 887061003819 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 887061003820 molybdopterin cofactor binding site; other site 887061003821 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 887061003822 NADH-dependant formate dehydrogenase delta subunit FdsD; Region: FdsD; pfam11390 887061003823 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 887061003824 substrate binding site; other site 887061003825 dimer interface; other site 887061003826 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 887061003827 homotrimer interaction site [polypeptide binding]; other site 887061003828 zinc binding site [ion binding]; other site 887061003829 CDP-binding sites; other site 887061003830 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061003831 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061003832 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061003833 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061003834 Outer membrane efflux protein; Region: OEP; pfam02321 887061003835 Outer membrane efflux protein; Region: OEP; pfam02321 887061003836 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 887061003837 dimer interface [polypeptide binding]; other site 887061003838 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 887061003839 metal binding site [ion binding]; metal-binding site 887061003840 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 887061003841 Smr domain; Region: Smr; pfam01713 887061003842 thioredoxin reductase; Provisional; Region: PRK10262 887061003843 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 887061003844 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 887061003845 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 887061003846 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 887061003847 dimerization interface [polypeptide binding]; other site 887061003848 DPS ferroxidase diiron center [ion binding]; other site 887061003849 ion pore; other site 887061003850 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 887061003851 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 887061003852 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 887061003853 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 887061003854 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 887061003855 recombination factor protein RarA; Reviewed; Region: PRK13342 887061003856 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061003857 Walker A motif; other site 887061003858 ATP binding site [chemical binding]; other site 887061003859 Walker B motif; other site 887061003860 arginine finger; other site 887061003861 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 887061003862 seryl-tRNA synthetase; Provisional; Region: PRK05431 887061003863 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 887061003864 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 887061003865 dimer interface [polypeptide binding]; other site 887061003866 active site 887061003867 motif 1; other site 887061003868 motif 2; other site 887061003869 motif 3; other site 887061003870 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 887061003871 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 887061003872 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 887061003873 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061003874 substrate binding pocket [chemical binding]; other site 887061003875 membrane-bound complex binding site; other site 887061003876 hinge residues; other site 887061003877 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...; Region: LT_GEWL; cd00254 887061003878 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061003879 catalytic residue [active] 887061003880 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 887061003881 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR1; cd08267 887061003882 putative NAD(P) binding site [chemical binding]; other site 887061003883 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 887061003884 Ly49-like protein, N-terminal region; Region: Ly49; pfam08391 887061003885 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 887061003886 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 887061003887 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 887061003888 dimer interface [polypeptide binding]; other site 887061003889 active site 887061003890 acyl carrier protein; Provisional; Region: acpP; PRK00982 887061003891 Esterase/lipase [General function prediction only]; Region: COG1647 887061003892 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 887061003893 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 887061003894 inhibitor-cofactor binding pocket; inhibition site 887061003895 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061003896 catalytic residue [active] 887061003897 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 887061003898 Autotransporter beta-domain; Region: Autotransporter; cl17461 887061003899 Autotransporter beta-domain; Region: Autotransporter; smart00869 887061003900 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 887061003901 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 887061003902 Cu(I) binding site [ion binding]; other site 887061003903 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 887061003904 UbiA prenyltransferase family; Region: UbiA; pfam01040 887061003905 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 887061003906 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 887061003907 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 887061003908 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 887061003909 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 887061003910 Subunit III/VIIa interface [polypeptide binding]; other site 887061003911 Phospholipid binding site [chemical binding]; other site 887061003912 Subunit I/III interface [polypeptide binding]; other site 887061003913 Subunit III/VIb interface [polypeptide binding]; other site 887061003914 Subunit III/VIa interface; other site 887061003915 Subunit III/Vb interface [polypeptide binding]; other site 887061003916 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 887061003917 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 887061003918 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 887061003919 Subunit I/III interface [polypeptide binding]; other site 887061003920 D-pathway; other site 887061003921 Subunit I/VIIc interface [polypeptide binding]; other site 887061003922 Subunit I/IV interface [polypeptide binding]; other site 887061003923 Subunit I/II interface [polypeptide binding]; other site 887061003924 Low-spin heme (heme a) binding site [chemical binding]; other site 887061003925 Subunit I/VIIa interface [polypeptide binding]; other site 887061003926 Subunit I/VIa interface [polypeptide binding]; other site 887061003927 Dimer interface; other site 887061003928 Putative water exit pathway; other site 887061003929 Binuclear center (heme a3/CuB) [ion binding]; other site 887061003930 K-pathway; other site 887061003931 Subunit I/Vb interface [polypeptide binding]; other site 887061003932 Putative proton exit pathway; other site 887061003933 Subunit I/VIb interface; other site 887061003934 Subunit I/VIc interface [polypeptide binding]; other site 887061003935 Electron transfer pathway; other site 887061003936 Subunit I/VIIIb interface [polypeptide binding]; other site 887061003937 Subunit I/VIIb interface [polypeptide binding]; other site 887061003938 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 887061003939 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 887061003940 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 887061003941 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 887061003942 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 887061003943 Yip1 domain; Region: Yip1; cl17815 887061003944 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 887061003945 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 887061003946 FtsX-like permease family; Region: FtsX; pfam02687 887061003947 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 887061003948 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 887061003949 Walker A/P-loop; other site 887061003950 ATP binding site [chemical binding]; other site 887061003951 Q-loop/lid; other site 887061003952 ABC transporter signature motif; other site 887061003953 Walker B; other site 887061003954 D-loop; other site 887061003955 H-loop/switch region; other site 887061003956 macrolide transporter subunit MacA; Provisional; Region: PRK11578 887061003957 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061003958 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061003959 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 887061003960 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 887061003961 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061003962 Walker A/P-loop; other site 887061003963 ATP binding site [chemical binding]; other site 887061003964 Q-loop/lid; other site 887061003965 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 887061003966 ABC transporter signature motif; other site 887061003967 Walker B; other site 887061003968 D-loop; other site 887061003969 ABC transporter; Region: ABC_tran_2; pfam12848 887061003970 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 887061003971 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 887061003972 dimer interface [polypeptide binding]; other site 887061003973 FMN binding site [chemical binding]; other site 887061003974 transcription elongation factor regulatory protein; Validated; Region: PRK06342 887061003975 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 887061003976 GMP synthase; Reviewed; Region: guaA; PRK00074 887061003977 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 887061003978 AMP/PPi binding site [chemical binding]; other site 887061003979 candidate oxyanion hole; other site 887061003980 catalytic triad [active] 887061003981 potential glutamine specificity residues [chemical binding]; other site 887061003982 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 887061003983 ATP Binding subdomain [chemical binding]; other site 887061003984 Ligand Binding sites [chemical binding]; other site 887061003985 Dimerization subdomain; other site 887061003986 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 887061003987 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; cl17186 887061003988 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...; Region: CBS_pair_IMPDH; cd04601 887061003989 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...; Region: IMPDH; cd00381 887061003990 active site 887061003991 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 887061003992 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2914 887061003993 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 887061003994 putative coenzyme Q binding site [chemical binding]; other site 887061003995 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 887061003996 SmpB-tmRNA interface; other site 887061003997 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 887061003998 CheW-like domain; Region: CheW; pfam01584 887061003999 putative DNA modification/repair radical SAM protein; Region: rSAM_link_UDG; TIGR03916 887061004000 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 887061004001 FeS/SAM binding site; other site 887061004002 probable DNA metabolism protein; Region: SAM_7_link_chp; TIGR03915 887061004003 elongation factor P; Validated; Region: PRK00529 887061004004 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 887061004005 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 887061004006 RNA binding site [nucleotide binding]; other site 887061004007 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 887061004008 RNA binding site [nucleotide binding]; other site 887061004009 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 887061004010 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 887061004011 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 887061004012 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 887061004013 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 887061004014 probable DNA repair protein; Region: TIGR03623 887061004015 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 887061004016 Part of AAA domain; Region: AAA_19; pfam13245 887061004017 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 887061004018 Family description; Region: UvrD_C_2; pfam13538 887061004019 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 887061004020 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 887061004021 choice-of-anchor A domain; Region: choice_anch_A; TIGR04215 887061004022 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 887061004023 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 887061004024 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 887061004025 ATP binding site [chemical binding]; other site 887061004026 putative Mg++ binding site [ion binding]; other site 887061004027 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 887061004028 nucleotide binding region [chemical binding]; other site 887061004029 ATP-binding site [chemical binding]; other site 887061004030 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 887061004031 Protein of unknown function (DUF2934); Region: DUF2934; pfam11154 887061004032 protease TldD; Provisional; Region: tldD; PRK10735 887061004033 nitrilase; Region: PLN02798 887061004034 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 887061004035 putative active site [active] 887061004036 catalytic triad [active] 887061004037 dimer interface [polypeptide binding]; other site 887061004038 TIGR02099 family protein; Region: TIGR02099 887061004039 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 887061004040 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 887061004041 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 887061004042 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 887061004043 ABC transporter; Region: ABC_tran_2; pfam12848 887061004044 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 887061004045 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 887061004046 dimer interface [polypeptide binding]; other site 887061004047 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 887061004048 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061004049 active site 887061004050 phosphorylation site [posttranslational modification] 887061004051 intermolecular recognition site; other site 887061004052 dimerization interface [polypeptide binding]; other site 887061004053 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061004054 DNA binding site [nucleotide binding] 887061004055 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061004056 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061004057 dimerization interface [polypeptide binding]; other site 887061004058 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061004059 dimer interface [polypeptide binding]; other site 887061004060 phosphorylation site [posttranslational modification] 887061004061 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 887061004062 ATP binding site [chemical binding]; other site 887061004063 Mg2+ binding site [ion binding]; other site 887061004064 G-X-G motif; other site 887061004065 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061004066 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 887061004067 ligand binding site [chemical binding]; other site 887061004068 flexible hinge region; other site 887061004069 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 887061004070 non-specific DNA interactions [nucleotide binding]; other site 887061004071 DNA binding site [nucleotide binding] 887061004072 sequence specific DNA binding site [nucleotide binding]; other site 887061004073 putative cAMP binding site [chemical binding]; other site 887061004074 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 887061004075 PilZ domain; Region: PilZ; pfam07238 887061004076 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 887061004077 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 887061004078 Sulfatase; Region: Sulfatase; pfam00884 887061004079 Helix-turn-helix domain; Region: HTH_18; pfam12833 887061004080 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061004081 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 887061004082 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 887061004083 aspartate aminotransferase; Provisional; Region: PRK05764 887061004084 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 887061004085 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004086 homodimer interface [polypeptide binding]; other site 887061004087 catalytic residue [active] 887061004088 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 887061004089 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 887061004090 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 887061004091 TPR repeat; Region: TPR_11; pfam13414 887061004092 binding surface 887061004093 TPR motif; other site 887061004094 excinuclease ABC subunit B; Provisional; Region: PRK05298 887061004095 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 887061004096 ATP binding site [chemical binding]; other site 887061004097 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 887061004098 nucleotide binding region [chemical binding]; other site 887061004099 ATP-binding site [chemical binding]; other site 887061004100 Ultra-violet resistance protein B; Region: UvrB; pfam12344 887061004101 UvrB/uvrC motif; Region: UVR; pfam02151 887061004102 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 887061004103 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 887061004104 homodimer interface [polypeptide binding]; other site 887061004105 oligonucleotide binding site [chemical binding]; other site 887061004106 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 887061004107 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 887061004108 RNA binding surface [nucleotide binding]; other site 887061004109 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 887061004110 active site 887061004111 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061004112 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 887061004113 motif II; other site 887061004114 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 887061004115 iron-sulfur cluster [ion binding]; other site 887061004116 [2Fe-2S] cluster binding site [ion binding]; other site 887061004117 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 887061004118 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 887061004119 tandem repeat interface [polypeptide binding]; other site 887061004120 oligomer interface [polypeptide binding]; other site 887061004121 active site residues [active] 887061004122 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 887061004123 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 887061004124 active site 887061004125 dimer interface [polypeptide binding]; other site 887061004126 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 887061004127 dimer interface [polypeptide binding]; other site 887061004128 active site 887061004129 glycogen branching enzyme; Provisional; Region: PRK05402 887061004130 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 887061004131 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 887061004132 active site 887061004133 catalytic site [active] 887061004134 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 887061004135 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK00725 887061004136 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 887061004137 ligand binding site; other site 887061004138 oligomer interface; other site 887061004139 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 887061004140 dimer interface [polypeptide binding]; other site 887061004141 N-terminal domain interface [polypeptide binding]; other site 887061004142 sulfate 1 binding site; other site 887061004143 Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins; Region: GH38-57_N_LamB_YdjC_SF; cl17191 887061004144 N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57); Region: GH57N_APU; cd10796 887061004145 putative active site [active] 887061004146 catalytic site [active] 887061004147 N-terminal catalytic domain of 4-alpha-glucanotransferase; glycoside hydrolase family 57 (GH57); Region: GH57N_TLGT_like; cd10793 887061004148 Glycosyl hydrolase family 57; Region: Glyco_hydro_57; pfam03065 887061004149 active site 887061004150 catalytic site [active] 887061004151 homodimer interface [polypeptide binding]; other site 887061004152 Lid 1; other site 887061004153 Domain of unknown function (DUF1925); Region: DUF1925; pfam09094 887061004154 Domain of unknown function (DUF1926); Region: DUF1926; pfam09095 887061004155 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 887061004156 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 887061004157 nucleotide binding site [chemical binding]; other site 887061004158 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 887061004159 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 887061004160 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061004161 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004162 metal binding site [ion binding]; metal-binding site 887061004163 active site 887061004164 I-site; other site 887061004165 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 887061004166 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 887061004167 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 887061004168 active site 887061004169 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]; Region: COG5309 887061004170 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 887061004171 putative active site [active] 887061004172 YdjC motif; other site 887061004173 Mg binding site [ion binding]; other site 887061004174 putative homodimer interface [polypeptide binding]; other site 887061004175 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 887061004176 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 887061004177 Ligand binding site; other site 887061004178 Putative Catalytic site; other site 887061004179 DXD motif; other site 887061004180 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 887061004181 epoxyqueuosine reductase; Region: TIGR00276 887061004182 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 887061004183 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 887061004184 AMIN domain; Region: AMIN; pfam11741 887061004185 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 887061004186 active site 887061004187 metal binding site [ion binding]; metal-binding site 887061004188 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 887061004189 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 887061004190 Beta-Casp domain; Region: Beta-Casp; smart01027 887061004191 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 887061004192 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 887061004193 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 887061004194 ATP binding site [chemical binding]; other site 887061004195 Mg2+ binding site [ion binding]; other site 887061004196 G-X-G motif; other site 887061004197 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 887061004198 ATP binding site [chemical binding]; other site 887061004199 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 887061004200 Protein of unknown function (DUF817); Region: DUF817; pfam05675 887061004201 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 887061004202 dimer interface [polypeptide binding]; other site 887061004203 substrate binding site [chemical binding]; other site 887061004204 ATP binding site [chemical binding]; other site 887061004205 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 887061004206 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 887061004207 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 887061004208 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 887061004209 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004210 homodimer interface [polypeptide binding]; other site 887061004211 catalytic residue [active] 887061004212 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 887061004213 EamA-like transporter family; Region: EamA; pfam00892 887061004214 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 887061004215 putative active site [active] 887061004216 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 887061004217 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 887061004218 ATP binding site [chemical binding]; other site 887061004219 Walker B motif; other site 887061004220 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 887061004221 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 887061004222 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004223 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061004224 metal binding site [ion binding]; metal-binding site 887061004225 active site 887061004226 I-site; other site 887061004227 Cache domain; Region: Cache_1; pfam02743 887061004228 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 887061004229 binding surface 887061004230 TPR motif; other site 887061004231 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 887061004232 TPR repeat; Region: TPR_11; pfam13414 887061004233 binding surface 887061004234 TPR motif; other site 887061004235 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 887061004236 binding surface 887061004237 TPR motif; other site 887061004238 TPR repeat; Region: TPR_11; pfam13414 887061004239 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 887061004240 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 887061004241 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 887061004242 Uncharacterized conserved protein [Function unknown]; Region: COG4121 887061004243 hydroxyglutarate oxidase; Provisional; Region: PRK11728 887061004244 Methyltransferase domain; Region: Methyltransf_23; pfam13489 887061004245 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 887061004246 S-adenosylmethionine binding site [chemical binding]; other site 887061004247 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 887061004248 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; cl17173 887061004249 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 887061004250 S-adenosylmethionine binding site [chemical binding]; other site 887061004251 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 887061004252 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 887061004253 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 887061004254 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 887061004255 Fatty acid desaturase; Region: FA_desaturase; pfam00487 887061004256 Di-iron ligands [ion binding]; other site 887061004257 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 887061004258 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 887061004259 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 887061004260 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 887061004261 Protein of unknown function (DUF2878); Region: DUF2878; pfam11086 887061004262 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 887061004263 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 887061004264 S-adenosylmethionine binding site [chemical binding]; other site 887061004265 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 887061004266 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 887061004267 DNA binding residues [nucleotide binding] 887061004268 B12 binding domain; Region: B12-binding_2; pfam02607 887061004269 B12 binding domain; Region: B12-binding; pfam02310 887061004270 B12 binding site [chemical binding]; other site 887061004271 Anti-sigma-K factor rskA; Region: RskA; pfam10099 887061004272 RNA polymerase sigma factor; Provisional; Region: PRK12514 887061004273 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061004274 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061004275 DNA binding residues [nucleotide binding] 887061004276 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061004277 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 887061004278 Trp docking motif [polypeptide binding]; other site 887061004279 active site 887061004280 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cl00248 887061004281 substrate binding site [chemical binding]; other site 887061004282 dimerization interface [polypeptide binding]; other site 887061004283 active site 887061004284 calcium binding site [ion binding]; other site 887061004285 Cache domain; Region: Cache_1; pfam02743 887061004286 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061004287 dimerization interface [polypeptide binding]; other site 887061004288 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061004289 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061004290 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061004291 dimer interface [polypeptide binding]; other site 887061004292 putative CheW interface [polypeptide binding]; other site 887061004293 choice-of-anchor A domain; Region: choice_anch_A; TIGR04215 887061004294 PEP-CTERM motif; Region: VPEP; pfam07589 887061004295 Domain of unknown function (DUF2383); Region: DUF2383; cl17556 887061004296 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 887061004297 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 887061004298 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 887061004299 Walker A/P-loop; other site 887061004300 ATP binding site [chemical binding]; other site 887061004301 Q-loop/lid; other site 887061004302 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 887061004303 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 887061004304 ABC transporter signature motif; other site 887061004305 Walker B; other site 887061004306 D-loop; other site 887061004307 H-loop/switch region; other site 887061004308 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 887061004309 FtsZ protein binding site [polypeptide binding]; other site 887061004310 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 887061004311 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 887061004312 nucleotide binding pocket [chemical binding]; other site 887061004313 K-X-D-G motif; other site 887061004314 catalytic site [active] 887061004315 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 887061004316 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 887061004317 Helix-hairpin-helix motif; Region: HHH; pfam00633 887061004318 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 887061004319 Dimer interface [polypeptide binding]; other site 887061004320 BRCT sequence motif; other site 887061004321 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 887061004322 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...; Region: CysQ; cd01638 887061004323 active site 887061004324 Tetratricopeptide repeat; Region: TPR_12; pfam13424 887061004325 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 887061004326 TPR motif; other site 887061004327 binding surface 887061004328 TMAO/DMSO reductase; Reviewed; Region: PRK05363 887061004329 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 887061004330 Moco binding site; other site 887061004331 metal coordination site [ion binding]; other site 887061004332 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 887061004333 Predicted membrane protein [Function unknown]; Region: COG2259 887061004334 Conserved TM helix; Region: TM_helix; pfam05552 887061004335 Conserved TM helix; Region: TM_helix; pfam05552 887061004336 hypothetical protein; Provisional; Region: PRK02237 887061004337 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 887061004338 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_1; cd09140 887061004339 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 887061004340 putative active site [active] 887061004341 putative active site [active] 887061004342 catalytic site [active] 887061004343 catalytic site [active] 887061004344 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2; Region: PLDc_vPLD1_2_like_bac_2; cd09143 887061004345 PLD-like domain; Region: PLDc_2; pfam13091 887061004346 putative active site [active] 887061004347 catalytic site [active] 887061004348 Uncharacterized conserved protein [Function unknown]; Region: COG0398 887061004349 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 887061004350 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 887061004351 putative catalytic site [active] 887061004352 putative metal binding site [ion binding]; other site 887061004353 putative phosphate binding site [ion binding]; other site 887061004354 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 to...; Region: EFh; cd00051 887061004355 EF-hand domain pair; Region: EF_hand_5; pfam13499 887061004356 Ca2+ binding site [ion binding]; other site 887061004357 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 887061004358 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 887061004359 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 887061004360 inhibitor site; inhibition site 887061004361 active site 887061004362 dimer interface [polypeptide binding]; other site 887061004363 catalytic residue [active] 887061004364 short chain dehydrogenase; Provisional; Region: PRK06179 887061004365 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 887061004366 NADP binding site [chemical binding]; other site 887061004367 active site 887061004368 steroid binding site; other site 887061004369 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061004370 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061004371 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 887061004372 short chain dehydrogenase; Provisional; Region: PRK06701 887061004373 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 887061004374 NAD binding site [chemical binding]; other site 887061004375 metal binding site [ion binding]; metal-binding site 887061004376 active site 887061004377 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061004378 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061004379 active site 887061004380 phosphorylation site [posttranslational modification] 887061004381 intermolecular recognition site; other site 887061004382 dimerization interface [polypeptide binding]; other site 887061004383 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 887061004384 DNA binding residues [nucleotide binding] 887061004385 dimerization interface [polypeptide binding]; other site 887061004386 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 887061004387 YceI-like domain; Region: YceI; pfam04264 887061004388 Succinylglutamate desuccinylase / Aspartoacylase family; Region: AstE_AspA; pfam04952 887061004389 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily; Region: M14_ASTE_ASPA_like; cd06230 887061004390 active site 887061004391 Zn binding site [ion binding]; other site 887061004392 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 887061004393 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 887061004394 metal-binding site [ion binding] 887061004395 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 887061004396 Soluble P-type ATPase [General function prediction only]; Region: COG4087 887061004397 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...; Region: CSP_CDS; cd04458 887061004398 DNA-binding site [nucleotide binding]; DNA binding site 887061004399 RNA-binding motif; other site 887061004400 CsbD-like; Region: CsbD; cl17424 887061004401 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061004402 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061004403 DNA binding residues [nucleotide binding] 887061004404 dimerization interface [polypeptide binding]; other site 887061004405 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 887061004406 Na binding site [ion binding]; other site 887061004407 Protein of unknown function (DUF3396); Region: DUF3396; pfam11876 887061004408 This model contains proteins with the VRR-NUC domain; Region: VRR_NUC; smart00990 887061004409 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 887061004410 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 887061004411 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 887061004412 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 887061004413 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 887061004414 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061004415 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061004416 active site 887061004417 phosphorylation site [posttranslational modification] 887061004418 intermolecular recognition site; other site 887061004419 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061004420 DNA binding residues [nucleotide binding] 887061004421 dimerization interface [polypeptide binding]; other site 887061004422 ferredoxin-NADP reductase; Provisional; Region: PRK10926 887061004423 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 887061004424 FAD binding pocket [chemical binding]; other site 887061004425 FAD binding motif [chemical binding]; other site 887061004426 phosphate binding motif [ion binding]; other site 887061004427 beta-alpha-beta structure motif; other site 887061004428 NAD binding pocket [chemical binding]; other site 887061004429 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 887061004430 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 887061004431 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 887061004432 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 887061004433 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 887061004434 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 887061004435 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 887061004436 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 887061004437 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 887061004438 catalytic loop [active] 887061004439 iron binding site [ion binding]; other site 887061004440 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 887061004441 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 887061004442 Ligand binding site; other site 887061004443 metal-binding site 887061004444 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 887061004445 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 887061004446 XdhC Rossmann domain; Region: XdhC_C; pfam13478 887061004447 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061004448 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061004449 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 887061004450 putative effector binding pocket; other site 887061004451 dimerization interface [polypeptide binding]; other site 887061004452 putative hydrolase; Provisional; Region: PRK02113 887061004453 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 887061004454 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 887061004455 active site 887061004456 PilZ domain; Region: PilZ; cl01260 887061004457 DNA polymerase III subunit delta'; Validated; Region: PRK06964 887061004458 DNA polymerase III subunit delta'; Validated; Region: PRK08485 887061004459 thymidylate kinase; Validated; Region: tmk; PRK00698 887061004460 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 887061004461 TMP-binding site; other site 887061004462 ATP-binding site [chemical binding]; other site 887061004463 YceG-like family; Region: YceG; pfam02618 887061004464 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 887061004465 dimerization interface [polypeptide binding]; other site 887061004466 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 887061004467 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 887061004468 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004469 catalytic residue [active] 887061004470 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 887061004471 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 887061004472 dimer interface [polypeptide binding]; other site 887061004473 active site 887061004474 acyl carrier protein; Provisional; Region: acpP; PRK00982 887061004475 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 887061004476 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 887061004477 NAD(P) binding site [chemical binding]; other site 887061004478 homotetramer interface [polypeptide binding]; other site 887061004479 homodimer interface [polypeptide binding]; other site 887061004480 active site 887061004481 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 887061004482 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 887061004483 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 887061004484 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 887061004485 dimer interface [polypeptide binding]; other site 887061004486 active site 887061004487 CoA binding pocket [chemical binding]; other site 887061004488 putative phosphate acyltransferase; Provisional; Region: PRK05331 887061004489 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 887061004490 pyruvate carboxylase subunit A; Validated; Region: PRK07178 887061004491 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061004492 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061004493 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 887061004494 pyruvate carboxylase subunit B; Validated; Region: PRK09282 887061004495 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 887061004496 active site 887061004497 metal binding site [ion binding]; metal-binding site 887061004498 homodimer binding site [polypeptide binding]; other site 887061004499 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 887061004500 carboxyltransferase (CT) interaction site; other site 887061004501 biotinylation site [posttranslational modification]; other site 887061004502 Maf-like protein; Region: Maf; pfam02545 887061004503 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 887061004504 active site 887061004505 dimer interface [polypeptide binding]; other site 887061004506 Uncharacterized conserved protein [Function unknown]; Region: COG5316 887061004507 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 887061004508 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 887061004509 putative SAM binding site [chemical binding]; other site 887061004510 homodimer interface [polypeptide binding]; other site 887061004511 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 887061004512 RNA/DNA hybrid binding site [nucleotide binding]; other site 887061004513 active site 887061004514 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 887061004515 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 887061004516 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 887061004517 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 887061004518 active site 887061004519 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 887061004520 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 887061004521 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 887061004522 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 887061004523 trimer interface [polypeptide binding]; other site 887061004524 active site 887061004525 UDP-GlcNAc binding site [chemical binding]; other site 887061004526 lipid binding site [chemical binding]; lipid-binding site 887061004527 periplasmic chaperone; Provisional; Region: PRK10780 887061004528 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 887061004529 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 887061004530 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 887061004531 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 887061004532 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 887061004533 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 887061004534 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 887061004535 Surface antigen; Region: Bac_surface_Ag; pfam01103 887061004536 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 887061004537 zinc metallopeptidase RseP; Provisional; Region: PRK10779 887061004538 active site 887061004539 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 887061004540 protein binding site [polypeptide binding]; other site 887061004541 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 887061004542 protein binding site [polypeptide binding]; other site 887061004543 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 887061004544 putative substrate binding region [chemical binding]; other site 887061004545 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 887061004546 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 887061004547 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 887061004548 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 887061004549 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 887061004550 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 887061004551 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 887061004552 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 887061004553 catalytic residue [active] 887061004554 putative FPP diphosphate binding site; other site 887061004555 putative FPP binding hydrophobic cleft; other site 887061004556 dimer interface [polypeptide binding]; other site 887061004557 putative IPP diphosphate binding site; other site 887061004558 ribosome recycling factor; Reviewed; Region: frr; PRK00083 887061004559 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...; Region: RRF; cd00520 887061004560 hinge region; other site 887061004561 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 887061004562 putative nucleotide binding site [chemical binding]; other site 887061004563 uridine monophosphate binding site [chemical binding]; other site 887061004564 homohexameric interface [polypeptide binding]; other site 887061004565 elongation factor Ts; Provisional; Region: tsf; PRK09377 887061004566 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 887061004567 Elongation factor TS; Region: EF_TS; pfam00889 887061004568 Elongation factor TS; Region: EF_TS; pfam00889 887061004569 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 887061004570 rRNA interaction site [nucleotide binding]; other site 887061004571 S8 interaction site; other site 887061004572 putative laminin-1 binding site; other site 887061004573 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 887061004574 active site 887061004575 PII uridylyl-transferase; Provisional; Region: PRK03059 887061004576 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 887061004577 metal binding triad; other site 887061004578 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 887061004579 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061004580 Zn2+ binding site [ion binding]; other site 887061004581 Mg2+ binding site [ion binding]; other site 887061004582 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 887061004583 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 887061004584 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 887061004585 active site 887061004586 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 887061004587 DNA binding site [nucleotide binding] 887061004588 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 887061004589 classical (c) SDRs; Region: SDR_c; cd05233 887061004590 NAD(P) binding site [chemical binding]; other site 887061004591 active site 887061004592 Protein of unknown function (DUF861); Region: Cupin_3; pfam05899 887061004593 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 887061004594 active site 887061004595 catalytic residues [active] 887061004596 metal binding site [ion binding]; metal-binding site 887061004597 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 887061004598 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 887061004599 active site lid residues [active] 887061004600 substrate binding pocket [chemical binding]; other site 887061004601 catalytic residues [active] 887061004602 substrate-Mg2+ binding site; other site 887061004603 aspartate-rich region 1; other site 887061004604 aspartate-rich region 2; other site 887061004605 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 887061004606 catalytic residues [active] 887061004607 substrate binding pocket [chemical binding]; other site 887061004608 substrate-Mg2+ binding site; other site 887061004609 aspartate-rich region 1; other site 887061004610 aspartate-rich region 2; other site 887061004611 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 887061004612 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 887061004613 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 887061004614 Membrane protein of unknown function; Region: DUF360; pfam04020 887061004615 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 887061004616 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061004617 NAD(P) binding site [chemical binding]; other site 887061004618 active site 887061004619 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 887061004620 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061004621 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 887061004622 motif II; other site 887061004623 DNA repair protein RadA; Provisional; Region: PRK11823 887061004624 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 887061004625 Walker A motif/ATP binding site; other site 887061004626 ATP binding site [chemical binding]; other site 887061004627 Walker B motif; other site 887061004628 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 887061004629 alanine racemase; Reviewed; Region: alr; PRK00053 887061004630 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 887061004631 active site 887061004632 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 887061004633 substrate binding site [chemical binding]; other site 887061004634 catalytic residues [active] 887061004635 dimer interface [polypeptide binding]; other site 887061004636 replicative DNA helicase; Region: DnaB; TIGR00665 887061004637 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 887061004638 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 887061004639 Walker A motif; other site 887061004640 ATP binding site [chemical binding]; other site 887061004641 Walker B motif; other site 887061004642 DNA binding loops [nucleotide binding] 887061004643 cystathionine beta-lyase; Provisional; Region: PRK07050 887061004644 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 887061004645 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061004646 catalytic residue [active] 887061004647 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 887061004648 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 887061004649 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 887061004650 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 887061004651 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 887061004652 generic binding surface II; other site 887061004653 generic binding surface I; other site 887061004654 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 887061004655 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 887061004656 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 887061004657 Protein of unknown function (DUF1504); Region: DUF1504; pfam07399 887061004658 glycogen synthase; Provisional; Region: glgA; PRK00654 887061004659 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 887061004660 ADP-binding pocket [chemical binding]; other site 887061004661 homodimer interface [polypeptide binding]; other site 887061004662 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 887061004663 catalytic site [active] 887061004664 putative active site [active] 887061004665 putative substrate binding site [chemical binding]; other site 887061004666 dimer interface [polypeptide binding]; other site 887061004667 Peptidase family M48; Region: Peptidase_M48; pfam01435 887061004668 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 887061004669 GTPase RsgA; Reviewed; Region: PRK00098 887061004670 RNA binding site [nucleotide binding]; other site 887061004671 homodimer interface [polypeptide binding]; other site 887061004672 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 887061004673 GTPase/Zn-binding domain interface [polypeptide binding]; other site 887061004674 GTP/Mg2+ binding site [chemical binding]; other site 887061004675 G4 box; other site 887061004676 G5 box; other site 887061004677 G1 box; other site 887061004678 Switch I region; other site 887061004679 G2 box; other site 887061004680 G3 box; other site 887061004681 Switch II region; other site 887061004682 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 887061004683 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 887061004684 putative active site [active] 887061004685 Zn binding site [ion binding]; other site 887061004686 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 887061004687 active site 887061004688 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 887061004689 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 887061004690 NADP binding site [chemical binding]; other site 887061004691 active site 887061004692 putative substrate binding site [chemical binding]; other site 887061004693 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 887061004694 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 887061004695 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 887061004696 substrate binding site; other site 887061004697 tetramer interface; other site 887061004698 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 887061004699 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 887061004700 NAD binding site [chemical binding]; other site 887061004701 substrate binding site [chemical binding]; other site 887061004702 homodimer interface [polypeptide binding]; other site 887061004703 active site 887061004704 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 887061004705 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 887061004706 active site 887061004707 catalytic site [active] 887061004708 substrate binding site [chemical binding]; other site 887061004709 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 887061004710 RNA/DNA hybrid binding site [nucleotide binding]; other site 887061004711 active site 887061004712 Methyltransferase domain; Region: Methyltransf_11; pfam08241 887061004713 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 887061004714 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...; Region: LT_GEWL; cd00254 887061004715 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061004716 catalytic residue [active] 887061004717 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 887061004718 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 887061004719 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 887061004720 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 887061004721 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 887061004722 peptide binding site [polypeptide binding]; other site 887061004723 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 887061004724 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061004725 dimer interface [polypeptide binding]; other site 887061004726 conserved gate region; other site 887061004727 putative PBP binding loops; other site 887061004728 ABC-ATPase subunit interface; other site 887061004729 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 887061004730 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061004731 dimer interface [polypeptide binding]; other site 887061004732 conserved gate region; other site 887061004733 putative PBP binding loops; other site 887061004734 ABC-ATPase subunit interface; other site 887061004735 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 887061004736 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 887061004737 NAD binding site [chemical binding]; other site 887061004738 homotetramer interface [polypeptide binding]; other site 887061004739 homodimer interface [polypeptide binding]; other site 887061004740 substrate binding site [chemical binding]; other site 887061004741 active site 887061004742 periplasmic folding chaperone; Provisional; Region: PRK10788 887061004743 SurA N-terminal domain; Region: SurA_N_3; cl07813 887061004744 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 887061004745 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 887061004746 IHF dimer interface [polypeptide binding]; other site 887061004747 IHF - DNA interface [nucleotide binding]; other site 887061004748 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 887061004749 Found in ATP-dependent protease La (LON); Region: LON; smart00464 887061004750 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061004751 Walker A motif; other site 887061004752 ATP binding site [chemical binding]; other site 887061004753 Walker B motif; other site 887061004754 arginine finger; other site 887061004755 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 887061004756 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 887061004757 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 887061004758 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 887061004759 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061004760 Walker A motif; other site 887061004761 ATP binding site [chemical binding]; other site 887061004762 Walker B motif; other site 887061004763 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 887061004764 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 887061004765 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 887061004766 oligomer interface [polypeptide binding]; other site 887061004767 active site residues [active] 887061004768 trigger factor; Provisional; Region: tig; PRK01490 887061004769 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 887061004770 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 887061004771 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 887061004772 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 887061004773 active site 887061004774 DNA binding site [nucleotide binding] 887061004775 Int/Topo IB signature motif; other site 887061004776 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 887061004777 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 887061004778 active site 887061004779 DNA binding site [nucleotide binding] 887061004780 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 887061004781 Outer membrane efflux protein; Region: OEP; pfam02321 887061004782 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061004783 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061004784 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 887061004785 PAS domain; Region: PAS_8; pfam13188 887061004786 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061004787 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004788 metal binding site [ion binding]; metal-binding site 887061004789 active site 887061004790 I-site; other site 887061004791 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 887061004792 aromatic arch; other site 887061004793 DCoH dimer interaction site [polypeptide binding]; other site 887061004794 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 887061004795 DCoH tetramer interaction site [polypeptide binding]; other site 887061004796 substrate binding site [chemical binding]; other site 887061004797 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 887061004798 substrate binding site [chemical binding]; other site 887061004799 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 887061004800 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 887061004801 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 887061004802 Predicted transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: COG1548; cl00668 887061004803 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061004804 hisA/hisF family protein; Region: hisAF_rel; TIGR00734 887061004805 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 887061004806 active site 887061004807 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 887061004808 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 887061004809 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 887061004810 tetramer interface [polypeptide binding]; other site 887061004811 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 887061004812 active site 887061004813 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 887061004814 active site 887061004815 dimer interface [polypeptide binding]; other site 887061004816 magnesium binding site [ion binding]; other site 887061004817 transaldolase-like protein; Provisional; Region: PTZ00411 887061004818 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 887061004819 active site 887061004820 dimer interface [polypeptide binding]; other site 887061004821 catalytic residue [active] 887061004822 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; pfam01874 887061004823 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 887061004824 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061004825 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase; Provisional; Region: PRK02264 887061004826 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), N...; Region: MCH; cd00545 887061004827 trimer interface I [polypeptide binding]; other site 887061004828 putative substrate binding pocket [chemical binding]; other site 887061004829 trimer interface II [polypeptide binding]; other site 887061004830 Predicted ATP-dependent carboligase related to biotin carboxylase [General function prediction only]; Region: COG2232 887061004831 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061004832 Methylene-tetrahydromethanopterin dehydrogenase, N-terminal; Region: Mpt_N; pfam09176 887061004833 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 887061004834 NAD(P) binding pocket [chemical binding]; other site 887061004835 Predicted archaeal sugar kinases [General function prediction only]; Region: COG1907 887061004836 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 887061004837 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 887061004838 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 887061004839 formylmethanofuran dehydrogenase subunit B; Region: one_C_dehyd_B; TIGR03129 887061004840 putative [4Fe-4S] binding site [ion binding]; other site 887061004841 putative molybdopterin cofactor binding site [chemical binding]; other site 887061004842 formylmethanofuran dehydrogenase subunit A; Region: one_C_dehyd_A; TIGR03121 887061004843 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 887061004844 active site 887061004845 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional; Region: PRK02114 887061004846 Formylmethanofuran-tetrahydromethanopterin formyltransferase; Region: FTR; pfam01913 887061004847 FTR, proximal lobe; Region: FTR_C; pfam02741 887061004848 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 887061004849 domain_subunit interface; other site 887061004850 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 887061004851 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061004852 ligand binding site [chemical binding]; other site 887061004853 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 887061004854 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 887061004855 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 887061004856 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 887061004857 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 887061004858 Domain of unknown function DUF302; Region: DUF302; cl01364 887061004859 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 887061004860 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061004861 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 887061004862 substrate binding site [chemical binding]; other site 887061004863 dimerization interface [polypeptide binding]; other site 887061004864 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 887061004865 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 887061004866 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 887061004867 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 887061004868 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 887061004869 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 887061004870 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 887061004871 Active Sites [active] 887061004872 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 887061004873 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 887061004874 Active Sites [active] 887061004875 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 887061004876 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 887061004877 CysD dimerization site [polypeptide binding]; other site 887061004878 G1 box; other site 887061004879 putative GEF interaction site [polypeptide binding]; other site 887061004880 GTP/Mg2+ binding site [chemical binding]; other site 887061004881 Switch I region; other site 887061004882 G2 box; other site 887061004883 G3 box; other site 887061004884 Switch II region; other site 887061004885 G4 box; other site 887061004886 G5 box; other site 887061004887 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 887061004888 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 887061004889 Ferredoxin [Energy production and conversion]; Region: COG1146 887061004890 4Fe-4S binding domain; Region: Fer4; cl02805 887061004891 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 887061004892 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 887061004893 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 887061004894 ATP binding site [chemical binding]; other site 887061004895 putative Mg++ binding site [ion binding]; other site 887061004896 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 887061004897 nucleotide binding region [chemical binding]; other site 887061004898 ATP-binding site [chemical binding]; other site 887061004899 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 887061004900 HRDC domain; Region: HRDC; pfam00570 887061004901 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 887061004902 putative substrate translocation pore; other site 887061004903 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061004904 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 887061004905 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 887061004906 FeS/SAM binding site; other site 887061004907 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 887061004908 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 887061004909 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 887061004910 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 887061004911 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 887061004912 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061004913 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 887061004914 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 887061004915 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 887061004916 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 887061004917 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004918 homodimer interface [polypeptide binding]; other site 887061004919 catalytic residue [active] 887061004920 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061004921 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061004922 metal binding site [ion binding]; metal-binding site 887061004923 active site 887061004924 I-site; other site 887061004925 Chorismate mutase type II; Region: CM_2; pfam01817 887061004926 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 887061004927 Prephenate dehydratase; Region: PDT; pfam00800 887061004928 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 887061004929 putative L-Phe binding site [chemical binding]; other site 887061004930 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 887061004931 homodimer interface [polypeptide binding]; other site 887061004932 substrate-cofactor binding pocket; other site 887061004933 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004934 catalytic residue [active] 887061004935 DNA gyrase subunit A; Validated; Region: PRK05560 887061004936 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...; Region: TOP4c; cd00187 887061004937 CAP-like domain; other site 887061004938 active site 887061004939 primary dimer interface [polypeptide binding]; other site 887061004940 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004941 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004942 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004943 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004944 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004945 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 887061004946 peroxidase; Provisional; Region: PRK15000 887061004947 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 887061004948 dimer interface [polypeptide binding]; other site 887061004949 decamer (pentamer of dimers) interface [polypeptide binding]; other site 887061004950 catalytic triad [active] 887061004951 peroxidatic and resolving cysteines [active] 887061004952 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 887061004953 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 887061004954 homodimer interface [polypeptide binding]; other site 887061004955 substrate-cofactor binding pocket; other site 887061004956 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004957 catalytic residue [active] 887061004958 amidophosphoribosyltransferase; Provisional; Region: PRK09246 887061004959 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 887061004960 active site 887061004961 tetramer interface [polypeptide binding]; other site 887061004962 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061004963 active site 887061004964 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 887061004965 Colicin V production protein; Region: Colicin_V; pfam02674 887061004966 Sporulation related domain; Region: SPOR; pfam05036 887061004967 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional; Region: PRK10846 887061004968 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 887061004969 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 887061004970 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 887061004971 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 887061004972 substrate binding site [chemical binding]; other site 887061004973 active site 887061004974 catalytic residues [active] 887061004975 heterodimer interface [polypeptide binding]; other site 887061004976 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 887061004977 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 887061004978 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061004979 catalytic residue [active] 887061004980 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...; Region: PRAI; cd00405 887061004981 active site 887061004982 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 887061004983 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 887061004984 active site 887061004985 dimerization interface 3.5A [polypeptide binding]; other site 887061004986 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 887061004987 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 887061004988 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 887061004989 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 887061004990 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 887061004991 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 887061004992 tartrate dehydrogenase; Region: TTC; TIGR02089 887061004993 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 887061004994 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 887061004995 substrate binding site [chemical binding]; other site 887061004996 Entericidin EcnA/B family; Region: Entericidin; pfam08085 887061004997 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 887061004998 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 887061004999 substrate binding site [chemical binding]; other site 887061005000 ligand binding site [chemical binding]; other site 887061005001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 887061005002 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 887061005003 DinB family; Region: DinB; cl17821 887061005004 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 887061005005 argininosuccinate synthase; Provisional; Region: PRK13820 887061005006 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 887061005007 ANP binding site [chemical binding]; other site 887061005008 Substrate Binding Site II [chemical binding]; other site 887061005009 Substrate Binding Site I [chemical binding]; other site 887061005010 ornithine carbamoyltransferase; Provisional; Region: PRK00779 887061005011 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 887061005012 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 887061005013 acetylornithine aminotransferase; Provisional; Region: PRK02627 887061005014 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 887061005015 inhibitor-cofactor binding pocket; inhibition site 887061005016 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061005017 catalytic residue [active] 887061005018 Protein of unknown function (DUF989); Region: DUF989; pfam06181 887061005019 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 887061005020 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 887061005021 [2Fe-2S] cluster binding site [ion binding]; other site 887061005022 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 887061005023 alpha subunit interface [polypeptide binding]; other site 887061005024 active site 887061005025 substrate binding site [chemical binding]; other site 887061005026 Fe binding site [ion binding]; other site 887061005027 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 887061005028 EamA-like transporter family; Region: EamA; pfam00892 887061005029 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061005030 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061005031 active site 887061005032 phosphorylation site [posttranslational modification] 887061005033 intermolecular recognition site; other site 887061005034 dimerization interface [polypeptide binding]; other site 887061005035 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061005036 DNA binding residues [nucleotide binding] 887061005037 dimerization interface [polypeptide binding]; other site 887061005038 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061005039 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061005040 dimerization interface [polypeptide binding]; other site 887061005041 PAS domain S-box; Region: sensory_box; TIGR00229 887061005042 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 887061005043 putative active site [active] 887061005044 heme pocket [chemical binding]; other site 887061005045 Histidine kinase; Region: HisKA_3; pfam07730 887061005046 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 887061005047 ATP binding site [chemical binding]; other site 887061005048 Mg2+ binding site [ion binding]; other site 887061005049 G-X-G motif; other site 887061005050 Cache domain; Region: Cache_1; pfam02743 887061005051 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 887061005052 dimerization interface [polypeptide binding]; other site 887061005053 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061005054 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061005055 dimer interface [polypeptide binding]; other site 887061005056 putative CheW interface [polypeptide binding]; other site 887061005057 HPP family; Region: HPP; pfam04982 887061005058 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 887061005059 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 887061005060 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 887061005061 metal binding triad; other site 887061005062 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 887061005063 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 887061005064 metal binding triad; other site 887061005065 acetyl-CoA synthetase; Provisional; Region: PRK00174 887061005066 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 887061005067 active site 887061005068 CoA binding site [chemical binding]; other site 887061005069 acyl-activating enzyme (AAE) consensus motif; other site 887061005070 AMP binding site [chemical binding]; other site 887061005071 acetate binding site [chemical binding]; other site 887061005072 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 887061005073 PepSY-associated TM helix; Region: PepSY_TM_3; pfam13706 887061005074 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 887061005075 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 887061005076 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 887061005077 N-terminal plug; other site 887061005078 ligand-binding site [chemical binding]; other site 887061005079 fec operon regulator FecR; Reviewed; Region: PRK09774 887061005080 FecR protein; Region: FecR; pfam04773 887061005081 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061005082 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005083 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 887061005084 DNA binding residues [nucleotide binding] 887061005085 Putative phosphatase (DUF442); Region: DUF442; cl17385 887061005086 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 887061005087 dimerization interface [polypeptide binding]; other site 887061005088 putative DNA binding site [nucleotide binding]; other site 887061005089 putative Zn2+ binding site [ion binding]; other site 887061005090 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 887061005091 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 887061005092 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 887061005093 G1 box; other site 887061005094 putative GEF interaction site [polypeptide binding]; other site 887061005095 GTP/Mg2+ binding site [chemical binding]; other site 887061005096 Switch I region; other site 887061005097 G2 box; other site 887061005098 G3 box; other site 887061005099 Switch II region; other site 887061005100 G4 box; other site 887061005101 G5 box; other site 887061005102 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 887061005103 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061005104 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 887061005105 ligand binding site [chemical binding]; other site 887061005106 flexible hinge region; other site 887061005107 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 887061005108 putative switch regulator; other site 887061005109 non-specific DNA interactions [nucleotide binding]; other site 887061005110 DNA binding site [nucleotide binding] 887061005111 sequence specific DNA binding site [nucleotide binding]; other site 887061005112 putative cAMP binding site [chemical binding]; other site 887061005113 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005114 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061005115 active site 887061005116 phosphorylation site [posttranslational modification] 887061005117 intermolecular recognition site; other site 887061005118 dimerization interface [polypeptide binding]; other site 887061005119 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 887061005120 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 887061005121 Phytochrome region; Region: PHY; pfam00360 887061005122 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061005123 dimer interface [polypeptide binding]; other site 887061005124 phosphorylation site [posttranslational modification] 887061005125 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 887061005126 ATP binding site [chemical binding]; other site 887061005127 Mg2+ binding site [ion binding]; other site 887061005128 G-X-G motif; other site 887061005129 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; cl17299 887061005130 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 887061005131 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 887061005132 Glucose/sorbosone dehydrogenases [Carbohydrate transport and metabolism]; Region: COG2133 887061005133 CHASE domain; Region: CHASE; pfam03924 887061005134 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 887061005135 putative active site [active] 887061005136 PAS fold; Region: PAS_3; pfam08447 887061005137 heme pocket [chemical binding]; other site 887061005138 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061005139 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061005140 metal binding site [ion binding]; metal-binding site 887061005141 active site 887061005142 I-site; other site 887061005143 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 887061005144 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 887061005145 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061005146 DNA-binding site [nucleotide binding]; DNA binding site 887061005147 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 887061005148 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061005149 homodimer interface [polypeptide binding]; other site 887061005150 catalytic residue [active] 887061005151 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 887061005152 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 887061005153 putative molybdopterin cofactor binding site [chemical binding]; other site 887061005154 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 887061005155 putative molybdopterin cofactor binding site; other site 887061005156 serine/threonine protein kinase; Provisional; Region: PRK11768 887061005157 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 887061005158 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 887061005159 catalytic residues [active] 887061005160 dimer interface [polypeptide binding]; other site 887061005161 Adenylyl- / guanylyl cyclase, catalytic domain; Region: CYCc; smart00044 887061005162 cyclase homology domain; Region: CHD; cd07302 887061005163 nucleotidyl binding site; other site 887061005164 metal binding site [ion binding]; metal-binding site 887061005165 dimer interface [polypeptide binding]; other site 887061005166 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 887061005167 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061005168 Walker A motif; other site 887061005169 ATP binding site [chemical binding]; other site 887061005170 DNA polymerase III subunit delta'; Validated; Region: PRK08485 887061005171 Walker B motif; other site 887061005172 arginine finger; other site 887061005173 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 887061005174 hypothetical protein; Validated; Region: PRK00153 887061005175 recombination protein RecR; Reviewed; Region: recR; PRK00076 887061005176 RecR protein; Region: RecR; pfam02132 887061005177 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 887061005178 putative active site [active] 887061005179 putative metal-binding site [ion binding]; other site 887061005180 tetramer interface [polypeptide binding]; other site 887061005181 phosphoglycolate phosphatase; Provisional; Region: PRK13222 887061005182 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 887061005183 motif II; other site 887061005184 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 887061005185 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 887061005186 S-adenosylmethionine binding site [chemical binding]; other site 887061005187 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 887061005188 Amidohydrolase; Region: Amidohydro_4; pfam13147 887061005189 active site 887061005190 putative substrate binding pocket [chemical binding]; other site 887061005191 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 887061005192 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 887061005193 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061005194 ligand binding site [chemical binding]; other site 887061005195 hypothetical protein; Provisional; Region: PRK02227 887061005196 Protein of unknown function (DUF447); Region: DUF447; pfam04289 887061005197 dihydropteroate synthase-related protein; Region: TIGR00284 887061005198 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 887061005199 substrate binding pocket [chemical binding]; other site 887061005200 dimer interface [polypeptide binding]; other site 887061005201 inhibitor binding site; inhibition site 887061005202 Archaeal flavoproteins [Energy production and conversion]; Region: COG1036 887061005203 Flavoprotein; Region: Flavoprotein; pfam02441 887061005204 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 887061005205 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 887061005206 GDP-binding site [chemical binding]; other site 887061005207 ACT binding site; other site 887061005208 IMP binding site; other site 887061005209 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 887061005210 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...; Region: HisRS-like_core; cd00773 887061005211 dimer interface [polypeptide binding]; other site 887061005212 motif 1; other site 887061005213 active site 887061005214 motif 2; other site 887061005215 motif 3; other site 887061005216 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 887061005217 HflC protein; Region: hflC; TIGR01932 887061005218 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 887061005219 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 887061005220 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 887061005221 HflK protein; Region: hflK; TIGR01933 887061005222 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 887061005223 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 887061005224 HflX GTPase family; Region: HflX; cd01878 887061005225 G1 box; other site 887061005226 GTP/Mg2+ binding site [chemical binding]; other site 887061005227 Switch I region; other site 887061005228 G2 box; other site 887061005229 G3 box; other site 887061005230 Switch II region; other site 887061005231 G4 box; other site 887061005232 G5 box; other site 887061005233 bacterial Hfq-like; Region: Hfq; cd01716 887061005234 hexamer interface [polypeptide binding]; other site 887061005235 Sm1 motif; other site 887061005236 RNA binding site [nucleotide binding]; other site 887061005237 Sm2 motif; other site 887061005238 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 887061005239 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 887061005240 active site 887061005241 HIGH motif; other site 887061005242 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 887061005243 active site 887061005244 KMSKS motif; other site 887061005245 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 887061005246 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 887061005247 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 887061005248 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061005249 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061005250 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061005251 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061005252 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 887061005253 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061005254 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 887061005255 putative active site [active] 887061005256 heme pocket [chemical binding]; other site 887061005257 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 887061005258 putative active site [active] 887061005259 heme pocket [chemical binding]; other site 887061005260 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061005261 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061005262 metal binding site [ion binding]; metal-binding site 887061005263 active site 887061005264 I-site; other site 887061005265 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 887061005266 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 887061005267 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 887061005268 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 887061005269 FeS/SAM binding site; other site 887061005270 TRAM domain; Region: TRAM; cl01282 887061005271 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 887061005272 ZIP Zinc transporter; Region: Zip; pfam02535 887061005273 PEP-CTERM motif; Region: VPEP; pfam07589 887061005274 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 887061005275 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061005276 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 887061005277 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 887061005278 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 887061005279 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 887061005280 RNA binding surface [nucleotide binding]; other site 887061005281 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 887061005282 active site 887061005283 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 887061005284 GTP-binding protein Der; Reviewed; Region: PRK00093 887061005285 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 887061005286 G1 box; other site 887061005287 GTP/Mg2+ binding site [chemical binding]; other site 887061005288 Switch I region; other site 887061005289 G2 box; other site 887061005290 Switch II region; other site 887061005291 G3 box; other site 887061005292 G4 box; other site 887061005293 G5 box; other site 887061005294 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 887061005295 G1 box; other site 887061005296 GTP/Mg2+ binding site [chemical binding]; other site 887061005297 Switch I region; other site 887061005298 G2 box; other site 887061005299 G3 box; other site 887061005300 Switch II region; other site 887061005301 G4 box; other site 887061005302 G5 box; other site 887061005303 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 887061005304 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 887061005305 Trp docking motif [polypeptide binding]; other site 887061005306 active site 887061005307 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 887061005308 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 887061005309 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 887061005310 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 887061005311 Walker A/P-loop; other site 887061005312 ATP binding site [chemical binding]; other site 887061005313 Q-loop/lid; other site 887061005314 ABC transporter signature motif; other site 887061005315 Walker B; other site 887061005316 D-loop; other site 887061005317 H-loop/switch region; other site 887061005318 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 887061005319 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 887061005320 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 887061005321 Walker A/P-loop; other site 887061005322 ATP binding site [chemical binding]; other site 887061005323 Q-loop/lid; other site 887061005324 ABC transporter signature motif; other site 887061005325 Walker B; other site 887061005326 D-loop; other site 887061005327 H-loop/switch region; other site 887061005328 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 887061005329 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 887061005330 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...; Region: HisRS-like_core; cd00773 887061005331 dimer interface [polypeptide binding]; other site 887061005332 motif 1; other site 887061005333 active site 887061005334 motif 2; other site 887061005335 motif 3; other site 887061005336 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 887061005337 anticodon binding site; other site 887061005338 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 887061005339 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 887061005340 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 887061005341 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 887061005342 non-specific DNA binding site [nucleotide binding]; other site 887061005343 salt bridge; other site 887061005344 sequence-specific DNA binding site [nucleotide binding]; other site 887061005345 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 887061005346 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 887061005347 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 887061005348 binding surface 887061005349 TPR motif; other site 887061005350 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 887061005351 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 887061005352 FeS/SAM binding site; other site 887061005353 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 887061005354 active site 887061005355 multimer interface [polypeptide binding]; other site 887061005356 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 887061005357 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 887061005358 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 887061005359 ribonuclease R; Region: RNase_R; TIGR02063 887061005360 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 887061005361 RNB domain; Region: RNB; pfam00773 887061005362 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...; Region: S1_RNase_R; cd04471 887061005363 RNA binding site [nucleotide binding]; other site 887061005364 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061005365 active site 887061005366 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 887061005367 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 887061005368 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 887061005369 NAD(P) binding site [chemical binding]; other site 887061005370 homodimer interface [polypeptide binding]; other site 887061005371 substrate binding site [chemical binding]; other site 887061005372 active site 887061005373 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 887061005374 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 887061005375 NAD(P) binding site [chemical binding]; other site 887061005376 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 887061005377 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 887061005378 C factor cell-cell signaling protein; Provisional; Region: PRK09009 887061005379 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 887061005380 NADP binding site [chemical binding]; other site 887061005381 homodimer interface [polypeptide binding]; other site 887061005382 active site 887061005383 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 887061005384 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 887061005385 FeS/SAM binding site; other site 887061005386 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 887061005387 RNA binding surface [nucleotide binding]; other site 887061005388 Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]; Region: LonB; COG1067 887061005389 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 887061005390 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 887061005391 MoaE homodimer interface [polypeptide binding]; other site 887061005392 MoaD interaction [polypeptide binding]; other site 887061005393 active site residues [active] 887061005394 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 887061005395 MoaE interaction surface [polypeptide binding]; other site 887061005396 MoeB interaction surface [polypeptide binding]; other site 887061005397 thiocarboxylated glycine; other site 887061005398 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 887061005399 RmuC family; Region: RmuC; pfam02646 887061005400 CHASE2 domain; Region: CHASE2; pfam05226 887061005401 Bacterial SH3 domain; Region: SH3_3; cl17532 887061005402 Peptidase family M48; Region: Peptidase_M48; pfam01435 887061005403 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 887061005404 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 887061005405 G1 box; other site 887061005406 putative GEF interaction site [polypeptide binding]; other site 887061005407 GTP/Mg2+ binding site [chemical binding]; other site 887061005408 Switch I region; other site 887061005409 G2 box; other site 887061005410 G3 box; other site 887061005411 Switch II region; other site 887061005412 G4 box; other site 887061005413 G5 box; other site 887061005414 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 887061005415 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 887061005416 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 887061005417 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 887061005418 ATP binding site [chemical binding]; other site 887061005419 Mg++ binding site [ion binding]; other site 887061005420 motif III; other site 887061005421 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 887061005422 nucleotide binding region [chemical binding]; other site 887061005423 ATP-binding site [chemical binding]; other site 887061005424 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 887061005425 DEAD-like helicases superfamily; Region: DEXDc; smart00487 887061005426 ATP binding site [chemical binding]; other site 887061005427 Mg++ binding site [ion binding]; other site 887061005428 motif III; other site 887061005429 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 887061005430 nucleotide binding region [chemical binding]; other site 887061005431 ATP-binding site [chemical binding]; other site 887061005432 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 887061005433 apolar tunnel; other site 887061005434 heme binding site [chemical binding]; other site 887061005435 dimerization interface [polypeptide binding]; other site 887061005436 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 887061005437 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061005438 ATP-grasp domain; Region: ATP-grasp; pfam02222 887061005439 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061005440 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061005441 active site 887061005442 phosphorylation site [posttranslational modification] 887061005443 intermolecular recognition site; other site 887061005444 dimerization interface [polypeptide binding]; other site 887061005445 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061005446 Walker A motif; other site 887061005447 ATP binding site [chemical binding]; other site 887061005448 Walker B motif; other site 887061005449 arginine finger; other site 887061005450 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061005451 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061005452 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 887061005453 N-terminal plug; other site 887061005454 ligand-binding site [chemical binding]; other site 887061005455 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 887061005456 FtsX-like permease family; Region: FtsX; pfam02687 887061005457 FtsX-like permease family; Region: FtsX; pfam02687 887061005458 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 887061005459 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 887061005460 Walker A/P-loop; other site 887061005461 ATP binding site [chemical binding]; other site 887061005462 Q-loop/lid; other site 887061005463 ABC transporter signature motif; other site 887061005464 Walker B; other site 887061005465 D-loop; other site 887061005466 H-loop/switch region; other site 887061005467 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 887061005468 active site 887061005469 catalytic triad [active] 887061005470 oxyanion hole [active] 887061005471 switch loop; other site 887061005472 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 887061005473 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 887061005474 Ligand Binding Site [chemical binding]; other site 887061005475 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 887061005476 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 887061005477 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 887061005478 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 887061005479 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 887061005480 putative active site [active] 887061005481 putative PHP Thumb interface [polypeptide binding]; other site 887061005482 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 887061005483 generic binding surface II; other site 887061005484 generic binding surface I; other site 887061005485 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 887061005486 putative binding surface; other site 887061005487 active site 887061005488 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 887061005489 putative binding surface; other site 887061005490 active site 887061005491 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 887061005492 putative binding surface; other site 887061005493 active site 887061005494 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 887061005495 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 887061005496 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 887061005497 ATP binding site [chemical binding]; other site 887061005498 Mg2+ binding site [ion binding]; other site 887061005499 G-X-G motif; other site 887061005500 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 887061005501 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005502 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061005503 active site 887061005504 phosphorylation site [posttranslational modification] 887061005505 intermolecular recognition site; other site 887061005506 dimerization interface [polypeptide binding]; other site 887061005507 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061005508 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061005509 dimer interface [polypeptide binding]; other site 887061005510 putative CheW interface [polypeptide binding]; other site 887061005511 CheW-like domain; Region: CheW; pfam01584 887061005512 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005513 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061005514 active site 887061005515 phosphorylation site [posttranslational modification] 887061005516 intermolecular recognition site; other site 887061005517 dimerization interface [polypeptide binding]; other site 887061005518 Response regulator receiver domain; Region: Response_reg; pfam00072 887061005519 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061005520 active site 887061005521 phosphorylation site [posttranslational modification] 887061005522 intermolecular recognition site; other site 887061005523 dimerization interface [polypeptide binding]; other site 887061005524 Uncharacterized conserved protein [Function unknown]; Region: COG3287 887061005525 FIST N domain; Region: FIST; pfam08495 887061005526 FIST C domain; Region: FIST_C; pfam10442 887061005527 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 887061005528 dimer interface [polypeptide binding]; other site 887061005529 catalytic triad [active] 887061005530 peroxidatic and resolving cysteines [active] 887061005531 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 887061005532 Autotransporter beta-domain; Region: Autotransporter; smart00869 887061005533 SnoaL-like domain; Region: SnoaL_3; pfam13474 887061005534 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061005535 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061005536 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061005537 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061005538 fec operon regulator FecR; Reviewed; Region: PRK09774 887061005539 FecR protein; Region: FecR; pfam04773 887061005540 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061005541 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005542 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061005543 DNA binding residues [nucleotide binding] 887061005544 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 887061005545 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 887061005546 homodimer interface [polypeptide binding]; other site 887061005547 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 887061005548 active site pocket [active] 887061005549 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 887061005550 TolR protein; Region: tolR; TIGR02801 887061005551 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 887061005552 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 887061005553 Hemin uptake protein hemP; Region: hemP; pfam10636 887061005554 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 887061005555 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 887061005556 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 887061005557 RNA binding surface [nucleotide binding]; other site 887061005558 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 887061005559 heat shock protein 90; Provisional; Region: PRK05218 887061005560 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 887061005561 ATP binding site [chemical binding]; other site 887061005562 Mg2+ binding site [ion binding]; other site 887061005563 G-X-G motif; other site 887061005564 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; pfam10013 887061005565 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 887061005566 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 887061005567 putative ATP binding site [chemical binding]; other site 887061005568 putative substrate interface [chemical binding]; other site 887061005569 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 887061005570 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...; Region: PNPsynthase; cd00003 887061005571 active site 887061005572 hydrophilic channel; other site 887061005573 dimerization interface [polypeptide binding]; other site 887061005574 catalytic residues [active] 887061005575 active site lid [active] 887061005576 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 887061005577 Recombination protein O N terminal; Region: RecO_N; pfam11967 887061005578 Recombination protein O C terminal; Region: RecO_C; pfam02565 887061005579 GTPase Era; Reviewed; Region: era; PRK00089 887061005580 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 887061005581 G1 box; other site 887061005582 GTP/Mg2+ binding site [chemical binding]; other site 887061005583 Switch I region; other site 887061005584 G2 box; other site 887061005585 Switch II region; other site 887061005586 G3 box; other site 887061005587 G4 box; other site 887061005588 G5 box; other site 887061005589 KH domain; Region: KH_2; pfam07650 887061005590 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 887061005591 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 887061005592 dimerization interface [polypeptide binding]; other site 887061005593 active site 887061005594 metal binding site [ion binding]; metal-binding site 887061005595 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 887061005596 dsRNA binding site [nucleotide binding]; other site 887061005597 signal peptidase I; Provisional; Region: PRK10861 887061005598 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 887061005599 Catalytic site [active] 887061005600 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 887061005601 GTP-binding protein LepA; Provisional; Region: PRK05433 887061005602 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 887061005603 G1 box; other site 887061005604 putative GEF interaction site [polypeptide binding]; other site 887061005605 GTP/Mg2+ binding site [chemical binding]; other site 887061005606 Switch I region; other site 887061005607 G2 box; other site 887061005608 G3 box; other site 887061005609 Switch II region; other site 887061005610 G4 box; other site 887061005611 G5 box; other site 887061005612 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 887061005613 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 887061005614 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 887061005615 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 887061005616 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 887061005617 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 887061005618 protein binding site [polypeptide binding]; other site 887061005619 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 887061005620 protein binding site [polypeptide binding]; other site 887061005621 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 887061005622 anti-sigma E factor; Provisional; Region: rseB; PRK09455 887061005623 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 887061005624 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 887061005625 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005626 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061005627 DNA binding residues [nucleotide binding] 887061005628 L-aspartate oxidase; Provisional; Region: PRK09077 887061005629 L-aspartate oxidase; Provisional; Region: PRK06175 887061005630 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 887061005631 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 887061005632 hypothetical protein; Provisional; Region: PRK05409 887061005633 RNA polymerase sigma factor; Provisional; Region: PRK12520 887061005634 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061005635 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 887061005636 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 887061005637 FIST C domain; Region: FIST_C; pfam10442 887061005638 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 887061005639 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 887061005640 minor groove reading motif; other site 887061005641 helix-hairpin-helix signature motif; other site 887061005642 substrate binding pocket [chemical binding]; other site 887061005643 active site 887061005644 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 887061005645 ferredoxin; Provisional; Region: PRK08764 887061005646 4Fe-4S binding domain; Region: Fer4; pfam00037 887061005647 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 887061005648 dihydrodipicolinate synthase; Region: dapA; TIGR00674 887061005649 dimer interface [polypeptide binding]; other site 887061005650 active site 887061005651 catalytic residue [active] 887061005652 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 887061005653 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 887061005654 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 887061005655 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 887061005656 Uncharacterized conserved protein [Function unknown]; Region: COG2850 887061005657 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 887061005658 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 887061005659 catalytic triad [active] 887061005660 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 887061005661 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 887061005662 Ligand binding site; other site 887061005663 Putative Catalytic site; other site 887061005664 DXD motif; other site 887061005665 Mycoplasma P30 protein; Region: P30; pfam07390 887061005666 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 887061005667 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 887061005668 active site 887061005669 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 887061005670 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 887061005671 active site 887061005672 colanic acid exporter; Provisional; Region: PRK10459 887061005673 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 887061005674 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005675 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 887061005676 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 887061005677 Trp docking motif [polypeptide binding]; other site 887061005678 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061005679 active site 887061005680 Core-2/I-Branching enzyme; Region: Branch; pfam02485 887061005681 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 887061005682 ArsC family; Region: ArsC; pfam03960 887061005683 catalytic residues [active] 887061005684 Acyltransferase family; Region: Acyl_transf_3; pfam01757 887061005685 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 887061005686 MutS domain I; Region: MutS_I; pfam01624 887061005687 MutS domain II; Region: MutS_II; pfam05188 887061005688 MutS domain III; Region: MutS_III; pfam05192 887061005689 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 887061005690 Walker A/P-loop; other site 887061005691 ATP binding site [chemical binding]; other site 887061005692 Q-loop/lid; other site 887061005693 ABC transporter signature motif; other site 887061005694 Walker B; other site 887061005695 D-loop; other site 887061005696 H-loop/switch region; other site 887061005697 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 887061005698 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...; Region: LT_GEWL; cd00254 887061005699 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061005700 catalytic residue [active] 887061005701 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 887061005702 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 887061005703 active site 887061005704 tetramer interface; other site 887061005705 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 887061005706 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 887061005707 NAD binding site [chemical binding]; other site 887061005708 homodimer interface [polypeptide binding]; other site 887061005709 active site 887061005710 substrate binding site [chemical binding]; other site 887061005711 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 887061005712 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 887061005713 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 887061005714 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 887061005715 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 887061005716 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 887061005717 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 887061005718 DXD motif; other site 887061005719 colanic acid biosynthesis glycosyltransferase WcaL; Provisional; Region: PRK15427 887061005720 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 887061005721 putative ADP-binding pocket [chemical binding]; other site 887061005722 O-Antigen ligase; Region: Wzy_C; pfam04932 887061005723 Protein of unknown function (DUF3485); Region: DUF3485; pfam11984 887061005724 Predicted membrane protein [Function unknown]; Region: COG4083; cl15694 887061005725 Transmembrane exosortase (Exosortase_EpsH); Region: Exosortase_EpsH; pfam09721 887061005726 chain length determinant protein tyrosine kinase EpsG; Region: EpsG; TIGR03029 887061005727 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 887061005728 DTAP/Switch II; other site 887061005729 Switch I; other site 887061005730 chain length determinant protein EpsF; Region: EpsF; TIGR03017 887061005731 Chain length determinant protein; Region: Wzz; cl15801 887061005732 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 887061005733 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 887061005734 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 887061005735 SLBB domain; Region: SLBB; pfam10531 887061005736 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 887061005737 exopolysaccharide biosynthesis operon protein EpsL; Region: EpsL; TIGR03014 887061005738 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061005739 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 887061005740 ligand binding site [chemical binding]; other site 887061005741 flexible hinge region; other site 887061005742 transcriptional regulator EpsA; Region: EpsA; TIGR03020 887061005743 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061005744 DNA binding residues [nucleotide binding] 887061005745 dimerization interface [polypeptide binding]; other site 887061005746 Undecaprenyl-phosphate glucose phosphotransferase; Region: WcaJ_sugtrans; TIGR03023 887061005747 Bacterial sugar transferase; Region: Bac_transf; pfam02397 887061005748 PEP-CTERM motif; Region: VPEP; pfam07589 887061005749 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 887061005750 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 887061005751 active site 887061005752 dimerization interface [polypeptide binding]; other site 887061005753 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 887061005754 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 887061005755 serine O-acetyltransferase; Region: cysE; TIGR01172 887061005756 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 887061005757 trimer interface [polypeptide binding]; other site 887061005758 active site 887061005759 substrate binding site [chemical binding]; other site 887061005760 CoA binding site [chemical binding]; other site 887061005761 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 887061005762 Rrf2 family protein; Region: rrf2_super; TIGR00738 887061005763 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 887061005764 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 887061005765 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061005766 catalytic residue [active] 887061005767 cysteine desulfurase; Provisional; Region: PRK14012 887061005768 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 887061005769 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061005770 catalytic residue [active] 887061005771 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 887061005772 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 887061005773 trimerization site [polypeptide binding]; other site 887061005774 active site 887061005775 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 887061005776 co-chaperone HscB; Provisional; Region: hscB; PRK03578 887061005777 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 887061005778 HSP70 interaction site [polypeptide binding]; other site 887061005779 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 887061005780 chaperone protein HscA; Provisional; Region: hscA; PRK05183 887061005781 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 887061005782 nucleotide binding site [chemical binding]; other site 887061005783 putative NEF/HSP70 interaction site [polypeptide binding]; other site 887061005784 SBD interface [polypeptide binding]; other site 887061005785 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 887061005786 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 887061005787 catalytic loop [active] 887061005788 iron binding site [ion binding]; other site 887061005789 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 887061005790 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 887061005791 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 887061005792 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 887061005793 active site 887061005794 phosphorylation site [posttranslational modification] 887061005795 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 887061005796 dimerization domain swap beta strand [polypeptide binding]; other site 887061005797 regulatory protein interface [polypeptide binding]; other site 887061005798 active site 887061005799 regulatory phosphorylation site [posttranslational modification]; other site 887061005800 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 887061005801 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 887061005802 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 887061005803 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 887061005804 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 887061005805 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 887061005806 putative substrate binding site [chemical binding]; other site 887061005807 putative ATP binding site [chemical binding]; other site 887061005808 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 887061005809 active site 887061005810 P-loop; other site 887061005811 phosphorylation site [posttranslational modification] 887061005812 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 887061005813 active site 887061005814 P-loop; other site 887061005815 phosphorylation site [posttranslational modification] 887061005816 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; cl17425 887061005817 Phosphotransferase system, EIIC; Region: PTS_EIIC; pfam02378 887061005818 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...; Region: Maltoporin-like; cd01346 887061005819 sugar binding site [chemical binding]; other site 887061005820 trimer interface; other site 887061005821 fructose-1,6-bisphosphatase family protein; Region: PLN02628 887061005822 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 887061005823 AMP binding site [chemical binding]; other site 887061005824 metal binding site [ion binding]; metal-binding site 887061005825 active site 887061005826 putative diguanylate cyclase; Provisional; Region: PRK09776 887061005827 MASE1; Region: MASE1; pfam05231 887061005828 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 887061005829 putative active site [active] 887061005830 heme pocket [chemical binding]; other site 887061005831 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 887061005832 putative active site [active] 887061005833 heme pocket [chemical binding]; other site 887061005834 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 887061005835 putative active site [active] 887061005836 heme pocket [chemical binding]; other site 887061005837 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061005838 metal binding site [ion binding]; metal-binding site 887061005839 active site 887061005840 I-site; other site 887061005841 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 887061005842 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 887061005843 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 887061005844 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 887061005845 dimer interface [polypeptide binding]; other site 887061005846 putative anticodon binding site; other site 887061005847 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 887061005848 motif 1; other site 887061005849 active site 887061005850 motif 2; other site 887061005851 motif 3; other site 887061005852 peptide chain release factor 2; Validated; Region: prfB; PRK00578 887061005853 This domain is found in peptide chain release factors; Region: PCRF; smart00937 887061005854 RF-1 domain; Region: RF-1; pfam00472 887061005855 phosphate binding protein; Region: ptsS_2; TIGR02136 887061005856 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 887061005857 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061005858 dimer interface [polypeptide binding]; other site 887061005859 conserved gate region; other site 887061005860 putative PBP binding loops; other site 887061005861 ABC-ATPase subunit interface; other site 887061005862 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 887061005863 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061005864 dimer interface [polypeptide binding]; other site 887061005865 conserved gate region; other site 887061005866 putative PBP binding loops; other site 887061005867 ABC-ATPase subunit interface; other site 887061005868 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 887061005869 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 887061005870 Walker A/P-loop; other site 887061005871 ATP binding site [chemical binding]; other site 887061005872 Q-loop/lid; other site 887061005873 ABC transporter signature motif; other site 887061005874 Walker B; other site 887061005875 D-loop; other site 887061005876 H-loop/switch region; other site 887061005877 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 887061005878 hydroxyglutarate oxidase; Provisional; Region: PRK11728 887061005879 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005880 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; Region: GT1_UGDG_like; cd03817 887061005881 putative ADP-binding pocket [chemical binding]; other site 887061005882 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 887061005883 Zinc dependent phospholipase C; Region: Zn_dep_PLPC; pfam00882 887061005884 Cupin domain; Region: Cupin_2; pfam07883 887061005885 Helix-turn-helix domain; Region: HTH_18; pfam12833 887061005886 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061005887 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 887061005888 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; cd01610 887061005889 active site 887061005890 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 887061005891 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 887061005892 active site 887061005893 substrate binding site [chemical binding]; other site 887061005894 metal binding site [ion binding]; metal-binding site 887061005895 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 887061005896 dihydropteroate synthase; Region: DHPS; TIGR01496 887061005897 substrate binding pocket [chemical binding]; other site 887061005898 dimer interface [polypeptide binding]; other site 887061005899 inhibitor binding site; inhibition site 887061005900 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 887061005901 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061005902 Walker A motif; other site 887061005903 ATP binding site [chemical binding]; other site 887061005904 Walker B motif; other site 887061005905 arginine finger; other site 887061005906 Peptidase family M41; Region: Peptidase_M41; pfam01434 887061005907 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 887061005908 FtsJ-like methyltransferase; Region: FtsJ; cl17430 887061005909 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; pfam01985 887061005910 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 887061005911 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 887061005912 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 887061005913 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 887061005914 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 887061005915 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061005916 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 887061005917 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 887061005918 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 887061005919 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061005920 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 887061005921 IMP binding site; other site 887061005922 dimer interface [polypeptide binding]; other site 887061005923 interdomain contacts; other site 887061005924 partial ornithine binding site; other site 887061005925 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 887061005926 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 887061005927 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 887061005928 catalytic site [active] 887061005929 subunit interface [polypeptide binding]; other site 887061005930 dihydrodipicolinate reductase; Provisional; Region: PRK00048 887061005931 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 887061005932 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 887061005933 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 887061005934 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 887061005935 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 887061005936 metal binding site 2 [ion binding]; metal-binding site 887061005937 putative DNA binding helix; other site 887061005938 metal binding site 1 [ion binding]; metal-binding site 887061005939 dimer interface [polypeptide binding]; other site 887061005940 structural Zn2+ binding site [ion binding]; other site 887061005941 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 887061005942 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 887061005943 Walker A/P-loop; other site 887061005944 ATP binding site [chemical binding]; other site 887061005945 Q-loop/lid; other site 887061005946 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 887061005947 ABC transporter signature motif; other site 887061005948 Walker B; other site 887061005949 D-loop; other site 887061005950 H-loop/switch region; other site 887061005951 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 887061005952 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 887061005953 Domain of unknown function (DUF3413); Region: DUF3413; pfam11893 887061005954 Sulfatase; Region: Sulfatase; pfam00884 887061005955 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 887061005956 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 887061005957 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 887061005958 Flagellar protein YcgR; Region: YcgR_2; pfam12945 887061005959 PilZ domain; Region: PilZ; pfam07238 887061005960 ferrochelatase; Reviewed; Region: hemH; PRK00035 887061005961 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 887061005962 C-terminal domain interface [polypeptide binding]; other site 887061005963 active site 887061005964 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 887061005965 active site 887061005966 N-terminal domain interface [polypeptide binding]; other site 887061005967 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 887061005968 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 887061005969 NADP binding site [chemical binding]; other site 887061005970 homopentamer interface [polypeptide binding]; other site 887061005971 substrate binding site [chemical binding]; other site 887061005972 active site 887061005973 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 887061005974 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 887061005975 dimer interface [polypeptide binding]; other site 887061005976 active site 887061005977 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 887061005978 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 887061005979 putative ribose interaction site [chemical binding]; other site 887061005980 putative ADP binding site [chemical binding]; other site 887061005981 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 887061005982 active site 887061005983 nucleotide binding site [chemical binding]; other site 887061005984 HIGH motif; other site 887061005985 KMSKS motif; other site 887061005986 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 887061005987 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 887061005988 putative active site [active] 887061005989 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005990 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 887061005991 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 887061005992 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061005993 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 887061005994 putative ADP-binding pocket [chemical binding]; other site 887061005995 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; cl17270 887061005996 active site 887061005997 ATP binding site [chemical binding]; other site 887061005998 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 887061005999 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 887061006000 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 887061006001 active site 887061006002 intersubunit interface [polypeptide binding]; other site 887061006003 catalytic residue [active] 887061006004 phosphogluconate dehydratase; Validated; Region: PRK09054 887061006005 6-phosphogluconate dehydratase; Region: edd; TIGR01196 887061006006 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 887061006007 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 887061006008 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 887061006009 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 887061006010 active site 887061006011 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 887061006012 lipopolysaccharide core heptose(I) kinase RfaP; Provisional; Region: PRK15123 887061006013 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061006014 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 887061006015 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 887061006016 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 887061006017 putative active site [active] 887061006018 GrpE; Region: GrpE; pfam01025 887061006019 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 887061006020 dimer interface [polypeptide binding]; other site 887061006021 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 887061006022 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 887061006023 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 887061006024 nucleotide binding site [chemical binding]; other site 887061006025 chaperone protein DnaJ; Provisional; Region: PRK10767 887061006026 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 887061006027 HSP70 interaction site [polypeptide binding]; other site 887061006028 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 887061006029 substrate binding site [polypeptide binding]; other site 887061006030 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 887061006031 Zn binding sites [ion binding]; other site 887061006032 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 887061006033 dimer interface [polypeptide binding]; other site 887061006034 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 887061006035 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 887061006036 putative active site [active] 887061006037 O-Antigen ligase; Region: Wzy_C; pfam04932 887061006038 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 887061006039 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 887061006040 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 887061006041 putative active site [active] 887061006042 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061006043 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 887061006044 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 887061006045 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 887061006046 putative ADP-binding pocket [chemical binding]; other site 887061006047 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 887061006048 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 887061006049 2-isopropylmalate synthase; Validated; Region: PRK03739 887061006050 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 887061006051 active site 887061006052 catalytic residues [active] 887061006053 metal binding site [ion binding]; metal-binding site 887061006054 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 887061006055 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; cd00312 887061006056 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 887061006057 substrate binding pocket [chemical binding]; other site 887061006058 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 887061006059 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 887061006060 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 887061006061 dimer interface [polypeptide binding]; other site 887061006062 active site 887061006063 metal binding site [ion binding]; metal-binding site 887061006064 glutathione binding site [chemical binding]; other site 887061006065 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061006066 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061006067 dimer interface [polypeptide binding]; other site 887061006068 putative CheW interface [polypeptide binding]; other site 887061006069 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061006070 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 887061006071 substrate binding pocket [chemical binding]; other site 887061006072 membrane-bound complex binding site; other site 887061006073 hinge residues; other site 887061006074 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 887061006075 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 887061006076 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 887061006077 active site 887061006078 (T/H)XGH motif; other site 887061006079 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 887061006080 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 887061006081 S-adenosylmethionine binding site [chemical binding]; other site 887061006082 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 887061006083 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 887061006084 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 887061006085 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 887061006086 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 887061006087 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 887061006088 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 887061006089 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 887061006090 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 887061006091 P loop; other site 887061006092 GTP binding site [chemical binding]; other site 887061006093 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 887061006094 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061006095 Walker A/P-loop; other site 887061006096 ATP binding site [chemical binding]; other site 887061006097 Q-loop/lid; other site 887061006098 ABC transporter signature motif; other site 887061006099 Walker B; other site 887061006100 D-loop; other site 887061006101 H-loop/switch region; other site 887061006102 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 887061006103 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 887061006104 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 887061006105 dimerization interface [polypeptide binding]; other site 887061006106 active site 887061006107 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 887061006108 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 887061006109 FAD binding pocket [chemical binding]; other site 887061006110 FAD binding motif [chemical binding]; other site 887061006111 phosphate binding motif [ion binding]; other site 887061006112 beta-alpha-beta structure motif; other site 887061006113 NAD binding pocket [chemical binding]; other site 887061006114 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 887061006115 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 887061006116 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 887061006117 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 887061006118 Ligand binding site [chemical binding]; other site 887061006119 Electron transfer flavoprotein domain; Region: ETF; pfam01012 887061006120 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 887061006121 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061006122 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 887061006123 putative dimerization interface [polypeptide binding]; other site 887061006124 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 887061006125 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 887061006126 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 887061006127 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 887061006128 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 887061006129 PhnA protein; Region: PhnA; pfam03831 887061006130 thiopurine S-methyltransferase, Se/Te detoxification family; Region: TMPT_Se_Te; TIGR03840 887061006131 Predicted membrane protein (DUF2214); Region: DUF2214; cl01427 887061006132 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 887061006133 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 887061006134 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 887061006135 homodimer interface [polypeptide binding]; other site 887061006136 substrate-cofactor binding pocket; other site 887061006137 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061006138 catalytic residue [active] 887061006139 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 887061006140 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 887061006141 Walker A/P-loop; other site 887061006142 ATP binding site [chemical binding]; other site 887061006143 Q-loop/lid; other site 887061006144 ABC transporter signature motif; other site 887061006145 Walker B; other site 887061006146 D-loop; other site 887061006147 H-loop/switch region; other site 887061006148 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 887061006149 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 887061006150 putative ligand binding site [chemical binding]; other site 887061006151 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 887061006152 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 887061006153 TM-ABC transporter signature motif; other site 887061006154 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 887061006155 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 887061006156 TM-ABC transporter signature motif; other site 887061006157 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 887061006158 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 887061006159 Walker A/P-loop; other site 887061006160 ATP binding site [chemical binding]; other site 887061006161 Q-loop/lid; other site 887061006162 ABC transporter signature motif; other site 887061006163 Walker B; other site 887061006164 D-loop; other site 887061006165 H-loop/switch region; other site 887061006166 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 887061006167 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 887061006168 dimethyl sulfone monooxygenase SfnG; Region: LLM_DMSO2_sfnG; TIGR04021 887061006169 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 887061006170 active site 887061006171 dimer interface [polypeptide binding]; other site 887061006172 non-prolyl cis peptide bond; other site 887061006173 insertion regions; other site 887061006174 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 887061006175 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 887061006176 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 887061006177 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 887061006178 Flavin binding site [chemical binding]; other site 887061006179 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061006180 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061006181 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 887061006182 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 887061006183 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061006184 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061006185 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 887061006186 Protein export membrane protein; Region: SecD_SecF; cl14618 887061006187 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG2159 887061006188 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 887061006189 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 887061006190 active site 887061006191 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 887061006192 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 887061006193 active site 887061006194 dimer interface [polypeptide binding]; other site 887061006195 non-prolyl cis peptide bond; other site 887061006196 insertion regions; other site 887061006197 sulfur acquisition oxidoreductase, SfnB family; Region: sulfur_SfnB; TIGR04022 887061006198 Dibenzothiophene (DBT) desulfurization enzyme C; Region: DszC; cd01163 887061006199 Flavin binding site [chemical binding]; other site 887061006200 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 887061006201 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061006202 Walker A motif; other site 887061006203 ATP binding site [chemical binding]; other site 887061006204 Walker B motif; other site 887061006205 arginine finger; other site 887061006206 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061006207 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 887061006208 dimerization interface [polypeptide binding]; other site 887061006209 active site 887061006210 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 887061006211 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061006212 substrate binding pocket [chemical binding]; other site 887061006213 membrane-bound complex binding site; other site 887061006214 hinge residues; other site 887061006215 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061006216 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006217 metal binding site [ion binding]; metal-binding site 887061006218 active site 887061006219 I-site; other site 887061006220 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 887061006221 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 887061006222 active site 887061006223 nucleophile elbow; other site 887061006224 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 887061006225 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 887061006226 N-terminal plug; other site 887061006227 ligand-binding site [chemical binding]; other site 887061006228 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 887061006229 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 887061006230 N-terminal plug; other site 887061006231 ligand-binding site [chemical binding]; other site 887061006232 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 887061006233 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 887061006234 Predicted thiol oxidoreductase [Energy production and conversion]; Region: COG3488 887061006235 Protein of unknown function (DUF1111); Region: DUF1111; pfam06537 887061006236 Bestrophin, RFP-TM, chloride channel; Region: Bestrophin; pfam01062 887061006237 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 887061006238 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 887061006239 putative substrate translocation pore; other site 887061006240 Cytochrome c; Region: Cytochrom_C; cl11414 887061006241 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 887061006242 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 887061006243 hypothetical protein; Provisional; Region: PRK10649 887061006244 Sulfatase; Region: Sulfatase; pfam00884 887061006245 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 887061006246 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 887061006247 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 887061006248 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 887061006249 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061006250 Coenzyme A binding pocket [chemical binding]; other site 887061006251 Protein of unknown function (DUF330); Region: DUF330; pfam03886 887061006252 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 887061006253 mce related protein; Region: MCE; pfam02470 887061006254 mce related protein; Region: MCE; pfam02470 887061006255 mce related protein; Region: MCE; pfam02470 887061006256 Paraquat-inducible protein A; Region: PqiA; pfam04403 887061006257 Paraquat-inducible protein A; Region: PqiA; pfam04403 887061006258 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 887061006259 Autotransporter beta-domain; Region: Autotransporter; smart00869 887061006260 Predicted membrane protein [Function unknown]; Region: COG2510 887061006261 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 887061006262 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 887061006263 Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases [Carbohydrate transport and metabolism]; Region: AraD; COG0235 887061006264 intersubunit interface [polypeptide binding]; other site 887061006265 active site 887061006266 Zn2+ binding site [ion binding]; other site 887061006267 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061006268 Q-loop/lid; other site 887061006269 ABC transporter signature motif; other site 887061006270 Walker B; other site 887061006271 D-loop; other site 887061006272 H-loop/switch region; other site 887061006273 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 887061006274 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061006275 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061006276 hypothetical protein; Validated; Region: PRK09039 887061006277 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061006278 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061006279 putative hydrophobic ligand binding site [chemical binding]; other site 887061006280 protein interface [polypeptide binding]; other site 887061006281 gate; other site 887061006282 putative transcriptional regulator; Provisional; Region: PRK11640 887061006283 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061006284 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 887061006285 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 887061006286 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061006287 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061006288 DNA binding residues [nucleotide binding] 887061006289 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 887061006290 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 887061006291 Dynamin family; Region: Dynamin_N; pfam00350 887061006292 G1 box; other site 887061006293 GTP/Mg2+ binding site [chemical binding]; other site 887061006294 G2 box; other site 887061006295 Switch I region; other site 887061006296 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 887061006297 G3 box; other site 887061006298 Switch II region; other site 887061006299 GTP/Mg2+ binding site [chemical binding]; other site 887061006300 G4 box; other site 887061006301 G5 box; other site 887061006302 Protein of unknown function (DUF971); Region: DUF971; pfam06155 887061006303 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 887061006304 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 887061006305 S-adenosylmethionine binding site [chemical binding]; other site 887061006306 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 887061006307 SCP-2 sterol transfer family; Region: SCP2; pfam02036 887061006308 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 887061006309 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 887061006310 active site 887061006311 substrate binding site [chemical binding]; other site 887061006312 ATP binding site [chemical binding]; other site 887061006313 HDOD domain; Region: HDOD; pfam08668 887061006314 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 887061006315 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 887061006316 Na binding site [ion binding]; other site 887061006317 putative glycosylation site [posttranslational modification]; other site 887061006318 putative glycosylation site [posttranslational modification]; other site 887061006319 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 887061006320 H2TH interface [polypeptide binding]; other site 887061006321 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 887061006322 DNA binding site [nucleotide binding] 887061006323 putative catalytic residues [active] 887061006324 turnover-facilitating residue; other site 887061006325 intercalation triad [nucleotide binding]; other site 887061006326 8OG recognition residue [nucleotide binding]; other site 887061006327 putative reading head residues; other site 887061006328 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 887061006329 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 887061006330 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 887061006331 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 887061006332 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 887061006333 ABC-2 family transporter protein; Region: ABC2_membrane_4; pfam12730 887061006334 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 887061006335 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061006336 Walker A/P-loop; other site 887061006337 ATP binding site [chemical binding]; other site 887061006338 Q-loop/lid; other site 887061006339 ABC transporter signature motif; other site 887061006340 Walker B; other site 887061006341 D-loop; other site 887061006342 H-loop/switch region; other site 887061006343 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 887061006344 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 887061006345 binding surface 887061006346 TPR motif; other site 887061006347 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 887061006348 TPR motif; other site 887061006349 binding surface 887061006350 TPR repeat; Region: TPR_11; pfam13414 887061006351 TPR repeat; Region: TPR_11; pfam13414 887061006352 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 887061006353 binding surface 887061006354 TPR motif; other site 887061006355 TPR repeat; Region: TPR_11; pfam13414 887061006356 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 887061006357 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 887061006358 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 887061006359 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 887061006360 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 887061006361 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 887061006362 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061006363 active site 887061006364 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 887061006365 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 887061006366 5S rRNA interface [nucleotide binding]; other site 887061006367 CTC domain interface [polypeptide binding]; other site 887061006368 L16 interface [polypeptide binding]; other site 887061006369 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 887061006370 putative active site [active] 887061006371 catalytic residue [active] 887061006372 GTP-binding protein YchF; Reviewed; Region: PRK09601 887061006373 YchF GTPase; Region: YchF; cd01900 887061006374 G1 box; other site 887061006375 GTP/Mg2+ binding site [chemical binding]; other site 887061006376 Switch I region; other site 887061006377 G2 box; other site 887061006378 Switch II region; other site 887061006379 G3 box; other site 887061006380 G4 box; other site 887061006381 G5 box; other site 887061006382 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 887061006383 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 887061006384 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 887061006385 cofactor binding site; other site 887061006386 DNA binding site [nucleotide binding] 887061006387 substrate interaction site [chemical binding]; other site 887061006388 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 887061006389 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061006390 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061006391 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 887061006392 dimerization interface [polypeptide binding]; other site 887061006393 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 887061006394 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 887061006395 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 887061006396 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061006397 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 887061006398 Coenzyme A binding pocket [chemical binding]; other site 887061006399 Staphylococcal nuclease homologues; Region: SNc; smart00318 887061006400 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 887061006401 Catalytic site; other site 887061006402 putative metal dependent hydrolase; Provisional; Region: PRK11598 887061006403 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 887061006404 Sulfatase; Region: Sulfatase; pfam00884 887061006405 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 887061006406 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 887061006407 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 887061006408 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 887061006409 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 887061006410 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 887061006411 Predicted membrane protein [Function unknown]; Region: COG2259 887061006412 Pirin-related protein [General function prediction only]; Region: COG1741 887061006413 Pirin; Region: Pirin; pfam02678 887061006414 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 887061006415 Acyl carrier protein phosphodiesterase [Lipid metabolism]; Region: AcpD; COG1182 887061006416 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 887061006417 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061006418 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061006419 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 887061006420 putative effector binding pocket; other site 887061006421 dimerization interface [polypeptide binding]; other site 887061006422 LexA repressor; Validated; Region: PRK00215 887061006423 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 887061006424 Catalytic site [active] 887061006425 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 887061006426 Protein of unknown function, DUF482; Region: DUF482; pfam04339 887061006427 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 to...; Region: EFh; cd00051 887061006428 EF-hand domain pair; Region: EF_hand_5; pfam13499 887061006429 Ca2+ binding site [ion binding]; other site 887061006430 osmolarity response regulator; Provisional; Region: ompR; PRK09468 887061006431 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061006432 active site 887061006433 phosphorylation site [posttranslational modification] 887061006434 intermolecular recognition site; other site 887061006435 dimerization interface [polypeptide binding]; other site 887061006436 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061006437 DNA binding site [nucleotide binding] 887061006438 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061006439 dimerization interface [polypeptide binding]; other site 887061006440 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061006441 dimer interface [polypeptide binding]; other site 887061006442 phosphorylation site [posttranslational modification] 887061006443 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 887061006444 ATP binding site [chemical binding]; other site 887061006445 Mg2+ binding site [ion binding]; other site 887061006446 G-X-G motif; other site 887061006447 siroheme synthase; Provisional; Region: cysG; PRK10637 887061006448 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 887061006449 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 887061006450 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 887061006451 active site 887061006452 SAM binding site [chemical binding]; other site 887061006453 homodimer interface [polypeptide binding]; other site 887061006454 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 887061006455 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 887061006456 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 887061006457 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 887061006458 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 887061006459 putative hemin binding site; other site 887061006460 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 887061006461 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 887061006462 ABC-ATPase subunit interface; other site 887061006463 dimer interface [polypeptide binding]; other site 887061006464 putative PBP binding regions; other site 887061006465 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13547 887061006466 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 887061006467 Walker A/P-loop; other site 887061006468 ATP binding site [chemical binding]; other site 887061006469 Q-loop/lid; other site 887061006470 ABC transporter signature motif; other site 887061006471 Walker B; other site 887061006472 D-loop; other site 887061006473 H-loop/switch region; other site 887061006474 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 887061006475 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 887061006476 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 887061006477 FeS/SAM binding site; other site 887061006478 TRAM domain; Region: TRAM; pfam01938 887061006479 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 887061006480 PhoH-like protein; Region: PhoH; pfam02562 887061006481 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 887061006482 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 887061006483 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 887061006484 Transporter associated domain; Region: CorC_HlyC; smart01091 887061006485 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 887061006486 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 887061006487 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 887061006488 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 887061006489 putative active site [active] 887061006490 catalytic triad [active] 887061006491 putative dimer interface [polypeptide binding]; other site 887061006492 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 887061006493 dimer interface [polypeptide binding]; other site 887061006494 motif 1; other site 887061006495 active site 887061006496 motif 2; other site 887061006497 motif 3; other site 887061006498 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 887061006499 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 887061006500 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 887061006501 active site 887061006502 motif I; other site 887061006503 motif II; other site 887061006504 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 887061006505 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 887061006506 putative acyl-acceptor binding pocket; other site 887061006507 Protein of unknown function DUF45; Region: DUF45; pfam01863 887061006508 Predicted transcriptional regulator [Transcription]; Region: COG1959 887061006509 Transcriptional regulator; Region: Rrf2; cl17282 887061006510 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 887061006511 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 887061006512 heme-binding site [chemical binding]; other site 887061006513 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 887061006514 FAD binding pocket [chemical binding]; other site 887061006515 FAD binding motif [chemical binding]; other site 887061006516 phosphate binding motif [ion binding]; other site 887061006517 beta-alpha-beta structure motif; other site 887061006518 NAD binding pocket [chemical binding]; other site 887061006519 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 887061006520 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 887061006521 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 887061006522 heme binding site [chemical binding]; other site 887061006523 ferroxidase pore; other site 887061006524 ferroxidase diiron center [ion binding]; other site 887061006525 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 887061006526 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 887061006527 heme binding site [chemical binding]; other site 887061006528 ferroxidase pore; other site 887061006529 ferroxidase diiron center [ion binding]; other site 887061006530 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 887061006531 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 887061006532 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 887061006533 metal-binding site [ion binding] 887061006534 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 887061006535 Soluble P-type ATPase [General function prediction only]; Region: COG4087 887061006536 FixH; Region: FixH; pfam05751 887061006537 YtkA-like; Region: YtkA; pfam13115 887061006538 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 887061006539 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 887061006540 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 887061006541 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 887061006542 Cytochrome c; Region: Cytochrom_C; pfam00034 887061006543 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 887061006544 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 887061006545 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 887061006546 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 887061006547 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 887061006548 Low-spin heme binding site [chemical binding]; other site 887061006549 Putative water exit pathway; other site 887061006550 Binuclear center (active site) [active] 887061006551 Putative proton exit pathway; other site 887061006552 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 887061006553 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 887061006554 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 887061006555 homodimer interface [polypeptide binding]; other site 887061006556 substrate-cofactor binding pocket; other site 887061006557 catalytic residue [active] 887061006558 Zinc-finger domain; Region: zf-CHCC; cl01821 887061006559 glutamate racemase; Provisional; Region: PRK00865 887061006560 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 887061006561 Uncharacterized small protein (DUF2292); Region: DUF2292; pfam10055 887061006562 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 887061006563 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 887061006564 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 887061006565 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 887061006566 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 887061006567 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 887061006568 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 887061006569 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061006570 catalytic residue [active] 887061006571 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 887061006572 serine O-acetyltransferase; Region: cysE; TIGR01172 887061006573 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 887061006574 trimer interface [polypeptide binding]; other site 887061006575 active site 887061006576 substrate binding site [chemical binding]; other site 887061006577 CoA binding site [chemical binding]; other site 887061006578 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 887061006579 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 887061006580 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 887061006581 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 887061006582 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061006583 dimer interface [polypeptide binding]; other site 887061006584 conserved gate region; other site 887061006585 putative PBP binding loops; other site 887061006586 ABC-ATPase subunit interface; other site 887061006587 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 887061006588 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061006589 dimer interface [polypeptide binding]; other site 887061006590 conserved gate region; other site 887061006591 putative PBP binding loops; other site 887061006592 ABC-ATPase subunit interface; other site 887061006593 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 887061006594 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 887061006595 Walker A/P-loop; other site 887061006596 ATP binding site [chemical binding]; other site 887061006597 Q-loop/lid; other site 887061006598 ABC transporter signature motif; other site 887061006599 Walker B; other site 887061006600 D-loop; other site 887061006601 H-loop/switch region; other site 887061006602 TOBE-like domain; Region: TOBE_3; pfam12857 887061006603 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 887061006604 Predicted transporter component [General function prediction only]; Region: COG2391 887061006605 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 887061006606 Predicted transporter component [General function prediction only]; Region: COG2391 887061006607 Sulphur transport; Region: Sulf_transp; pfam04143 887061006608 poly(A) polymerase; Region: pcnB; TIGR01942 887061006609 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 887061006610 active site 887061006611 NTP binding site [chemical binding]; other site 887061006612 metal binding triad [ion binding]; metal-binding site 887061006613 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 887061006614 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 887061006615 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 887061006616 catalytic center binding site [active] 887061006617 ATP binding site [chemical binding]; other site 887061006618 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 887061006619 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 2.7.1; Region: dNK; cd01673 887061006620 Substrate-binding site [chemical binding]; other site 887061006621 Substrate specificity [chemical binding]; other site 887061006622 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 887061006623 oligomerization interface [polypeptide binding]; other site 887061006624 active site 887061006625 metal binding site [ion binding]; metal-binding site 887061006626 Pantoate-beta-alanine ligase; Region: PanC; cd00560 887061006627 pantoate--beta-alanine ligase; Region: panC; TIGR00018 887061006628 active site 887061006629 ATP-binding site [chemical binding]; other site 887061006630 pantoate-binding site; other site 887061006631 HXXH motif; other site 887061006632 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 887061006633 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; cd00312 887061006634 substrate binding pocket [chemical binding]; other site 887061006635 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 887061006636 tetramerization interface [polypeptide binding]; other site 887061006637 active site 887061006638 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 887061006639 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 887061006640 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 887061006641 DNA photolyase; Region: DNA_photolyase; pfam00875 887061006642 MFS transporter, sugar porter (SP) family; Region: SP; TIGR00879 887061006643 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 887061006644 putative substrate translocation pore; other site 887061006645 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 887061006646 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 887061006647 AMP binding site [chemical binding]; other site 887061006648 metal binding site [ion binding]; metal-binding site 887061006649 active site 887061006650 VacJ like lipoprotein; Region: VacJ; cl01073 887061006651 peptidase PmbA; Provisional; Region: PRK11040 887061006652 hypothetical protein; Provisional; Region: PRK05255 887061006653 Site-specific recombinase; Region: SpecificRecomb; pfam10136 887061006654 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 887061006655 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 887061006656 MPT binding site; other site 887061006657 trimer interface [polypeptide binding]; other site 887061006658 thiamine monophosphate kinase; Provisional; Region: PRK05731 887061006659 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 887061006660 ATP binding site [chemical binding]; other site 887061006661 dimerization interface [polypeptide binding]; other site 887061006662 probable extracellular repeat, HAF family; Region: HAF_rpt; TIGR02913 887061006663 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 887061006664 tetramer interfaces [polypeptide binding]; other site 887061006665 binuclear metal-binding site [ion binding]; other site 887061006666 Competence-damaged protein; Region: CinA; pfam02464 887061006667 recombinase A; Provisional; Region: recA; PRK09354 887061006668 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 887061006669 hexamer interface [polypeptide binding]; other site 887061006670 Walker A motif; other site 887061006671 ATP binding site [chemical binding]; other site 887061006672 Walker B motif; other site 887061006673 RecX family; Region: RecX; pfam02631 887061006674 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 887061006675 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...; Region: AlaRS_core; cd00673 887061006676 motif 1; other site 887061006677 active site 887061006678 motif 2; other site 887061006679 motif 3; other site 887061006680 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 887061006681 aspartate kinase; Reviewed; Region: PRK06635 887061006682 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 887061006683 putative nucleotide binding site [chemical binding]; other site 887061006684 putative catalytic residues [active] 887061006685 putative Mg ion binding site [ion binding]; other site 887061006686 putative aspartate binding site [chemical binding]; other site 887061006687 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 887061006688 putative allosteric regulatory site; other site 887061006689 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 887061006690 putative allosteric regulatory residue; other site 887061006691 hydroperoxidase II; Provisional; Region: katE; PRK11249 887061006692 Clade 2 of the heme-binding enzyme catalase; Region: catalase_clade_2; cd08155 887061006693 tetramer interface [polypeptide binding]; other site 887061006694 heme binding pocket [chemical binding]; other site 887061006695 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 887061006696 domain interactions; other site 887061006697 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 887061006698 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 887061006699 non-specific DNA binding site [nucleotide binding]; other site 887061006700 salt bridge; other site 887061006701 sequence-specific DNA binding site [nucleotide binding]; other site 887061006702 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 887061006703 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061006704 dimer interface [polypeptide binding]; other site 887061006705 putative CheW interface [polypeptide binding]; other site 887061006706 Malic enzyme, N-terminal domain; Region: malic; pfam00390 887061006707 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 887061006708 putative NAD(P) binding site [chemical binding]; other site 887061006709 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061006710 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061006711 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 887061006712 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061006713 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 887061006714 CHASE3 domain; Region: CHASE3; pfam05227 887061006715 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061006716 dimer interface [polypeptide binding]; other site 887061006717 phosphorylation site [posttranslational modification] 887061006718 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 887061006719 ATP binding site [chemical binding]; other site 887061006720 Mg2+ binding site [ion binding]; other site 887061006721 G-X-G motif; other site 887061006722 Response regulator receiver domain; Region: Response_reg; pfam00072 887061006723 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061006724 active site 887061006725 phosphorylation site [posttranslational modification] 887061006726 intermolecular recognition site; other site 887061006727 dimerization interface [polypeptide binding]; other site 887061006728 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 887061006729 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061006730 active site 887061006731 phosphorylation site [posttranslational modification] 887061006732 intermolecular recognition site; other site 887061006733 dimerization interface [polypeptide binding]; other site 887061006734 PAS fold; Region: PAS_4; pfam08448 887061006735 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 887061006736 putative active site [active] 887061006737 heme pocket [chemical binding]; other site 887061006738 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 887061006739 PAS domain; Region: PAS_9; pfam13426 887061006740 putative active site [active] 887061006741 heme pocket [chemical binding]; other site 887061006742 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061006743 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061006744 metal binding site [ion binding]; metal-binding site 887061006745 active site 887061006746 I-site; other site 887061006747 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 887061006748 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 887061006749 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 887061006750 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 887061006751 HPP family; Region: HPP; pfam04982 887061006752 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 887061006753 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 887061006754 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 887061006755 dinuclear metal binding motif [ion binding]; other site 887061006756 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061006757 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061006758 YyzF-like protein; Region: YyzF; cl15733 887061006759 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 887061006760 dimer interface [polypeptide binding]; other site 887061006761 PEP synthetase regulatory protein; Provisional; Region: PRK05339 887061006762 phosphoenolpyruvate synthase; Validated; Region: PRK06464 887061006763 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 887061006764 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 887061006765 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 887061006766 Protein of unknown function, DUF481; Region: DUF481; pfam04338 887061006767 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 887061006768 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 887061006769 active site 887061006770 motif I; other site 887061006771 motif II; other site 887061006772 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 887061006773 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 887061006774 active site 887061006775 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 887061006776 YaeQ protein; Region: YaeQ; pfam07152 887061006777 signal recognition particle protein; Provisional; Region: PRK10867 887061006778 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 887061006779 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 887061006780 P loop; other site 887061006781 GTP binding site [chemical binding]; other site 887061006782 Signal peptide binding domain; Region: SRP_SPB; pfam02978 887061006783 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 887061006784 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 887061006785 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 887061006786 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 887061006787 Predicted membrane protein [Function unknown]; Region: COG3235 887061006788 2-isopropylmalate synthase; Validated; Region: PRK00915 887061006789 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 887061006790 active site 887061006791 catalytic residues [active] 887061006792 metal binding site [ion binding]; metal-binding site 887061006793 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 887061006794 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 887061006795 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 887061006796 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 887061006797 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 887061006798 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 887061006799 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 887061006800 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 887061006801 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 887061006802 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 887061006803 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 887061006804 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 887061006805 Protein export membrane protein; Region: SecD_SecF; pfam02355 887061006806 Domain of unknown function DUF21; Region: DUF21; pfam01595 887061006807 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 887061006808 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 887061006809 Transporter associated domain; Region: CorC_HlyC; smart01091 887061006810 Uncharacterized conserved protein [Function unknown]; Region: COG2127 887061006811 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 887061006812 Clp amino terminal domain; Region: Clp_N; pfam02861 887061006813 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061006814 Walker A motif; other site 887061006815 ATP binding site [chemical binding]; other site 887061006816 Walker B motif; other site 887061006817 arginine finger; other site 887061006818 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061006819 Walker A motif; other site 887061006820 ATP binding site [chemical binding]; other site 887061006821 Walker B motif; other site 887061006822 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 887061006823 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 887061006824 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 887061006825 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 887061006826 putative N-terminal domain interface [polypeptide binding]; other site 887061006827 putative dimer interface [polypeptide binding]; other site 887061006828 putative substrate binding pocket (H-site) [chemical binding]; other site 887061006829 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 887061006830 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 887061006831 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 887061006832 quinone interaction residues [chemical binding]; other site 887061006833 active site 887061006834 catalytic residues [active] 887061006835 FMN binding site [chemical binding]; other site 887061006836 substrate binding site [chemical binding]; other site 887061006837 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 887061006838 Nitrogen regulatory protein P-II; Region: P-II; smart00938 887061006839 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061006840 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 887061006841 Nitrogen regulatory protein P-II; Region: P-II; smart00938 887061006842 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 887061006843 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061006844 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 887061006845 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061006846 Outer membrane efflux protein; Region: OEP; pfam02321 887061006847 Outer membrane efflux protein; Region: OEP; pfam02321 887061006848 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 887061006849 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 887061006850 active site 887061006851 HIGH motif; other site 887061006852 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 887061006853 KMSKS motif; other site 887061006854 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 887061006855 tRNA binding surface [nucleotide binding]; other site 887061006856 anticodon binding site; other site 887061006857 TPR repeat; Region: TPR_11; pfam13414 887061006858 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 887061006859 binding surface 887061006860 TPR motif; other site 887061006861 Tetratricopeptide repeat; Region: TPR_16; pfam13432 887061006862 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 887061006863 SnoaL-like domain; Region: SnoaL_3; pfam13474 887061006864 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 887061006865 binding surface 887061006866 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 887061006867 SnoaL-like domain; Region: SnoaL_3; pfam13474 887061006868 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 887061006869 active site 887061006870 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 887061006871 substrate binding site [chemical binding]; other site 887061006872 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 887061006873 putative active site [active] 887061006874 putative metal binding site [ion binding]; other site 887061006875 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 887061006876 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 887061006877 phosphopeptide binding site; other site 887061006878 transcription antitermination factor NusB; Region: nusB; TIGR01951 887061006879 putative RNA binding site [nucleotide binding]; other site 887061006880 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 887061006881 homopentamer interface [polypeptide binding]; other site 887061006882 active site 887061006883 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061006884 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 887061006885 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061006886 active site 887061006887 phosphorylation site [posttranslational modification] 887061006888 intermolecular recognition site; other site 887061006889 dimerization interface [polypeptide binding]; other site 887061006890 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061006891 DNA binding site [nucleotide binding] 887061006892 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 887061006893 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 887061006894 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 887061006895 putative active site [active] 887061006896 heme pocket [chemical binding]; other site 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...; 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 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 887061006905 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 887061006906 FAD binding domain; Region: FAD_binding_4; pfam01565 887061006907 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 887061006908 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 887061006909 Cysteine-rich domain; Region: CCG; pfam02754 887061006910 Cysteine-rich domain; Region: CCG; pfam02754 887061006911 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 887061006912 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 887061006913 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 887061006914 catalytic residues [active] 887061006915 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 887061006916 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 887061006917 putative hydrophobic ligand binding site [chemical binding]; other site 887061006918 protein interface [polypeptide binding]; other site 887061006919 gate; other site 887061006920 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061006921 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061006922 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 887061006923 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 887061006924 substrate binding site [chemical binding]; other site 887061006925 ATP binding site [chemical binding]; other site 887061006926 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 887061006927 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 887061006928 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 887061006929 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 887061006930 putative acyl-acceptor binding pocket; other site 887061006931 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 887061006932 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 887061006933 active site 887061006934 metal binding site [ion binding]; metal-binding site 887061006935 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 887061006936 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 887061006937 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 887061006938 Sulfatase; Region: Sulfatase; cl17466 887061006939 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 887061006940 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 887061006941 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 887061006942 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 887061006943 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...; Region: LT_GEWL; cd00254 887061006944 N-acetyl-D-glucosamine binding site [chemical binding]; other site 887061006945 catalytic residue [active] 887061006946 prolyl-tRNA synthetase; Provisional; Region: PRK09194 887061006947 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...; Region: ProRS_core_prok; cd00779 887061006948 dimer interface [polypeptide binding]; other site 887061006949 motif 1; other site 887061006950 active site 887061006951 motif 2; other site 887061006952 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 887061006953 putative deacylase active site [active] 887061006954 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 887061006955 active site 887061006956 motif 3; other site 887061006957 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 887061006958 anticodon binding site; other site 887061006959 Repair protein; Region: Repair_PSII; pfam04536 887061006960 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 887061006961 Repair protein; Region: Repair_PSII; pfam04536 887061006962 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 887061006963 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 887061006964 Fe-S cluster binding site [ion binding]; other site 887061006965 active site 887061006966 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 887061006967 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061006968 Coenzyme A binding pocket [chemical binding]; other site 887061006969 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 887061006970 Glycoprotease family; Region: Peptidase_M22; pfam00814 887061006971 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 887061006972 hypothetical protein; Provisional; Region: PRK09256 887061006973 protein structure with unknown function; Region: DUF4144; pfam13642 887061006974 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 887061006975 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 887061006976 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 887061006977 EamA-like transporter family; Region: EamA; pfam00892 887061006978 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 887061006979 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 887061006980 ring oligomerisation interface [polypeptide binding]; other site 887061006981 ATP/Mg binding site [chemical binding]; other site 887061006982 stacking interactions; other site 887061006983 hinge regions; other site 887061006984 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 887061006985 oligomerisation interface [polypeptide binding]; other site 887061006986 mobile loop; other site 887061006987 roof hairpin; other site 887061006988 Domain of unknown function (DUF202); Region: DUF202; pfam02656 887061006989 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 887061006990 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 887061006991 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 887061006992 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061006993 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061006994 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 887061006995 putative effector binding pocket; other site 887061006996 dimerization interface [polypeptide binding]; other site 887061006997 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 887061006998 DEAD/DEAH box helicase; Region: DEAD; pfam00270 887061006999 DEAD_2; Region: DEAD_2; pfam06733 887061007000 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 887061007001 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 887061007002 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 887061007003 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 887061007004 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 887061007005 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 887061007006 active site 887061007007 catalytic tetrad [active] 887061007008 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 887061007009 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 887061007010 apolar tunnel; other site 887061007011 heme binding site [chemical binding]; other site 887061007012 dimerization interface [polypeptide binding]; other site 887061007013 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl17499 887061007014 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061007015 dimerization interface [polypeptide binding]; other site 887061007016 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061007017 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007018 metal binding site [ion binding]; metal-binding site 887061007019 active site 887061007020 I-site; other site 887061007021 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 887061007022 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 887061007023 active site 887061007024 substrate binding pocket [chemical binding]; other site 887061007025 dimer interface [polypeptide binding]; other site 887061007026 Predicted methyltransferases [General function prediction only]; Region: COG0313 887061007027 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 887061007028 putative homodimer interface [polypeptide binding]; other site 887061007029 putative SAM binding site [chemical binding]; other site 887061007030 LppC putative lipoprotein; Region: LppC; pfam04348 887061007031 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 887061007032 putative ligand binding site [chemical binding]; other site 887061007033 hypothetical protein; Reviewed; Region: PRK12497 887061007034 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 887061007035 dimer interface [polypeptide binding]; other site 887061007036 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 887061007037 active site 887061007038 BON domain; Region: BON; pfam04972 887061007039 bacterial OsmY and nodulation domain; Region: BON; smart00749 887061007040 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 887061007041 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 887061007042 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 887061007043 catalytic residues [active] 887061007044 Uncharacterized protein family, UPF0114; Region: UPF0114; pfam03350 887061007045 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 887061007046 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 887061007047 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 887061007048 catalytic residues [active] 887061007049 transcription termination factor Rho; Provisional; Region: rho; PRK09376 887061007050 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 887061007051 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 887061007052 RNA binding site [nucleotide binding]; other site 887061007053 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 887061007054 multimer interface [polypeptide binding]; other site 887061007055 Walker A motif; other site 887061007056 ATP binding site [chemical binding]; other site 887061007057 Walker B motif; other site 887061007058 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 887061007059 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 887061007060 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 887061007061 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 887061007062 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061007063 Walker A/P-loop; other site 887061007064 ATP binding site [chemical binding]; other site 887061007065 Q-loop/lid; other site 887061007066 ABC transporter signature motif; other site 887061007067 Walker B; other site 887061007068 D-loop; other site 887061007069 H-loop/switch region; other site 887061007070 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 887061007071 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061007072 dimer interface [polypeptide binding]; other site 887061007073 conserved gate region; other site 887061007074 putative PBP binding loops; other site 887061007075 ABC-ATPase subunit interface; other site 887061007076 molybdate transporter periplasmic protein; Provisional; Region: modA; PRK10677 887061007077 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 887061007078 Phosphate-selective porin [Inorganic ion transport and metabolism]; Region: OprP; COG3746 887061007079 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 887061007080 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 887061007081 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 887061007082 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 887061007083 FeS/SAM binding site; other site 887061007084 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 887061007085 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 887061007086 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 887061007087 GTP binding site; other site 887061007088 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 887061007089 Walker A motif; other site 887061007090 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 887061007091 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 887061007092 dimer interface [polypeptide binding]; other site 887061007093 putative functional site; other site 887061007094 putative MPT binding site; other site 887061007095 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 887061007096 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 887061007097 dimer interface [polypeptide binding]; other site 887061007098 putative metal binding site [ion binding]; other site 887061007099 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061007100 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 887061007101 N-terminal plug; other site 887061007102 ligand-binding site [chemical binding]; other site 887061007103 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 887061007104 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 887061007105 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 887061007106 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 887061007107 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 887061007108 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 887061007109 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061007110 dimerization interface [polypeptide binding]; other site 887061007111 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061007112 dimer interface [polypeptide binding]; other site 887061007113 phosphorylation site [posttranslational modification] 887061007114 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 887061007115 ATP binding site [chemical binding]; other site 887061007116 G-X-G motif; other site 887061007117 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 887061007118 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 887061007119 catalytic triad [active] 887061007120 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 887061007121 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 887061007122 putative active site [active] 887061007123 PhoH-like protein; Region: PhoH; pfam02562 887061007124 lysophospholipid transporter LplT; Provisional; Region: PRK11195 887061007125 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 887061007126 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 887061007127 Cytochrome c; Region: Cytochrom_C; cl11414 887061007128 Cytochrome c; Region: Cytochrom_C; cl11414 887061007129 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein; Region: ABC_peri_MoxJ_2; TIGR03871 887061007130 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061007131 substrate binding pocket [chemical binding]; other site 887061007132 membrane-bound complex binding site; other site 887061007133 hinge residues; other site 887061007134 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 887061007135 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 887061007136 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 887061007137 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 887061007138 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061007139 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 887061007140 ligand binding site [chemical binding]; other site 887061007141 flexible hinge region; other site 887061007142 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 887061007143 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 887061007144 active site residue [active] 887061007145 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 887061007146 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 887061007147 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 887061007148 phosphorylation site [posttranslational modification] 887061007149 intermolecular recognition site; other site 887061007150 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 887061007151 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 887061007152 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 887061007153 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 887061007154 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 887061007155 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061007156 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 887061007157 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061007158 DNA binding residues [nucleotide binding] 887061007159 DNA primase; Validated; Region: dnaG; PRK05667 887061007160 CHC2 zinc finger; Region: zf-CHC2; pfam01807 887061007161 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 887061007162 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 887061007163 active site 887061007164 metal binding site [ion binding]; metal-binding site 887061007165 interdomain interaction site; other site 887061007166 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 887061007167 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; cl07879 887061007168 Yqey-like protein; Region: YqeY; pfam09424 887061007169 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 887061007170 UGMP family protein; Validated; Region: PRK09604 887061007171 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 887061007172 Fumble; Region: Fumble; cl17357 887061007173 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 887061007174 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 887061007175 homooctamer interface [polypeptide binding]; other site 887061007176 active site 887061007177 TIGR03790 family protein; Region: TIGR03790 887061007178 hypothetical protein; Provisional; Region: PRK04233 887061007179 Putative cell wall binding repeat; Region: CW_binding_1; pfam01473 887061007180 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 887061007181 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 887061007182 active site 887061007183 Int/Topo IB signature motif; other site 887061007184 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 887061007185 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 887061007186 DNA binding site [nucleotide binding] 887061007187 active site 887061007188 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 887061007189 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 887061007190 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 887061007191 RimM N-terminal domain; Region: RimM; pfam01782 887061007192 PRC-barrel domain; Region: PRC; pfam05239 887061007193 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 887061007194 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 887061007195 Ligand Binding Site [chemical binding]; other site 887061007196 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 887061007197 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 887061007198 FeS/SAM binding site; other site 887061007199 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 887061007200 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 887061007201 TPR motif; other site 887061007202 binding surface 887061007203 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 887061007204 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 887061007205 ligand binding site [chemical binding]; other site 887061007206 translocation protein TolB; Provisional; Region: tolB; PRK02889 887061007207 TolB amino-terminal domain; Region: TolB_N; pfam04052 887061007208 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061007209 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061007210 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061007211 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 887061007212 TonB C terminal; Region: TonB_2; pfam13103 887061007213 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 887061007214 TolR protein; Region: tolR; TIGR02801 887061007215 TolQ protein; Region: tolQ; TIGR02796 887061007216 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 887061007217 active site 887061007218 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 887061007219 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061007220 Walker A motif; other site 887061007221 ATP binding site [chemical binding]; other site 887061007222 Walker B motif; other site 887061007223 arginine finger; other site 887061007224 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 887061007225 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 887061007226 RuvA N terminal domain; Region: RuvA_N; pfam01330 887061007227 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 887061007228 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...; Region: RuvC_resolvase; cd00529 887061007229 active site 887061007230 putative DNA-binding cleft [nucleotide binding]; other site 887061007231 dimer interface [polypeptide binding]; other site 887061007232 hypothetical protein; Validated; Region: PRK00110 887061007233 EamA-like transporter family; Region: EamA; pfam00892 887061007234 EamA-like transporter family; Region: EamA; pfam00892 887061007235 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 887061007236 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 887061007237 MarR family; Region: MarR_2; cl17246 887061007238 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 887061007239 FOG: CBS domain [General function prediction only]; Region: COG0517 887061007240 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 887061007241 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 887061007242 TrkA-N domain; Region: TrkA_N; pfam02254 887061007243 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 887061007244 Uncharacterized conserved protein [Function unknown]; Region: COG0432 887061007245 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 887061007246 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 887061007247 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 887061007248 catalytic triad [active] 887061007249 Maltose operon periplasmic protein precursor (MalM); Region: MalM; cl11647 887061007250 Domain of Unknown Function with PDB structure (DUF3857); Region: DUF3857; pfam12969 887061007251 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 887061007252 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061007253 Transglutaminase/protease-like homologues; Region: TGc; smart00460 887061007254 Lipoprotein NlpI, contains TPR repeats [General function prediction only]; Region: NlpI; COG4785 887061007255 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 887061007256 binding surface 887061007257 TPR motif; other site 887061007258 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 887061007259 catalytic residue [active] 887061007260 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 887061007261 Conserved region in glutamate synthase; Region: Glu_synthase; pfam01645 887061007262 active site 887061007263 FMN binding site [chemical binding]; other site 887061007264 substrate binding site [chemical binding]; other site 887061007265 3Fe-4S cluster binding site [ion binding]; other site 887061007266 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 887061007267 domain_subunit interface; other site 887061007268 Glutamate synthase domain 1 [Amino acid transport and metabolism]; Region: GltB; COG0067 887061007269 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 887061007270 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 887061007271 putative active site [active] 887061007272 glutamine synthetase, type III; Region: gln_synth_III; TIGR03105 887061007273 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 887061007274 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 887061007275 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 887061007276 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 887061007277 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_4; pfam13510 887061007278 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 887061007279 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 887061007280 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 887061007281 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 887061007282 Sarcosine oxidase, delta subunit family; Region: SoxD; pfam04267 887061007283 sarcosine oxidase, beta subunit family, heterotetrameric form; Region: soxB; TIGR01373 887061007284 hydroxyglutarate oxidase; Provisional; Region: PRK11728 887061007285 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 887061007286 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 887061007287 non-specific DNA binding site [nucleotide binding]; other site 887061007288 salt bridge; other site 887061007289 sequence-specific DNA binding site [nucleotide binding]; other site 887061007290 Cupin domain; Region: Cupin_2; pfam07883 887061007291 Histone acetyltransferase HPA2 and related acetyltransferases [Transcription / General function prediction only]; Region: WecD; COG0454 887061007292 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061007293 Coenzyme A binding pocket [chemical binding]; other site 887061007294 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 887061007295 Permease; Region: Permease; pfam02405 887061007296 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 887061007297 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 887061007298 Walker A/P-loop; other site 887061007299 ATP binding site [chemical binding]; other site 887061007300 Q-loop/lid; other site 887061007301 ABC transporter signature motif; other site 887061007302 Walker B; other site 887061007303 D-loop; other site 887061007304 H-loop/switch region; other site 887061007305 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 887061007306 mce related protein; Region: MCE; pfam02470 887061007307 Protein of unknown function (DUF330); Region: DUF330; cl01135 887061007308 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 887061007309 Phospholipase D delta; Region: PLN03008 887061007310 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 887061007311 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins; Region: PLDc_vPLD1_2_like_2; cd09105 887061007312 putative active site [active] 887061007313 catalytic site [active] 887061007314 CCC1-related family of proteins; Region: CCC1_like; cl00278 887061007315 PAS fold; Region: PAS; pfam00989 887061007316 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 887061007317 putative active site [active] 887061007318 heme pocket [chemical binding]; other site 887061007319 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061007320 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007321 metal binding site [ion binding]; metal-binding site 887061007322 active site 887061007323 I-site; other site 887061007324 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 887061007325 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 887061007326 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 887061007327 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 887061007328 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 887061007329 putative active site [active] 887061007330 putative metal binding site [ion binding]; other site 887061007331 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 887061007332 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 887061007333 active site 887061007334 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 887061007335 GAF domain; Region: GAF; pfam01590 887061007336 PAS domain S-box; Region: sensory_box; TIGR00229 887061007337 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 887061007338 putative active site [active] 887061007339 heme pocket [chemical binding]; other site 887061007340 PAS domain S-box; Region: sensory_box; TIGR00229 887061007341 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 887061007342 putative active site [active] 887061007343 heme pocket [chemical binding]; other site 887061007344 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061007345 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007346 metal binding site [ion binding]; metal-binding site 887061007347 active site 887061007348 I-site; other site 887061007349 PEP-CTERM motif; Region: VPEP; pfam07589 887061007350 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 887061007351 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061007352 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 887061007353 putative active site [active] 887061007354 catalytic site [active] 887061007355 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 887061007356 putative active site [active] 887061007357 catalytic site [active] 887061007358 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 887061007359 putative catalytic site [active] 887061007360 putative metal binding site [ion binding]; other site 887061007361 putative phosphate binding site [ion binding]; other site 887061007362 quinolinate synthetase; Provisional; Region: PRK09375 887061007363 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 887061007364 nudix motif; other site 887061007365 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061007366 active site 887061007367 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 887061007368 TPR repeat; Region: TPR_11; pfam13414 887061007369 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 887061007370 binding surface 887061007371 TPR motif; other site 887061007372 TPR repeat; Region: TPR_11; pfam13414 887061007373 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 887061007374 binding surface 887061007375 TPR motif; other site 887061007376 TPR repeat; Region: TPR_11; pfam13414 887061007377 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 887061007378 binding surface 887061007379 TPR repeat; Region: TPR_11; pfam13414 887061007380 TPR motif; other site 887061007381 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 887061007382 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 887061007383 dimer interface [polypeptide binding]; other site 887061007384 anticodon binding site; other site 887061007385 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...; Region: AspRS_core; cd00777 887061007386 homodimer interface [polypeptide binding]; other site 887061007387 motif 1; other site 887061007388 active site 887061007389 motif 2; other site 887061007390 GAD domain; Region: GAD; pfam02938 887061007391 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...; Region: AspRS_core; cd00777 887061007392 motif 3; other site 887061007393 Uncharacterized conserved protein [Function unknown]; Region: COG2928 887061007394 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 887061007395 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 887061007396 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 887061007397 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 887061007398 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 887061007399 Ligand binding site [chemical binding]; other site 887061007400 Electron transfer flavoprotein domain; Region: ETF; pfam01012 887061007401 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 887061007402 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 887061007403 4Fe-4S binding domain; Region: Fer4; pfam00037 887061007404 Cysteine-rich domain; Region: CCG; pfam02754 887061007405 Cysteine-rich domain; Region: CCG; pfam02754 887061007406 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 887061007407 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 887061007408 FMN binding site [chemical binding]; other site 887061007409 active site 887061007410 homodimer interface [polypeptide binding]; other site 887061007411 putative catalytic residue [active] 887061007412 4Fe-4S cluster binding site [ion binding]; other site 887061007413 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 887061007414 Amino acid permease; Region: AA_permease_2; pfam13520 887061007415 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 887061007416 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 887061007417 transcriptional regulator NarL; Provisional; Region: PRK10651 887061007418 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061007419 active site 887061007420 phosphorylation site [posttranslational modification] 887061007421 intermolecular recognition site; other site 887061007422 dimerization interface [polypeptide binding]; other site 887061007423 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 887061007424 DNA binding residues [nucleotide binding] 887061007425 dimerization interface [polypeptide binding]; other site 887061007426 Histidine kinase; Region: HisKA_3; pfam07730 887061007427 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 887061007428 ATP binding site [chemical binding]; other site 887061007429 Mg2+ binding site [ion binding]; other site 887061007430 G-X-G motif; other site 887061007431 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061007432 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 887061007433 putative active site [active] 887061007434 heme pocket [chemical binding]; other site 887061007435 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 887061007436 putative active site [active] 887061007437 heme pocket [chemical binding]; other site 887061007438 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 887061007439 PAS fold; Region: PAS_3; pfam08447 887061007440 putative active site [active] 887061007441 heme pocket [chemical binding]; other site 887061007442 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; pfam09694 887061007443 Protein of unknown function (DUF3445); Region: DUF3445; pfam11927 887061007444 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 887061007445 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 887061007446 FMN-binding pocket [chemical binding]; other site 887061007447 flavin binding motif; other site 887061007448 phosphate binding motif [ion binding]; other site 887061007449 beta-alpha-beta structure motif; other site 887061007450 NAD binding pocket [chemical binding]; other site 887061007451 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 887061007452 catalytic loop [active] 887061007453 iron binding site [ion binding]; other site 887061007454 Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]; Region: GcvT; COG0404 887061007455 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 887061007456 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 887061007457 NMT1/THI5 like; Region: NMT1; pfam09084 887061007458 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 887061007459 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 887061007460 PAS fold; Region: PAS_3; pfam08447 887061007461 putative active site [active] 887061007462 heme pocket [chemical binding]; other site 887061007463 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061007464 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007465 metal binding site [ion binding]; metal-binding site 887061007466 active site 887061007467 I-site; other site 887061007468 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 887061007469 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 887061007470 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 887061007471 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061007472 dimer interface [polypeptide binding]; other site 887061007473 phosphorylation site [posttranslational modification] 887061007474 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 887061007475 ATP binding site [chemical binding]; other site 887061007476 Mg2+ binding site [ion binding]; other site 887061007477 G-X-G motif; other site 887061007478 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 887061007479 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061007480 active site 887061007481 phosphorylation site [posttranslational modification] 887061007482 intermolecular recognition site; other site 887061007483 dimerization interface [polypeptide binding]; other site 887061007484 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 887061007485 DNA binding site [nucleotide binding] 887061007486 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 887061007487 putative hydrophobic ligand binding site [chemical binding]; other site 887061007488 Molybdenum cofactor biosynthesis protein F; Region: MoaF; pfam10703 887061007489 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061007490 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061007491 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 887061007492 putative effector binding pocket; other site 887061007493 putative dimerization interface [polypeptide binding]; other site 887061007494 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 887061007495 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061007496 NAD(P) binding site [chemical binding]; other site 887061007497 active site 887061007498 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; cd00312 887061007499 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 887061007500 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061007501 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061007502 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061007503 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 887061007504 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 887061007505 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007506 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 887061007507 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007508 DNA gyrase inhibitor [DNA replication, recombination, and repair]; Region: COG3449 887061007509 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 887061007510 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 887061007511 dimer interface [polypeptide binding]; other site 887061007512 ssDNA binding site [nucleotide binding]; other site 887061007513 tetramer (dimer of dimers) interface [polypeptide binding]; other site 887061007514 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 887061007515 Major Facilitator Superfamily; Region: MFS_1; pfam07690 887061007516 putative substrate translocation pore; other site 887061007517 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 887061007518 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 887061007519 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 887061007520 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 887061007521 HDOD domain; Region: HDOD; pfam08668 887061007522 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 887061007523 Transglycosylase; Region: Transgly; cl17702 887061007524 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 887061007525 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 887061007526 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 887061007527 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 887061007528 shikimate binding site; other site 887061007529 NAD(P) binding site [chemical binding]; other site 887061007530 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 887061007531 active site residue [active] 887061007532 glutamine synthetase; Provisional; Region: glnA; PRK09469 887061007533 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 887061007534 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 887061007535 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 887061007536 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 887061007537 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 887061007538 putative active site [active] 887061007539 heme pocket [chemical binding]; other site 887061007540 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061007541 dimer interface [polypeptide binding]; other site 887061007542 phosphorylation site [posttranslational modification] 887061007543 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 887061007544 ATP binding site [chemical binding]; other site 887061007545 Mg2+ binding site [ion binding]; other site 887061007546 G-X-G motif; other site 887061007547 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 887061007548 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061007549 active site 887061007550 phosphorylation site [posttranslational modification] 887061007551 intermolecular recognition site; other site 887061007552 dimerization interface [polypeptide binding]; other site 887061007553 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061007554 Walker A motif; other site 887061007555 ATP binding site [chemical binding]; other site 887061007556 Walker B motif; other site 887061007557 arginine finger; other site 887061007558 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061007559 TPR repeat; Region: TPR_11; pfam13414 887061007560 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 887061007561 binding surface 887061007562 TPR motif; other site 887061007563 TPR repeat; Region: TPR_11; pfam13414 887061007564 Methyltransferase domain; Region: Methyltransf_24; pfam13578 887061007565 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 887061007566 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 887061007567 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 887061007568 Zn2+ binding site [ion binding]; other site 887061007569 Mg2+ binding site [ion binding]; other site 887061007570 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 887061007571 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 887061007572 active site 887061007573 dimer interface [polypeptide binding]; other site 887061007574 metal binding site [ion binding]; metal-binding site 887061007575 shikimate kinase; Reviewed; Region: aroK; PRK00131 887061007576 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 887061007577 ADP binding site [chemical binding]; other site 887061007578 magnesium binding site [ion binding]; other site 887061007579 putative shikimate binding site; other site 887061007580 AMIN domain; Region: AMIN; pfam11741 887061007581 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 887061007582 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061007583 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 887061007584 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 887061007585 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 887061007586 Pilus assembly protein, PilP; Region: PilP; pfam04351 887061007587 Pilus assembly protein, PilO; Region: PilO; pfam04350 887061007588 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 887061007589 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 887061007590 Competence protein A; Region: Competence_A; pfam11104 887061007591 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 887061007592 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 887061007593 Transglycosylase; Region: Transgly; pfam00912 887061007594 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 887061007595 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 887061007596 dimer interface [polypeptide binding]; other site 887061007597 allosteric magnesium binding site [ion binding]; other site 887061007598 active site 887061007599 aspartate-rich active site metal binding site; other site 887061007600 Schiff base residues; other site 887061007601 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 887061007602 active site 887061007603 ribulose/triose binding site [chemical binding]; other site 887061007604 phosphate binding site [ion binding]; other site 887061007605 substrate (anthranilate) binding pocket [chemical binding]; other site 887061007606 product (indole) binding pocket [chemical binding]; other site 887061007607 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 887061007608 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 887061007609 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 887061007610 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 887061007611 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 887061007612 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 887061007613 glutamine binding [chemical binding]; other site 887061007614 catalytic triad [active] 887061007615 anthranilate synthase component I; Provisional; Region: PRK13565 887061007616 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 887061007617 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 887061007618 phosphoglycolate phosphatase; Provisional; Region: PRK13222 887061007619 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 887061007620 motif II; other site 887061007621 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 887061007622 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 887061007623 substrate binding site [chemical binding]; other site 887061007624 hexamer interface [polypeptide binding]; other site 887061007625 metal binding site [ion binding]; metal-binding site 887061007626 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 887061007627 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 887061007628 tRNA; other site 887061007629 putative tRNA binding site [nucleotide binding]; other site 887061007630 putative NADP binding site [chemical binding]; other site 887061007631 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 887061007632 peptide chain release factor 1; Validated; Region: prfA; PRK00591 887061007633 This domain is found in peptide chain release factors; Region: PCRF; smart00937 887061007634 RF-1 domain; Region: RF-1; pfam00472 887061007635 Predicted membrane protein (DUF2127); Region: DUF2127; pfam09900 887061007636 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 887061007637 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; cl17173 887061007638 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 887061007639 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 887061007640 trimer interface [polypeptide binding]; other site 887061007641 putative metal binding site [ion binding]; other site 887061007642 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 887061007643 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 887061007644 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; cl17173 887061007645 Family description; Region: DsbD_2; pfam13386 887061007646 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 887061007647 muropeptide transporter; Reviewed; Region: ampG; PRK11902 887061007648 putative substrate translocation pore; other site 887061007649 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 887061007650 putative active site [active] 887061007651 putative catalytic site [active] 887061007652 putative DNA binding site [nucleotide binding]; other site 887061007653 putative phosphate binding site [ion binding]; other site 887061007654 metal binding site A [ion binding]; metal-binding site 887061007655 putative AP binding site [nucleotide binding]; other site 887061007656 putative metal binding site B [ion binding]; other site 887061007657 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 887061007658 active site 887061007659 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 887061007660 putative active site [active] 887061007661 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 887061007662 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 887061007663 GatB domain; Region: GatB_Yqey; smart00845 887061007664 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 887061007665 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 887061007666 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 887061007667 rod shape-determining protein MreB; Provisional; Region: PRK13927 887061007668 MreB and similar proteins; Region: MreB_like; cd10225 887061007669 nucleotide binding site [chemical binding]; other site 887061007670 Mg binding site [ion binding]; other site 887061007671 putative protofilament interaction site [polypeptide binding]; other site 887061007672 RodZ interaction site [polypeptide binding]; other site 887061007673 rod shape-determining protein MreC; Provisional; Region: PRK13922 887061007674 rod shape-determining protein MreC; Region: MreC; pfam04085 887061007675 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 887061007676 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 887061007677 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 887061007678 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 887061007679 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 887061007680 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 887061007681 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 887061007682 Sporulation related domain; Region: SPOR; pfam05036 887061007683 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 887061007684 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 887061007685 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 887061007686 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 887061007687 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...; Region: D-AAT_like; cd01558 887061007688 homodimer interface [polypeptide binding]; other site 887061007689 substrate-cofactor binding pocket; other site 887061007690 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061007691 catalytic residue [active] 887061007692 Protein of unknown function (DUF493); Region: DUF493; cl01102 887061007693 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 887061007694 lipoyl synthase; Provisional; Region: PRK05481 887061007695 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 887061007696 FeS/SAM binding site; other site 887061007697 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 887061007698 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061007699 DNA-binding site [nucleotide binding]; DNA binding site 887061007700 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 887061007701 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061007702 homodimer interface [polypeptide binding]; other site 887061007703 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 887061007704 Large subunit of methanol dehydrogenase (moxF); Region: PQQ_MDH; cd10278 887061007705 Trp docking motif [polypeptide binding]; other site 887061007706 dimer interface [polypeptide binding]; other site 887061007707 active site 887061007708 small subunit binding site [polypeptide binding]; other site 887061007709 Uncharacterized protein conserved in bacteria (DUF2171); Region: DUF2171; pfam09939 887061007710 phosphoribosylamine--glycine ligase; Provisional; Region: PRK13790 887061007711 ATP-grasp domain; Region: ATP-grasp_4; cl17255 887061007712 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 887061007713 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 887061007714 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 887061007715 S-adenosylmethionine binding site [chemical binding]; other site 887061007716 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 887061007717 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 887061007718 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 887061007719 active site 887061007720 homodimer interface [polypeptide binding]; other site 887061007721 catalytic site [active] 887061007722 acceptor binding site [chemical binding]; other site 887061007723 trehalose synthase; Region: treS_nterm; TIGR02456 887061007724 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 887061007725 active site 887061007726 catalytic site [active] 887061007727 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 887061007728 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 887061007729 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 887061007730 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 887061007731 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 887061007732 catalytic site [active] 887061007733 active site 887061007734 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 887061007735 maltooligosyl trehalose synthase; Provisional; Region: PRK14511 887061007736 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 887061007737 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 887061007738 active site 887061007739 catalytic site [active] 887061007740 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 887061007741 Hemerythrin-like domain; Region: Hr-like; cd12108 887061007742 Fe binding site [ion binding]; other site 887061007743 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 887061007744 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061007745 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 887061007746 nucleotide binding site/active site [active] 887061007747 HIT family signature motif; other site 887061007748 catalytic residue [active] 887061007749 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 887061007750 dimer interface [polypeptide binding]; other site 887061007751 [2Fe-2S] cluster binding site [ion binding]; other site 887061007752 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 887061007753 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 887061007754 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 887061007755 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 887061007756 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 887061007757 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 887061007758 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 887061007759 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 887061007760 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 887061007761 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 887061007762 N-terminal plug; other site 887061007763 ligand-binding site [chemical binding]; other site 887061007764 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 887061007765 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 887061007766 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 887061007767 substrate binding pocket [chemical binding]; other site 887061007768 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 887061007769 B12 binding site [chemical binding]; other site 887061007770 cobalt ligand [ion binding]; other site 887061007771 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 887061007772 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_2; cd02433 887061007773 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 887061007774 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 887061007775 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061007776 Walker A motif; other site 887061007777 ATP binding site [chemical binding]; other site 887061007778 Walker B motif; other site 887061007779 arginine finger; other site 887061007780 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 887061007781 Membrane fusogenic activity; Region: BMFP; pfam04380 887061007782 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; pfam09694 887061007783 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 887061007784 Nitrogen regulatory protein P-II; Region: P-II; smart00938 887061007785 ammonium transporter; Provisional; Region: PRK10666 887061007786 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 887061007787 Glutamate-cysteine ligase; Region: GshA; pfam08886 887061007788 glutathione synthetase; Provisional; Region: PRK05246 887061007789 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 887061007790 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 887061007791 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 887061007792 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 887061007793 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 887061007794 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 887061007795 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 887061007796 Type II transport protein GspH; Region: GspH; pfam12019 887061007797 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 887061007798 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 887061007799 diaminopimelate decarboxylase; Region: lysA; TIGR01048 887061007800 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 887061007801 active site 887061007802 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 887061007803 substrate binding site [chemical binding]; other site 887061007804 catalytic residues [active] 887061007805 dimer interface [polypeptide binding]; other site 887061007806 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 887061007807 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 887061007808 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 887061007809 putative active site [active] 887061007810 putative substrate binding site [chemical binding]; other site 887061007811 putative cosubstrate binding site; other site 887061007812 catalytic site [active] 887061007813 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 887061007814 CobD/Cbib protein; Region: CobD_Cbib; cl00561 887061007815 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 887061007816 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 887061007817 Predicted membrane protein [Function unknown]; Region: COG2259 887061007818 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 887061007819 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 887061007820 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 887061007821 Coenzyme A binding pocket [chemical binding]; other site 887061007822 Formaldehyde-activating enzyme (Fae); Region: Fae; pfam08714 887061007823 putative transporter; Provisional; Region: PRK11660 887061007824 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 887061007825 Sulfate transporter family; Region: Sulfate_transp; pfam00916 887061007826 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 887061007827 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 887061007828 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 887061007829 minor groove reading motif; other site 887061007830 helix-hairpin-helix signature motif; other site 887061007831 substrate binding pocket [chemical binding]; other site 887061007832 active site 887061007833 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 887061007834 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 887061007835 DNA binding and oxoG recognition site [nucleotide binding] 887061007836 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 887061007837 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 887061007838 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 887061007839 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 887061007840 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 887061007841 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 887061007842 RNA binding surface [nucleotide binding]; other site 887061007843 Pseudouridine synthase, a subgroup of the RsuA family; Region: PSSA_1; cd02555 887061007844 active site 887061007845 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 887061007846 ThiC-associated domain; Region: ThiC-associated; pfam13667 887061007847 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 887061007848 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 887061007849 TPR motif; other site 887061007850 binding surface 887061007851 short chain dehydrogenase; Provisional; Region: PRK09072 887061007852 classical (c) SDRs; Region: SDR_c; cd05233 887061007853 NAD(P) binding site [chemical binding]; other site 887061007854 active site 887061007855 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 887061007856 heme binding pocket [chemical binding]; other site 887061007857 heme ligand [chemical binding]; other site 887061007858 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 887061007859 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_3; cd05914 887061007860 acyl-activating enzyme (AAE) consensus motif; other site 887061007861 putative AMP binding site [chemical binding]; other site 887061007862 putative active site [active] 887061007863 putative CoA binding site [chemical binding]; other site 887061007864 Thermostable hemolysin; Region: T_hemolysin; pfam12261 887061007865 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 887061007866 dimer interface [polypeptide binding]; other site 887061007867 phosphorylation site [posttranslational modification] 887061007868 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 887061007869 ATP binding site [chemical binding]; other site 887061007870 Mg2+ binding site [ion binding]; other site 887061007871 G-X-G motif; other site 887061007872 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 887061007873 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061007874 active site 887061007875 phosphorylation site [posttranslational modification] 887061007876 intermolecular recognition site; other site 887061007877 dimerization interface [polypeptide binding]; other site 887061007878 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 887061007879 Walker A motif; other site 887061007880 ATP binding site [chemical binding]; other site 887061007881 Walker B motif; other site 887061007882 arginine finger; other site 887061007883 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 887061007884 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 887061007885 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 887061007886 S-adenosylmethionine binding site [chemical binding]; other site 887061007887 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 887061007888 Isochorismatase family; Region: Isochorismatase; pfam00857 887061007889 catalytic triad [active] 887061007890 dimer interface [polypeptide binding]; other site 887061007891 conserved cis-peptide bond; other site 887061007892 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 887061007893 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 887061007894 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 887061007895 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 887061007896 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 887061007897 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 887061007898 active site 887061007899 dimer interface [polypeptide binding]; other site 887061007900 effector binding site; other site 887061007901 TSCPD domain; Region: TSCPD; pfam12637 887061007902 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 887061007903 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 887061007904 putative substrate translocation pore; other site 887061007905 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 887061007906 Sodium / potassium ATPase beta chain; Region: Na_K-ATPase; cl08255 887061007907 Pilin (bacterial filament); Region: Pilin; pfam00114 887061007908 Protein of unknown function (DUF3604); Region: DUF3604; pfam12228 887061007909 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 887061007910 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 887061007911 dimer interface [polypeptide binding]; other site 887061007912 conserved gate region; other site 887061007913 putative PBP binding loops; other site 887061007914 ABC-ATPase subunit interface; other site 887061007915 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 887061007916 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061007917 substrate binding pocket [chemical binding]; other site 887061007918 membrane-bound complex binding site; other site 887061007919 hinge residues; other site 887061007920 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 887061007921 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 887061007922 Walker A/P-loop; other site 887061007923 ATP binding site [chemical binding]; other site 887061007924 Q-loop/lid; other site 887061007925 ABC transporter signature motif; other site 887061007926 Walker B; other site 887061007927 D-loop; other site 887061007928 H-loop/switch region; other site 887061007929 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 887061007930 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061007931 DNA-binding site [nucleotide binding]; DNA binding site 887061007932 UTRA domain; Region: UTRA; pfam07702 887061007933 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 887061007934 DNA phosphorothioation-associated DGQHR protein 1; Region: DGQHR_dnd_1; TIGR04172 887061007935 Cupin; Region: Cupin_6; pfam12852 887061007936 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007937 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 887061007938 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061007939 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 887061007940 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 887061007941 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 887061007942 Acyl transferase domain; Region: Acyl_transf_1; cl08282 887061007943 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061007944 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 887061007945 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061007946 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061007947 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 887061007948 putative effector binding pocket; other site 887061007949 putative dimerization interface [polypeptide binding]; other site 887061007950 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 887061007951 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 887061007952 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...; Region: CSP_CDS; cd04458 887061007953 DNA-binding site [nucleotide binding]; DNA binding site 887061007954 RNA-binding motif; other site 887061007955 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 887061007956 BON domain; Region: BON; pfam04972 887061007957 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 887061007958 Protein of unknown function (DUF1469); Region: DUF1469; pfam07332 887061007959 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061007960 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 887061007961 ligand binding site [chemical binding]; other site 887061007962 flexible hinge region; other site 887061007963 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 887061007964 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061007965 active site 887061007966 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 887061007967 phosphorylation site [posttranslational modification] 887061007968 intermolecular recognition site; other site 887061007969 dimerization interface [polypeptide binding]; other site 887061007970 PAS fold; Region: PAS; pfam00989 887061007971 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 887061007972 putative active site [active] 887061007973 heme pocket [chemical binding]; other site 887061007974 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061007975 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061007976 metal binding site [ion binding]; metal-binding site 887061007977 active site 887061007978 I-site; other site 887061007979 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 887061007980 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 887061007981 ligand binding site [chemical binding]; other site 887061007982 flexible hinge region; other site 887061007983 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 887061007984 non-specific DNA interactions [nucleotide binding]; other site 887061007985 DNA binding site [nucleotide binding] 887061007986 sequence specific DNA binding site [nucleotide binding]; other site 887061007987 putative cAMP binding site [chemical binding]; other site 887061007988 Putative glucoamylase; Region: Glycoamylase; pfam10091 887061007989 Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_2_like; cd11753 887061007990 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 887061007991 First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains; Region: GH94N_ChvB_NdvB_1_like; cd11756 887061007992 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 887061007993 MarR family; Region: MarR_2; pfam12802 887061007994 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 887061007995 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 887061007996 FAD binding pocket [chemical binding]; other site 887061007997 FAD binding motif [chemical binding]; other site 887061007998 phosphate binding motif [ion binding]; other site 887061007999 NAD binding pocket [chemical binding]; other site 887061008000 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 887061008001 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061008002 putative active site [active] 887061008003 heme pocket [chemical binding]; other site 887061008004 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 887061008005 putative active site [active] 887061008006 heme pocket [chemical binding]; other site 887061008007 PAS domain; Region: PAS_9; pfam13426 887061008008 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 887061008009 putative active site [active] 887061008010 heme pocket [chemical binding]; other site 887061008011 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 887061008012 PAS domain; Region: PAS_9; pfam13426 887061008013 putative active site [active] 887061008014 heme pocket [chemical binding]; other site 887061008015 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008016 dimer interface [polypeptide binding]; other site 887061008017 putative CheW interface [polypeptide binding]; other site 887061008018 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 887061008019 PAS domain; Region: PAS_9; pfam13426 887061008020 putative active site [active] 887061008021 heme pocket [chemical binding]; other site 887061008022 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 887061008023 PAS domain; Region: PAS_9; pfam13426 887061008024 putative active site [active] 887061008025 heme pocket [chemical binding]; other site 887061008026 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 887061008027 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 887061008028 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 887061008029 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 887061008030 DNA-binding site [nucleotide binding]; DNA binding site 887061008031 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 887061008032 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061008033 homodimer interface [polypeptide binding]; other site 887061008034 catalytic residue [active] 887061008035 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 887061008036 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 887061008037 Protein export membrane protein; Region: SecD_SecF; cl14618 887061008038 Protein export membrane protein; Region: SecD_SecF; cl14618 887061008039 multidrug efflux system protein MdtE; Provisional; Region: PRK09859 887061008040 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061008041 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061008042 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061008043 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061008044 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008045 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008046 metal binding site [ion binding]; metal-binding site 887061008047 active site 887061008048 I-site; other site 887061008049 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 887061008050 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 887061008051 putative heme binding pocket [chemical binding]; other site 887061008052 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 887061008053 MarR family; Region: MarR; pfam01047 887061008054 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 887061008055 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061008056 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061008057 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061008058 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061008059 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 887061008060 dimerization interface [polypeptide binding]; other site 887061008061 Pirin-related protein [General function prediction only]; Region: COG1741 887061008062 Pirin; Region: Pirin; pfam02678 887061008063 triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs; Region: TMR_SDR_a; cd05269 887061008064 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 887061008065 NADP binding site [chemical binding]; other site 887061008066 Isochorismatase family; Region: Isochorismatase; pfam00857 887061008067 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 887061008068 catalytic triad [active] 887061008069 dimer interface [polypeptide binding]; other site 887061008070 conserved cis-peptide bond; other site 887061008071 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 887061008072 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 887061008073 active site 887061008074 Transmembrane secretion effector; Region: MFS_3; pfam05977 887061008075 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 887061008076 putative substrate translocation pore; other site 887061008077 XapX domain; Region: XapX; TIGR03510 887061008078 Cytosol aminopeptidase family, N-terminal domain; Region: Peptidase_M17_N; pfam02789 887061008079 Domain of unknown function (DUF4104); Region: DUF4104; pfam13372 887061008080 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061008081 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061008082 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 887061008083 putative effector binding pocket; other site 887061008084 dimerization interface [polypeptide binding]; other site 887061008085 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 887061008086 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 887061008087 MoxR-like ATPases [General function prediction only]; Region: COG0714 887061008088 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 887061008089 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 887061008090 Protein of unknown function DUF58; Region: DUF58; pfam01882 887061008091 von Willebrand factor type A domain; Region: VWA_2; pfam13519 887061008092 metal ion-dependent adhesion site (MIDAS); other site 887061008093 von Willebrand factor type A domain; Region: VWA_2; pfam13519 887061008094 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 887061008095 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 887061008096 putative NAD(P) binding site [chemical binding]; other site 887061008097 dimer interface [polypeptide binding]; other site 887061008098 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061008099 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061008100 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 887061008101 putative effector binding pocket; other site 887061008102 dimerization interface [polypeptide binding]; other site 887061008103 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 887061008104 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 887061008105 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 887061008106 PAS fold; Region: PAS_3; pfam08447 887061008107 putative active site [active] 887061008108 heme pocket [chemical binding]; other site 887061008109 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008110 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008111 metal binding site [ion binding]; metal-binding site 887061008112 active site 887061008113 I-site; other site 887061008114 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 887061008115 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 887061008116 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061008117 active site 887061008118 phosphorylation site [posttranslational modification] 887061008119 intermolecular recognition site; other site 887061008120 dimerization interface [polypeptide binding]; other site 887061008121 CheB methylesterase; Region: CheB_methylest; pfam01339 887061008122 CheD chemotactic sensory transduction; Region: CheD; cl00810 887061008123 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 887061008124 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 887061008125 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 887061008126 S-adenosylmethionine binding site [chemical binding]; other site 887061008127 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 887061008128 putative CheA interaction surface; other site 887061008129 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061008130 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008131 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008132 dimer interface [polypeptide binding]; other site 887061008133 putative CheW interface [polypeptide binding]; other site 887061008134 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 887061008135 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 887061008136 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061008137 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 887061008138 dimerization interface [polypeptide binding]; other site 887061008139 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008140 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061008141 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008142 dimer interface [polypeptide binding]; other site 887061008143 putative CheW interface [polypeptide binding]; other site 887061008144 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 887061008145 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 887061008146 putative CheA interaction surface; other site 887061008147 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 887061008148 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008149 dimer interface [polypeptide binding]; other site 887061008150 putative CheW interface [polypeptide binding]; other site 887061008151 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 887061008152 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061008153 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008154 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 887061008155 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 887061008156 putative binding surface; other site 887061008157 active site 887061008158 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 887061008159 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 887061008160 ATP binding site [chemical binding]; other site 887061008161 Mg2+ binding site [ion binding]; other site 887061008162 G-X-G motif; other site 887061008163 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 887061008164 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 887061008165 anti sigma factor interaction site; other site 887061008166 regulatory phosphorylation site [posttranslational modification]; other site 887061008167 Response regulator receiver domain; Region: Response_reg; pfam00072 887061008168 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 887061008169 active site 887061008170 phosphorylation site [posttranslational modification] 887061008171 intermolecular recognition site; other site 887061008172 dimerization interface [polypeptide binding]; other site 887061008173 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 887061008174 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 887061008175 dimer interface [polypeptide binding]; other site 887061008176 putative CheW interface [polypeptide binding]; other site 887061008177 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 887061008178 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 887061008179 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061008180 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 887061008181 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 887061008182 PAS domain S-box; Region: sensory_box; TIGR00229 887061008183 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 887061008184 putative active site [active] 887061008185 heme pocket [chemical binding]; other site 887061008186 PAS fold; Region: PAS_4; pfam08448 887061008187 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 887061008188 putative active site [active] 887061008189 heme pocket [chemical binding]; other site 887061008190 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008191 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008192 metal binding site [ion binding]; metal-binding site 887061008193 active site 887061008194 I-site; other site 887061008195 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 887061008196 Protein of unknown function, DUF399; Region: DUF399; cl01139 887061008197 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 887061008198 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 887061008199 classical (c) SDRs; Region: SDR_c; cd05233 887061008200 NAD(P) binding site [chemical binding]; other site 887061008201 active site 887061008202 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 887061008203 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 887061008204 conserved cys residue [active] 887061008205 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061008206 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 887061008207 PAS fold; Region: PAS_3; pfam08447 887061008208 putative active site [active] 887061008209 heme pocket [chemical binding]; other site 887061008210 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008211 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008212 metal binding site [ion binding]; metal-binding site 887061008213 active site 887061008214 I-site; other site 887061008215 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 887061008216 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 887061008217 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 887061008218 substrate binding pocket [chemical binding]; other site 887061008219 membrane-bound complex binding site; other site 887061008220 hinge residues; other site 887061008221 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 887061008222 PAS fold; Region: PAS_3; pfam08447 887061008223 putative active site [active] 887061008224 heme pocket [chemical binding]; other site 887061008225 PAS fold; Region: PAS_4; pfam08448 887061008226 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 887061008227 PAS domain; Region: PAS_9; pfam13426 887061008228 putative active site [active] 887061008229 heme pocket [chemical binding]; other site 887061008230 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008231 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008232 metal binding site [ion binding]; metal-binding site 887061008233 active site 887061008234 I-site; other site 887061008235 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 887061008236 Transcriptional regulator [Transcription]; Region: LysR; COG0583 887061008237 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 887061008238 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 887061008239 putative effector binding pocket; other site 887061008240 putative dimerization interface [polypeptide binding]; other site 887061008241 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 887061008242 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061008243 NAD(P) binding site [chemical binding]; other site 887061008244 active site 887061008245 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 887061008246 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 887061008247 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 887061008248 active site residue [active] 887061008249 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 887061008250 MgtC family; Region: MgtC; pfam02308 887061008251 putative chaperone; Provisional; Region: PRK11678 887061008252 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 887061008253 nucleotide binding site [chemical binding]; other site 887061008254 putative NEF/HSP70 interaction site [polypeptide binding]; other site 887061008255 SBD interface [polypeptide binding]; other site 887061008256 recombination associated protein; Reviewed; Region: rdgC; PRK00321 887061008257 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 887061008258 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 887061008259 Putative motility protein; Region: YjfB_motility; pfam14070 887061008260 Uncharacterized conserved protein [Function unknown]; Region: COG0397 887061008261 hypothetical protein; Validated; Region: PRK00029 887061008262 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 887061008263 binding surface 887061008264 TPR motif; other site 887061008265 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 887061008266 Sel1-like repeats; Region: SEL1; smart00671 887061008267 Sel1-like repeats; Region: SEL1; smart00671 887061008268 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 887061008269 Domain of unknown function DUF21; Region: DUF21; pfam01595 887061008270 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 887061008271 Transporter associated domain; Region: CorC_HlyC; smart01091 887061008272 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...; Region: CSP_CDS; cd04458 887061008273 DNA-binding site [nucleotide binding]; DNA binding site 887061008274 RNA-binding motif; other site 887061008275 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 887061008276 rRNA binding site [nucleotide binding]; other site 887061008277 predicted 30S ribosome binding site; other site 887061008278 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 887061008279 Helix-turn-helix domain; Region: HTH_18; pfam12833 887061008280 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 887061008281 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 887061008282 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 887061008283 HlyD family secretion protein; Region: HlyD_3; pfam13437 887061008284 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 887061008285 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 887061008286 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 887061008287 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 887061008288 Tetratricopeptide repeat; Region: TPR_16; pfam13432 887061008289 binding surface 887061008290 TPR motif; other site 887061008291 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 887061008292 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 887061008293 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 887061008294 RNA polymerase sigma factor; Provisional; Region: PRK12528 887061008295 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 887061008296 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 887061008297 DNA binding residues [nucleotide binding] 887061008298 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 887061008299 FecR protein; Region: FecR; pfam04773 887061008300 Secretin and TonB N terminus short domain; Region: STN; smart00965 887061008301 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 887061008302 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 887061008303 N-terminal plug; other site 887061008304 ligand-binding site [chemical binding]; other site 887061008305 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061008306 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 887061008307 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 887061008308 IHF dimer interface [polypeptide binding]; other site 887061008309 IHF - DNA interface [nucleotide binding]; other site 887061008310 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061008311 putative cation:proton antiport protein; Provisional; Region: PRK10669 887061008312 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 887061008313 TrkA-N domain; Region: TrkA_N; pfam02254 887061008314 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 887061008315 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 887061008316 putative substrate binding site [chemical binding]; other site 887061008317 putative ATP binding site [chemical binding]; other site 887061008318 sucrose-phosphate synthase, putative, glycosyltransferase domain; Region: sucr_P_syn_N; TIGR02472 887061008319 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 887061008320 putative ADP-binding pocket [chemical binding]; other site 887061008321 sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial; Region: sucr_syn_bact_C; TIGR02471 887061008322 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; cl17915 887061008323 active site 887061008324 motif I; other site 887061008325 motif II; other site 887061008326 Alpha amylase catalytic domain found in Amylosucrase; Region: AmyAc_Amylosucrase; cd11324 887061008327 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 887061008328 active site 887061008329 catalytic site [active] 887061008330 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 887061008331 Mechanosensitive ion channel; Region: MS_channel; pfam00924 887061008332 H+ Antiporter protein; Region: 2A0121; TIGR00900 887061008333 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; cl17904 887061008334 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008335 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008336 metal binding site [ion binding]; metal-binding site 887061008337 active site 887061008338 I-site; other site 887061008339 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 887061008340 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008341 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008342 metal binding site [ion binding]; metal-binding site 887061008343 active site 887061008344 I-site; other site 887061008345 Biofilm formation and stress response factor; Region: BsmA; pfam10014 887061008346 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 887061008347 dimerization interface [polypeptide binding]; other site 887061008348 putative DNA binding site [nucleotide binding]; other site 887061008349 putative Zn2+ binding site [ion binding]; other site 887061008350 bifunctional acyl-[acyl carrier protein] synthetase/2-acylglycerophosphoethanolamine acyltransferase; Validated; Region: PRK08043 887061008351 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 887061008352 putative acyl-acceptor binding pocket; other site 887061008353 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 887061008354 acyl-activating enzyme (AAE) consensus motif; other site 887061008355 putative AMP binding site [chemical binding]; other site 887061008356 lysophospholipid transporter LplT; Provisional; Region: PRK11195 887061008357 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 887061008358 putative substrate translocation pore; other site 887061008359 Predicted small secreted protein [Function unknown]; Region: COG5510 887061008360 coenzyme PQQ biosynthesis protein A; Provisional; Region: PRK14763 887061008361 SURF4 family; Region: SURF4; pfam02077 887061008362 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 887061008363 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 887061008364 putative active site [active] 887061008365 metal binding site [ion binding]; metal-binding site 887061008366 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 887061008367 MltA specific insert domain; Region: MltA; smart00925 887061008368 3D domain; Region: 3D; pfam06725 887061008369 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 887061008370 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 887061008371 ThiS interaction site; other site 887061008372 putative active site [active] 887061008373 tetramer interface [polypeptide binding]; other site 887061008374 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 887061008375 thiS-thiF/thiG interaction site; other site 887061008376 TPR repeat; Region: TPR_11; pfam13414 887061008377 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 887061008378 binding surface 887061008379 TPR motif; other site 887061008380 TPR repeat; Region: TPR_11; pfam13414 887061008381 Tetratricopeptide repeat; Region: TPR_16; pfam13432 887061008382 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 887061008383 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 887061008384 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 887061008385 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 887061008386 catalytic residue [active] 887061008387 Phosphopantetheine attachment site; Region: PP-binding; cl09936 887061008388 3-oxoacyl-[acyl-carrier-protein]; Region: FabH; COG0332 887061008389 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 887061008390 dimer interface [polypeptide binding]; other site 887061008391 active site 887061008392 CoA binding pocket [chemical binding]; other site 887061008393 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 887061008394 classical (c) SDRs; Region: SDR_c; cd05233 887061008395 NAD(P) binding site [chemical binding]; other site 887061008396 active site 887061008397 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 887061008398 classical (c) SDRs; Region: SDR_c; cd05233 887061008399 NAD(P) binding site [chemical binding]; other site 887061008400 active site 887061008401 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 887061008402 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 887061008403 putative trimer interface [polypeptide binding]; other site 887061008404 putative CoA binding site [chemical binding]; other site 887061008405 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 887061008406 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 887061008407 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 887061008408 [2Fe-2S] cluster binding site [ion binding]; other site 887061008409 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 887061008410 alpha subunit interface [polypeptide binding]; other site 887061008411 active site 887061008412 substrate binding site [chemical binding]; other site 887061008413 Fe binding site [ion binding]; other site 887061008414 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 887061008415 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 887061008416 putative trimer interface [polypeptide binding]; other site 887061008417 putative CoA binding site [chemical binding]; other site 887061008418 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 887061008419 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 887061008420 [2Fe-2S] cluster binding site [ion binding]; other site 887061008421 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 887061008422 alpha subunit interface [polypeptide binding]; other site 887061008423 active site 887061008424 substrate binding site [chemical binding]; other site 887061008425 Fe binding site [ion binding]; other site 887061008426 CsbD-like; Region: CsbD; cl17424 887061008427 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 887061008428 active site 887061008429 catalytic site [active] 887061008430 substrate binding site [chemical binding]; other site 887061008431 nucleotide excision repair endonuclease; Provisional; Region: PRK10545 887061008432 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 887061008433 GIY-YIG motif/motif A; other site 887061008434 active site 887061008435 catalytic site [active] 887061008436 putative DNA binding site [nucleotide binding]; other site 887061008437 metal binding site [ion binding]; metal-binding site 887061008438 Rubredoxin [Energy production and conversion]; Region: COG1773 887061008439 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 887061008440 iron binding site [ion binding]; other site 887061008441 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 887061008442 dimer interface [polypeptide binding]; other site 887061008443 substrate binding site [chemical binding]; other site 887061008444 ATP binding site [chemical binding]; other site 887061008445 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 887061008446 thiamine phosphate binding site [chemical binding]; other site 887061008447 active site 887061008448 pyrophosphate binding site [ion binding]; other site 887061008449 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 887061008450 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 887061008451 inhibitor-cofactor binding pocket; inhibition site 887061008452 pyridoxal 5'-phosphate binding site [chemical binding]; other site 887061008453 catalytic residue [active] 887061008454 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 887061008455 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 887061008456 active site 887061008457 dimer interface [polypeptide binding]; other site 887061008458 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 887061008459 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 887061008460 active site 887061008461 FMN binding site [chemical binding]; other site 887061008462 substrate binding site [chemical binding]; other site 887061008463 3Fe-4S cluster binding site [ion binding]; other site 887061008464 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 887061008465 domain interface; other site 887061008466 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 887061008467 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 887061008468 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 887061008469 substrate binding site [chemical binding]; other site 887061008470 active site 887061008471 primosome assembly protein PriA; Validated; Region: PRK05580 887061008472 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 887061008473 ATP binding site [chemical binding]; other site 887061008474 putative Mg++ binding site [ion binding]; other site 887061008475 helicase superfamily c-terminal domain; Region: HELICc; smart00490 887061008476 ATP-binding site [chemical binding]; other site 887061008477 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 887061008478 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 887061008479 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 887061008480 active site 887061008481 HIGH motif; other site 887061008482 KMSK motif region; other site 887061008483 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 887061008484 tRNA binding surface [nucleotide binding]; other site 887061008485 anticodon binding site; other site 887061008486 Sporulation related domain; Region: SPOR; pfam05036 887061008487 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 887061008488 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 887061008489 catalytic residues [active] 887061008490 hinge region; other site 887061008491 alpha helical domain; other site 887061008492 short chain dehydrogenase; Provisional; Region: PRK07024 887061008493 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 887061008494 NAD(P) binding site [chemical binding]; other site 887061008495 active site 887061008496 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 887061008497 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061008498 putative active site [active] 887061008499 heme pocket [chemical binding]; other site 887061008500 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 887061008501 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061008502 putative active site [active] 887061008503 heme pocket [chemical binding]; other site 887061008504 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 887061008505 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 887061008506 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 887061008507 metal binding site [ion binding]; metal-binding site 887061008508 active site 887061008509 I-site; other site 887061008510 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 887061008511 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 887061008512 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 887061008513 glutaminase active site [active] 887061008514 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 887061008515 dimer interface [polypeptide binding]; other site 887061008516 active site 887061008517 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 887061008518 dimer interface [polypeptide binding]; other site 887061008519 active site 887061008520 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 887061008521 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 887061008522 Substrate binding site; other site 887061008523 Mg++ binding site; other site 887061008524 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 887061008525 active site 887061008526 substrate binding site [chemical binding]; other site 887061008527 CoA binding site [chemical binding]; other site 887061008528 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 887061008529 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 887061008530 gamma subunit interface [polypeptide binding]; other site 887061008531 epsilon subunit interface [polypeptide binding]; other site 887061008532 LBP interface [polypeptide binding]; other site 887061008533 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 887061008534 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 887061008535 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 887061008536 alpha subunit interaction interface [polypeptide binding]; other site 887061008537 Walker A motif; other site 887061008538 ATP binding site [chemical binding]; other site 887061008539 Walker B motif; other site 887061008540 inhibitor binding site; inhibition site 887061008541 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 887061008542 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 887061008543 core domain interface [polypeptide binding]; other site 887061008544 delta subunit interface [polypeptide binding]; other site 887061008545 epsilon subunit interface [polypeptide binding]; other site 887061008546 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 887061008547 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 887061008548 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 887061008549 beta subunit interaction interface [polypeptide binding]; other site 887061008550 Walker A motif; other site 887061008551 ATP binding site [chemical binding]; other site 887061008552 Walker B motif; other site 887061008553 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 887061008554 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 887061008555 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 887061008556 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 887061008557 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 887061008558 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 887061008559 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 887061008560 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 887061008561 ParB-like nuclease domain; Region: ParBc; pfam02195 887061008562 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 887061008563 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 887061008564 P-loop; other site 887061008565 Magnesium ion binding site [ion binding]; other site 887061008566 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 887061008567 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 887061008568 S-adenosylmethionine binding site [chemical binding]; other site 887061008569 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 887061008570 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 887061008571 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 887061008572 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 887061008573 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 887061008574 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 887061008575 trmE is a tRNA modification GTPase; Region: trmE; cd04164 887061008576 G1 box; other site 887061008577 GTP/Mg2+ binding site [chemical binding]; other site 887061008578 Switch I region; other site 887061008579 G2 box; other site 887061008580 Switch II region; other site 887061008581 G3 box; other site 887061008582 G4 box; other site 887061008583 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 887061008584 membrane protein insertase; Provisional; Region: PRK01318 887061008585 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592