-- dump date 20140619_055136 -- class Genbank::misc_feature -- table misc_feature_note -- id note 385025000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 385025000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 385025000003 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 385025000004 Walker A motif; other site 385025000005 ATP binding site [chemical binding]; other site 385025000006 Walker B motif; other site 385025000007 arginine finger; other site 385025000008 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 385025000009 DnaA box-binding interface [nucleotide binding]; other site 385025000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 385025000011 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 385025000012 putative DNA binding surface [nucleotide binding]; other site 385025000013 dimer interface [polypeptide binding]; other site 385025000014 beta-clamp/clamp loader binding surface; other site 385025000015 beta-clamp/translesion DNA polymerase binding surface; other site 385025000016 recombination protein F; Reviewed; Region: recF; PRK00064 385025000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025000018 Walker A/P-loop; other site 385025000019 ATP binding site [chemical binding]; other site 385025000020 Q-loop/lid; other site 385025000021 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025000022 ABC transporter signature motif; other site 385025000023 Walker B; other site 385025000024 D-loop; other site 385025000025 H-loop/switch region; other site 385025000026 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 385025000027 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 385025000028 Mg2+ binding site [ion binding]; other site 385025000029 G-X-G motif; other site 385025000030 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 385025000031 anchoring element; other site 385025000032 dimer interface [polypeptide binding]; other site 385025000033 ATP binding site [chemical binding]; other site 385025000034 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 385025000035 active site 385025000036 putative metal-binding site [ion binding]; other site 385025000037 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 385025000038 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 385025000039 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 385025000040 putative ligand binding site [chemical binding]; other site 385025000041 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 385025000042 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 385025000043 TM-ABC transporter signature motif; other site 385025000044 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 385025000045 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 385025000046 TM-ABC transporter signature motif; other site 385025000047 urea ABC transporter, ATP-binding protein UrtD; Region: urea_trans_UrtD; TIGR03411 385025000048 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 385025000049 Walker A/P-loop; other site 385025000050 ATP binding site [chemical binding]; other site 385025000051 Q-loop/lid; other site 385025000052 ABC transporter signature motif; other site 385025000053 Walker B; other site 385025000054 D-loop; other site 385025000055 H-loop/switch region; other site 385025000056 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 385025000057 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 385025000058 Walker A/P-loop; other site 385025000059 ATP binding site [chemical binding]; other site 385025000060 Q-loop/lid; other site 385025000061 ABC transporter signature motif; other site 385025000062 Walker B; other site 385025000063 D-loop; other site 385025000064 H-loop/switch region; other site 385025000065 UreD urease accessory protein; Region: UreD; pfam01774 385025000066 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 385025000067 alpha-gamma subunit interface [polypeptide binding]; other site 385025000068 beta-gamma subunit interface [polypeptide binding]; other site 385025000069 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 385025000070 gamma-beta subunit interface [polypeptide binding]; other site 385025000071 alpha-beta subunit interface [polypeptide binding]; other site 385025000072 urease subunit alpha; Reviewed; Region: ureC; PRK13207 385025000073 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 385025000074 subunit interactions [polypeptide binding]; other site 385025000075 active site 385025000076 flap region; other site 385025000077 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 385025000078 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 385025000079 dimer interface [polypeptide binding]; other site 385025000080 catalytic residues [active] 385025000081 UreF; Region: UreF; pfam01730 385025000082 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 385025000083 G1 box; other site 385025000084 GTP/Mg2+ binding site [chemical binding]; other site 385025000085 G2 box; other site 385025000086 Switch I region; other site 385025000087 G3 box; other site 385025000088 Switch II region; other site 385025000089 G4 box; other site 385025000090 G5 box; other site 385025000091 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 385025000092 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 385025000093 putative acyl-acceptor binding pocket; other site 385025000094 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 385025000095 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 385025000096 active site 385025000097 motif I; other site 385025000098 motif II; other site 385025000099 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 385025000100 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 385025000101 dimer interface [polypeptide binding]; other site 385025000102 motif 1; other site 385025000103 active site 385025000104 motif 2; other site 385025000105 motif 3; other site 385025000106 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 385025000107 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 385025000108 Ligand Binding Site [chemical binding]; other site 385025000109 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 385025000110 CPxP motif; other site 385025000111 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 385025000112 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 385025000113 glutamine synthetase; Provisional; Region: glnA; PRK09469 385025000114 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 385025000115 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 385025000116 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 385025000117 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 385025000118 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 385025000119 putative active site [active] 385025000120 heme pocket [chemical binding]; other site 385025000121 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 385025000122 dimer interface [polypeptide binding]; other site 385025000123 phosphorylation site [posttranslational modification] 385025000124 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 385025000125 ATP binding site [chemical binding]; other site 385025000126 Mg2+ binding site [ion binding]; other site 385025000127 G-X-G motif; other site 385025000128 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 385025000129 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025000130 active site 385025000131 phosphorylation site [posttranslational modification] 385025000132 intermolecular recognition site; other site 385025000133 dimerization interface [polypeptide binding]; other site 385025000134 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 385025000135 Walker A motif; other site 385025000136 ATP binding site [chemical binding]; other site 385025000137 Walker B motif; other site 385025000138 arginine finger; other site 385025000139 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 385025000140 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. 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...; Region: DHOD_1B_like; cd04740 385025000141 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 385025000142 heterodimer interface [polypeptide binding]; other site 385025000143 active site 385025000144 FMN binding site [chemical binding]; other site 385025000145 homodimer interface [polypeptide binding]; other site 385025000146 substrate binding site [chemical binding]; other site 385025000147 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 385025000148 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 385025000149 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 385025000150 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 385025000151 preprotein translocase subunit SecB; Validated; Region: PRK05751 385025000152 SecA binding site; other site 385025000153 Preprotein binding site; other site 385025000154 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 385025000155 active site residue [active] 385025000156 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 385025000157 dimerization interface [polypeptide binding]; other site 385025000158 putative DNA binding site [nucleotide binding]; other site 385025000159 putative Zn2+ binding site [ion binding]; other site 385025000160 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 385025000161 phosphoglyceromutase; Provisional; Region: PRK05434 385025000162 AmiB activator; Provisional; Region: PRK11637 385025000163 Peptidase family M23; Region: Peptidase_M23; pfam01551 385025000164 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 385025000165 C-terminal peptidase (prc); Region: prc; TIGR00225 385025000166 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 385025000167 protein binding site [polypeptide binding]; other site 385025000168 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 385025000169 Catalytic dyad [active] 385025000170 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 385025000171 NodB motif; other site 385025000172 putative active site [active] 385025000173 putative catalytic site [active] 385025000174 Zn binding site [ion binding]; other site 385025000175 Uncharacterized conserved protein [Function unknown]; Region: COG3391 385025000176 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 385025000177 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 385025000178 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 385025000179 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 385025000180 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 385025000181 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 385025000182 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 385025000183 Domain of unknown function (DUF4426); Region: DUF4426; pfam14467 385025000184 muropeptide transporter; Validated; Region: ampG; cl17669 385025000185 muropeptide transporter; Validated; Region: ampG; cl17669 385025000186 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 385025000187 putative active site [active] 385025000188 putative catalytic site [active] 385025000189 putative DNA binding site [nucleotide binding]; other site 385025000190 putative phosphate binding site [ion binding]; other site 385025000191 metal binding site A [ion binding]; metal-binding site 385025000192 putative AP binding site [nucleotide binding]; other site 385025000193 putative metal binding site B [ion binding]; other site 385025000194 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 385025000195 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 385025000196 Peptidase family M48; Region: Peptidase_M48; pfam01435 385025000197 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 385025000198 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 385025000199 dimer interface [polypeptide binding]; other site 385025000200 active site 385025000201 citrylCoA binding site [chemical binding]; other site 385025000202 NADH binding [chemical binding]; other site 385025000203 cationic pore residues; other site 385025000204 oxalacetate/citrate binding site [chemical binding]; other site 385025000205 coenzyme A binding site [chemical binding]; other site 385025000206 catalytic triad [active] 385025000207 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 385025000208 Transglycosylase; Region: Transgly; pfam00912 385025000209 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 385025000210 Competence protein A; Region: Competence_A; pfam11104 385025000211 Cell division protein FtsA; Region: FtsA; cl17206 385025000212 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 385025000213 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 385025000214 Pilus assembly protein, PilO; Region: PilO; pfam04350 385025000215 Pilus assembly protein, PilP; Region: PilP; pfam04351 385025000216 AMIN domain; Region: AMIN; pfam11741 385025000217 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 385025000218 Secretin and TonB N terminus short domain; Region: STN; smart00965 385025000219 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 385025000220 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 385025000221 shikimate kinase; Reviewed; Region: aroK; PRK00131 385025000222 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 385025000223 ADP binding site [chemical binding]; other site 385025000224 magnesium binding site [ion binding]; other site 385025000225 putative shikimate binding site; other site 385025000226 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 385025000227 active site 385025000228 dimer interface [polypeptide binding]; other site 385025000229 metal binding site [ion binding]; metal-binding site 385025000230 AAA ATPase domain; Region: AAA_16; pfam13191 385025000231 AAA domain; Region: AAA_22; pfam13401 385025000232 cell division protein DamX; Validated; Region: PRK10905 385025000233 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 385025000234 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 385025000235 active site 385025000236 dimer interface [polypeptide binding]; other site 385025000237 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 385025000238 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 385025000239 active site 385025000240 FMN binding site [chemical binding]; other site 385025000241 substrate binding site [chemical binding]; other site 385025000242 3Fe-4S cluster binding site [ion binding]; other site 385025000243 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 385025000244 domain interface; other site 385025000245 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 385025000246 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025000247 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025000248 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 385025000249 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 385025000250 substrate binding site [chemical binding]; other site 385025000251 active site 385025000252 Rdx family; Region: Rdx; cl01407 385025000253 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 385025000254 TPR motif; other site 385025000255 binding surface 385025000256 Transposase IS200 like; Region: Y1_Tnp; pfam01797 385025000257 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 385025000258 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 385025000259 PemK-like protein; Region: PemK; cl00995 385025000260 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 385025000261 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 385025000262 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 385025000263 Type II transport protein GspH; Region: GspH; pfam12019 385025000264 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 385025000265 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 385025000266 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 385025000267 Walker A motif; other site 385025000268 ATP binding site [chemical binding]; other site 385025000269 Walker B motif; other site 385025000270 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 385025000271 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 385025000272 Walker A motif; other site 385025000273 ATP binding site [chemical binding]; other site 385025000274 Walker B motif; other site 385025000275 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 385025000276 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 385025000277 catalytic residue [active] 385025000278 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 385025000279 pyrroline-5-carboxylate reductase; Region: PLN02688 385025000280 YGGT family; Region: YGGT; pfam02325 385025000281 YGGT family; Region: YGGT; pfam02325 385025000282 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 385025000283 Dynamin family; Region: Dynamin_N; pfam00350 385025000284 G1 box; other site 385025000285 GTP/Mg2+ binding site [chemical binding]; other site 385025000286 G2 box; other site 385025000287 Switch I region; other site 385025000288 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 385025000289 G3 box; other site 385025000290 Switch II region; other site 385025000291 GTP/Mg2+ binding site [chemical binding]; other site 385025000292 G4 box; other site 385025000293 G5 box; other site 385025000294 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 385025000295 S-adenosylmethionine binding site [chemical binding]; other site 385025000296 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional; Region: PRK11840 385025000297 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 385025000298 thiS-thiF/thiG interaction site; other site 385025000299 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 385025000300 ThiS interaction site; other site 385025000301 putative active site [active] 385025000302 tetramer interface [polypeptide binding]; other site 385025000303 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 385025000304 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 385025000305 HDOD domain; Region: HDOD; pfam08668 385025000306 AsmA family; Region: AsmA; pfam05170 385025000307 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 385025000308 adenine DNA glycosylase; Provisional; Region: PRK10880 385025000309 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 385025000310 minor groove reading motif; other site 385025000311 helix-hairpin-helix signature motif; other site 385025000312 substrate binding pocket [chemical binding]; other site 385025000313 active site 385025000314 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 385025000315 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 385025000316 DNA binding and oxoG recognition site [nucleotide binding] 385025000317 oxidative damage protection protein; Provisional; Region: PRK05408 385025000318 YceI-like domain; Region: YceI; pfam04264 385025000319 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 385025000320 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 385025000321 ATP binding site [chemical binding]; other site 385025000322 putative Mg++ binding site [ion binding]; other site 385025000323 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 385025000324 nucleotide binding region [chemical binding]; other site 385025000325 ATP-binding site [chemical binding]; other site 385025000326 Helicase associated domain (HA2); Region: HA2; pfam04408 385025000327 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 385025000328 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 385025000329 OsmC-like protein; Region: OsmC; pfam02566 385025000330 Protein of unknown function (DUF2288); Region: DUF2288; pfam10052 385025000331 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 385025000332 Predicted transporter component [General function prediction only]; Region: COG2391 385025000333 Sulphur transport; Region: Sulf_transp; pfam04143 385025000334 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 385025000335 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 385025000336 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 385025000337 active site 385025000338 NTP binding site [chemical binding]; other site 385025000339 metal binding triad [ion binding]; metal-binding site 385025000340 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 385025000341 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 385025000342 Zn2+ binding site [ion binding]; other site 385025000343 Mg2+ binding site [ion binding]; other site 385025000344 pteridine reductase; Provisional; Region: PRK09135 385025000345 pteridine reductase (PR), classical (c) SDRs; Region: PR_SDR_c; cd05357 385025000346 NADP binding site [chemical binding]; other site 385025000347 substrate binding pocket [chemical binding]; other site 385025000348 active site 385025000349 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 385025000350 catalytic center binding site [active] 385025000351 ATP binding site [chemical binding]; other site 385025000352 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 385025000353 homooctamer interface [polypeptide binding]; other site 385025000354 active site 385025000355 UGMP family protein; Validated; Region: PRK09604 385025000356 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 385025000357 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 385025000358 Yqey-like protein; Region: YqeY; pfam09424 385025000359 DNA primase; Validated; Region: dnaG; PRK05667 385025000360 CHC2 zinc finger; Region: zf-CHC2; pfam01807 385025000361 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 385025000362 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 385025000363 active site 385025000364 metal binding site [ion binding]; metal-binding site 385025000365 interdomain interaction site; other site 385025000366 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 385025000367 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 385025000368 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 385025000369 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 385025000370 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 385025000371 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 385025000372 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025000373 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 385025000374 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 385025000375 DNA binding residues [nucleotide binding] 385025000376 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 385025000377 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 385025000378 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 385025000379 FeS/SAM binding site; other site 385025000380 HemN C-terminal domain; Region: HemN_C; pfam06969 385025000381 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 385025000382 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 385025000383 Beta-Casp domain; Region: Beta-Casp; smart01027 385025000384 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 385025000385 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 385025000386 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025000387 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025000388 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 385025000389 C-terminal domain interface [polypeptide binding]; other site 385025000390 GSH binding site (G-site) [chemical binding]; other site 385025000391 dimer interface [polypeptide binding]; other site 385025000392 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 385025000393 N-terminal domain interface [polypeptide binding]; other site 385025000394 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 385025000395 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 385025000396 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025000397 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 385025000398 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 385025000399 Walker A/P-loop; other site 385025000400 ATP binding site [chemical binding]; other site 385025000401 Q-loop/lid; other site 385025000402 ABC transporter signature motif; other site 385025000403 Walker B; other site 385025000404 D-loop; other site 385025000405 H-loop/switch region; other site 385025000406 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 385025000407 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 385025000408 FtsX-like permease family; Region: FtsX; pfam02687 385025000409 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 385025000410 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 385025000411 FtsX-like permease family; Region: FtsX; pfam02687 385025000412 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 385025000413 Major Facilitator Superfamily; Region: MFS_1; pfam07690 385025000414 putative substrate translocation pore; other site 385025000415 Membrane transport protein; Region: Mem_trans; cl09117 385025000416 Transmembrane secretion effector; Region: MFS_3; pfam05977 385025000417 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 385025000418 putative substrate translocation pore; other site 385025000419 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 385025000420 arsenical-resistance protein; Region: acr3; TIGR00832 385025000421 hypothetical protein; Provisional; Region: PRK09272 385025000422 Predicted membrane protein [Function unknown]; Region: COG1238 385025000423 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 385025000424 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 385025000425 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 385025000426 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 385025000427 catalytic triad [active] 385025000428 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 385025000429 Uncharacterized conserved protein [Function unknown]; Region: COG3461 385025000430 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 385025000431 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 385025000432 dimer interface [polypeptide binding]; other site 385025000433 active site 385025000434 heme binding site [chemical binding]; other site 385025000435 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 385025000436 Uncharacterized conserved protein [Function unknown]; Region: COG1432 385025000437 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 385025000438 putative metal binding site [ion binding]; other site 385025000439 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 385025000440 Predicted flavoprotein [General function prediction only]; Region: COG0431 385025000441 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 385025000442 Predicted membrane protein [Function unknown]; Region: COG1238 385025000443 A predicted NlpC/p60-like peptidase; Region: BtrH; pfam14399 385025000444 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_C39A; cd02549 385025000445 putative active site [active] 385025000446 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 385025000447 binding surface 385025000448 TPR motif; other site 385025000449 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 385025000450 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 385025000451 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 385025000452 cofactor binding site; other site 385025000453 DNA binding site [nucleotide binding] 385025000454 substrate interaction site [chemical binding]; other site 385025000455 NgoPII restriction endonuclease; Region: RE_NgoPII; pfam09521 385025000456 integron integrase; Region: integrase_gron; TIGR02249 385025000457 IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and...; Region: INT_IntI; cd01193 385025000458 Int/Topo IB signature motif; other site 385025000459 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 385025000460 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 385025000461 cobalamin binding residues [chemical binding]; other site 385025000462 putative BtuC binding residues; other site 385025000463 dimer interface [polypeptide binding]; other site 385025000464 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 385025000465 catalytic residues [active] 385025000466 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 385025000467 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 385025000468 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 385025000469 Late embryogenesis abundant protein; Region: LEA_2; cl12118 385025000470 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025000471 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025000472 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 385025000473 putative dimer interface [polypeptide binding]; other site 385025000474 putative N-terminal domain interface [polypeptide binding]; other site 385025000475 putative substrate binding pocket (H-site) [chemical binding]; other site 385025000476 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 385025000477 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 385025000478 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 385025000479 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 385025000480 active site 385025000481 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 385025000482 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 385025000483 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 385025000484 electron transport complex RsxE subunit; Provisional; Region: PRK12405 385025000485 FMN-binding domain; Region: FMN_bind; cl01081 385025000486 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 385025000487 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 385025000488 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 385025000489 SLBB domain; Region: SLBB; pfam10531 385025000490 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 385025000491 ferredoxin; Provisional; Region: PRK08764 385025000492 Putative Fe-S cluster; Region: FeS; pfam04060 385025000493 4Fe-4S binding domain; Region: Fer4; pfam00037 385025000494 electron transport complex protein RsxA; Provisional; Region: PRK05151 385025000495 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 385025000496 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 385025000497 active site 385025000498 HIGH motif; other site 385025000499 KMSKS motif; other site 385025000500 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 385025000501 anticodon binding site; other site 385025000502 tRNA binding surface [nucleotide binding]; other site 385025000503 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 385025000504 dimer interface [polypeptide binding]; other site 385025000505 putative tRNA-binding site [nucleotide binding]; other site 385025000506 Domain of unknown function DUF59; Region: DUF59; pfam01883 385025000507 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 385025000508 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 385025000509 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 385025000510 trimer interface [polypeptide binding]; other site 385025000511 active site 385025000512 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 385025000513 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 385025000514 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 385025000515 active site 385025000516 substrate binding site [chemical binding]; other site 385025000517 cosubstrate binding site; other site 385025000518 catalytic site [active] 385025000519 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 385025000520 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 385025000521 dimerization interface [polypeptide binding]; other site 385025000522 putative ATP binding site [chemical binding]; other site 385025000523 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3249 385025000524 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 385025000525 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 385025000526 Domain of unknown function DUF20; Region: UPF0118; pfam01594 385025000527 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 385025000528 superoxide dismutase; Provisional; Region: PRK10543 385025000529 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 385025000530 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 385025000531 Mechanosensitive ion channel; Region: MS_channel; pfam00924 385025000532 Protein of unknown function (DUF4197); Region: DUF4197; pfam13852 385025000533 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 385025000534 DnaA regulatory inactivator Hda; Region: DnaA_homol_Hda; TIGR03420 385025000535 Predicted membrane protein (DUF2069); Region: DUF2069; pfam09842 385025000536 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 385025000537 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 385025000538 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 385025000539 ArsC family; Region: ArsC; pfam03960 385025000540 catalytic residues [active] 385025000541 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 385025000542 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 385025000543 putative ribose interaction site [chemical binding]; other site 385025000544 putative ADP binding site [chemical binding]; other site 385025000545 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 385025000546 active site 385025000547 nucleotide binding site [chemical binding]; other site 385025000548 HIGH motif; other site 385025000549 KMSKS motif; other site 385025000550 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 385025000551 ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional; Region: rfaD; PRK11150 385025000552 NADP binding site [chemical binding]; other site 385025000553 homopentamer interface [polypeptide binding]; other site 385025000554 substrate binding site [chemical binding]; other site 385025000555 active site 385025000556 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 385025000557 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 385025000558 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 385025000559 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 385025000560 Major Facilitator Superfamily; Region: MFS_1; pfam07690 385025000561 putative substrate translocation pore; other site 385025000562 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 385025000563 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 385025000564 putative active site [active] 385025000565 dimerization interface [polypeptide binding]; other site 385025000566 putative tRNAtyr binding site [nucleotide binding]; other site 385025000567 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 385025000568 ligand binding site [chemical binding]; other site 385025000569 active site 385025000570 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 385025000571 active site residue [active] 385025000572 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 385025000573 ThiC-associated domain; Region: ThiC-associated; pfam13667 385025000574 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 385025000575 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 385025000576 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 385025000577 Methyltransferase domain; Region: Methyltransf_23; pfam13489 385025000578 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 385025000579 S-adenosylmethionine binding site [chemical binding]; other site 385025000580 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 385025000581 Part of AAA domain; Region: AAA_19; pfam13245 385025000582 Family description; Region: UvrD_C_2; pfam13538 385025000583 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 385025000584 Salicylaldehyde dehydrogenase, DoxF-like; Region: ALDH_SaliADH; cd07105 385025000585 NAD(P) binding site [chemical binding]; other site 385025000586 catalytic residues [active] 385025000587 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 385025000588 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 385025000589 active site 385025000590 catalytic tetrad [active] 385025000591 hypothetical protein; Provisional; Region: PRK05208 385025000592 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 385025000593 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 385025000594 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 385025000595 heme-binding site [chemical binding]; other site 385025000596 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 385025000597 5-histidylcysteine sulfoxide synthase; Region: ovoA_Nterm; TIGR04344 385025000598 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 385025000599 Methyltransferase domain; Region: Methyltransf_31; pfam13847 385025000600 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 385025000601 S-adenosylmethionine binding site [chemical binding]; other site 385025000602 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 385025000603 DctM-like transporters; Region: DctM; pfam06808 385025000604 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 385025000605 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 385025000606 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 385025000607 putative active site [active] 385025000608 putative substrate binding site [chemical binding]; other site 385025000609 ATP binding site [chemical binding]; other site 385025000610 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 385025000611 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 385025000612 DNA polymerase I; Provisional; Region: PRK05755 385025000613 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 385025000614 active site 385025000615 metal binding site 1 [ion binding]; metal-binding site 385025000616 putative 5' ssDNA interaction site; other site 385025000617 metal binding site 3; metal-binding site 385025000618 metal binding site 2 [ion binding]; metal-binding site 385025000619 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 385025000620 putative DNA binding site [nucleotide binding]; other site 385025000621 putative metal binding site [ion binding]; other site 385025000622 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 385025000623 active site 385025000624 catalytic site [active] 385025000625 substrate binding site [chemical binding]; other site 385025000626 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 385025000627 active site 385025000628 DNA binding site [nucleotide binding] 385025000629 catalytic site [active] 385025000630 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 385025000631 G1 box; other site 385025000632 GTP/Mg2+ binding site [chemical binding]; other site 385025000633 Switch I region; other site 385025000634 G2 box; other site 385025000635 G3 box; other site 385025000636 Switch II region; other site 385025000637 G4 box; other site 385025000638 G5 box; other site 385025000639 Cytochrome c; Region: Cytochrom_C; cl11414 385025000640 Cytochrome c553 [Energy production and conversion]; Region: COG2863 385025000641 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 385025000642 Cytochrome c; Region: Cytochrom_C; cl11414 385025000643 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 385025000644 ResB-like family; Region: ResB; pfam05140 385025000645 ResB-like family; Region: ResB; pfam05140 385025000646 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 385025000647 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 385025000648 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 385025000649 catalytic residues [active] 385025000650 hinge region; other site 385025000651 alpha helical domain; other site 385025000652 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 385025000653 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 385025000654 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 385025000655 PYR/PP interface [polypeptide binding]; other site 385025000656 dimer interface [polypeptide binding]; other site 385025000657 TPP binding site [chemical binding]; other site 385025000658 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 385025000659 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 385025000660 TPP-binding site [chemical binding]; other site 385025000661 dimer interface [polypeptide binding]; other site 385025000662 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 385025000663 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 385025000664 putative valine binding site [chemical binding]; other site 385025000665 dimer interface [polypeptide binding]; other site 385025000666 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 385025000667 ketol-acid reductoisomerase; Provisional; Region: PRK05479 385025000668 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 385025000669 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 385025000670 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 385025000671 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 385025000672 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 385025000673 Fe-S cluster binding site [ion binding]; other site 385025000674 active site 385025000675 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 385025000676 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 385025000677 Coenzyme A binding pocket [chemical binding]; other site 385025000678 Helix-turn-helix domain; Region: HTH_17; pfam12728 385025000679 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 385025000680 HsdM N-terminal domain; Region: HsdM_N; pfam12161 385025000681 Methyltransferase domain; Region: Methyltransf_26; pfam13659 385025000682 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 385025000683 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 385025000684 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 385025000685 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 385025000686 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 385025000687 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 385025000688 ATP binding site [chemical binding]; other site 385025000689 putative Mg++ binding site [ion binding]; other site 385025000690 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 385025000691 Antirestriction protein (ArdA); Region: ArdA; cl01953 385025000692 Protein of unknwon function (DUF2893); Region: DUF2893; pfam11459 385025000693 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 385025000694 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 385025000695 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 385025000696 G1 box; other site 385025000697 putative GEF interaction site [polypeptide binding]; other site 385025000698 GTP/Mg2+ binding site [chemical binding]; other site 385025000699 Switch I region; other site 385025000700 G2 box; other site 385025000701 G3 box; other site 385025000702 Switch II region; other site 385025000703 G4 box; other site 385025000704 G5 box; other site 385025000705 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 385025000706 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 385025000707 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 385025000708 thiopurine S-methyltransferase, Se/Te detoxification family; Region: TMPT_Se_Te; TIGR03840 385025000709 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 385025000710 prolyl-tRNA synthetase; Provisional; Region: PRK09194 385025000711 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 385025000712 dimer interface [polypeptide binding]; other site 385025000713 motif 1; other site 385025000714 active site 385025000715 motif 2; other site 385025000716 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 385025000717 putative deacylase active site [active] 385025000718 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 385025000719 active site 385025000720 motif 3; other site 385025000721 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 385025000722 anticodon binding site; other site 385025000723 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 385025000724 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 385025000725 Walker A motif; other site 385025000726 ATP binding site [chemical binding]; other site 385025000727 Walker B motif; other site 385025000728 arginine finger; other site 385025000729 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 385025000730 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 385025000731 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 385025000732 PBP superfamily domain; Region: PBP_like_2; pfam12849 385025000733 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 385025000734 Sodium Bile acid symporter family; Region: SBF; cl17470 385025000735 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 385025000736 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 385025000737 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 385025000738 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 385025000739 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 385025000740 Major Facilitator Superfamily; Region: MFS_1; pfam07690 385025000741 putative substrate translocation pore; other site 385025000742 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 385025000743 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 385025000744 dimer interface [polypeptide binding]; other site 385025000745 ssDNA binding site [nucleotide binding]; other site 385025000746 tetramer (dimer of dimers) interface [polypeptide binding]; other site 385025000747 short chain dehydrogenase; Provisional; Region: PRK09072 385025000748 classical (c) SDRs; Region: SDR_c; cd05233 385025000749 NAD(P) binding site [chemical binding]; other site 385025000750 active site 385025000751 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 385025000752 N-acetyl-D-glucosamine binding site [chemical binding]; other site 385025000753 catalytic residue [active] 385025000754 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 385025000755 N-acetyl-D-glucosamine binding site [chemical binding]; other site 385025000756 catalytic residue [active] 385025000757 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 385025000758 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025000759 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 385025000760 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025000761 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 385025000762 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 385025000763 catalytic site [active] 385025000764 putative active site [active] 385025000765 putative substrate binding site [chemical binding]; other site 385025000766 HRDC domain; Region: HRDC; pfam00570 385025000767 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 385025000768 hypothetical protein; Provisional; Region: PRK05255 385025000769 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 385025000770 transmembrane helices; other site 385025000771 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 385025000772 TrkA-C domain; Region: TrkA_C; pfam02080 385025000773 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 385025000774 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 385025000775 HSP70 interaction site [polypeptide binding]; other site 385025000776 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 385025000777 FMN-binding domain; Region: FMN_bind; pfam04205 385025000778 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 385025000779 oxidative damage protection protein; Provisional; Region: PRK05408 385025000780 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 385025000781 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 385025000782 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 385025000783 catalytic residues [active] 385025000784 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 385025000785 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 385025000786 putative ion selectivity filter; other site 385025000787 putative pore gating glutamate residue; other site 385025000788 putative H+/Cl- coupling transport residue; other site 385025000789 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 385025000790 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 385025000791 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 385025000792 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 385025000793 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 385025000794 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 385025000795 Opacity-associated protein A LysM-like domain; Region: OapA; pfam04225 385025000796 Peptidase family M23; Region: Peptidase_M23; pfam01551 385025000797 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 385025000798 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 385025000799 active site 385025000800 HIGH motif; other site 385025000801 dimer interface [polypeptide binding]; other site 385025000802 KMSKS motif; other site 385025000803 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 385025000804 RNA binding surface [nucleotide binding]; other site 385025000805 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 385025000806 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 385025000807 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 385025000808 substrate binding site [chemical binding]; other site 385025000809 ligand binding site [chemical binding]; other site 385025000810 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 385025000811 substrate binding site [chemical binding]; other site 385025000812 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 385025000813 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 385025000814 dimer interface [polypeptide binding]; other site 385025000815 active site 385025000816 citrylCoA binding site [chemical binding]; other site 385025000817 oxalacetate/citrate binding site [chemical binding]; other site 385025000818 coenzyme A binding site [chemical binding]; other site 385025000819 catalytic triad [active] 385025000820 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 385025000821 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 385025000822 tetramer interface [polypeptide binding]; other site 385025000823 active site 385025000824 Mg2+/Mn2+ binding site [ion binding]; other site 385025000825 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 385025000826 Propionyl-CoA synthetase (PrpE); Region: PrpE; cd05967 385025000827 acyl-activating enzyme (AAE) consensus motif; other site 385025000828 putative AMP binding site [chemical binding]; other site 385025000829 putative active site [active] 385025000830 putative CoA binding site [chemical binding]; other site 385025000831 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 385025000832 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 385025000833 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 385025000834 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 385025000835 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025000836 active site 385025000837 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 385025000838 acyl-CoA synthetase; Validated; Region: PRK08162 385025000839 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 385025000840 acyl-activating enzyme (AAE) consensus motif; other site 385025000841 putative active site [active] 385025000842 AMP binding site [chemical binding]; other site 385025000843 putative CoA binding site [chemical binding]; other site 385025000844 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 385025000845 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025000846 ligand binding site [chemical binding]; other site 385025000847 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 385025000848 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025000849 ligand binding site [chemical binding]; other site 385025000850 FOG: WD40 repeat [General function prediction only]; Region: COG2319 385025000851 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 385025000852 structural tetrad; other site 385025000853 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 385025000854 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cd00741 385025000855 nucleophilic elbow; other site 385025000856 catalytic triad; other site 385025000857 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 385025000858 siroheme synthase; Provisional; Region: cysG; PRK10637 385025000859 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 385025000860 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 385025000861 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 385025000862 active site 385025000863 SAM binding site [chemical binding]; other site 385025000864 homodimer interface [polypeptide binding]; other site 385025000865 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 385025000866 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 385025000867 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 385025000868 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 385025000869 putative active site [active] 385025000870 Ap4A binding site [chemical binding]; other site 385025000871 nudix motif; other site 385025000872 putative metal binding site [ion binding]; other site 385025000873 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 385025000874 active site 385025000875 metal binding site [ion binding]; metal-binding site 385025000876 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 385025000877 hexamer interface [polypeptide binding]; other site 385025000878 N-acetylglutamate synthase; Validated; Region: PRK05279 385025000879 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 385025000880 putative feedback inhibition sensing region; other site 385025000881 putative nucleotide binding site [chemical binding]; other site 385025000882 putative substrate binding site [chemical binding]; other site 385025000883 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 385025000884 Coenzyme A binding pocket [chemical binding]; other site 385025000885 acetylornithine deacetylase; Provisional; Region: PRK05111 385025000886 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 385025000887 metal binding site [ion binding]; metal-binding site 385025000888 putative dimer interface [polypeptide binding]; other site 385025000889 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 385025000890 Bacterial SH3 domain homologues; Region: SH3b; smart00287 385025000891 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 385025000892 ornithine carbamoyltransferase; Provisional; Region: PRK00779 385025000893 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 385025000894 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 385025000895 acetylornithine aminotransferase; Provisional; Region: PRK02627 385025000896 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 385025000897 inhibitor-cofactor binding pocket; inhibition site 385025000898 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025000899 catalytic residue [active] 385025000900 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 385025000901 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 385025000902 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 385025000903 putative GSH binding site [chemical binding]; other site 385025000904 catalytic residues [active] 385025000905 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 385025000906 DEDDh 3'-5' exonuclease domain of RNase T; Region: RNaseT; cd06134 385025000907 dimer interface [polypeptide binding]; other site 385025000908 catalytic site [active] 385025000909 putative active site [active] 385025000910 putative substrate binding site [chemical binding]; other site 385025000911 VacJ like lipoprotein; Region: VacJ; cl01073 385025000912 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 385025000913 active site 385025000914 substrate binding pocket [chemical binding]; other site 385025000915 dimer interface [polypeptide binding]; other site 385025000916 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 385025000917 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 385025000918 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 385025000919 dimer interface [polypeptide binding]; other site 385025000920 anticodon binding site; other site 385025000921 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 385025000922 homodimer interface [polypeptide binding]; other site 385025000923 motif 1; other site 385025000924 active site 385025000925 motif 2; other site 385025000926 GAD domain; Region: GAD; pfam02938 385025000927 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 385025000928 active site 385025000929 motif 3; other site 385025000930 quinolinate synthetase; Provisional; Region: PRK09375 385025000931 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 385025000932 TPR motif; other site 385025000933 binding surface 385025000934 Pilin (bacterial filament); Region: Pilin; pfam00114 385025000935 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 385025000936 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025000937 active site 385025000938 phosphorylation site [posttranslational modification] 385025000939 intermolecular recognition site; other site 385025000940 dimerization interface [polypeptide binding]; other site 385025000941 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 385025000942 Walker A motif; other site 385025000943 ATP binding site [chemical binding]; other site 385025000944 Walker B motif; other site 385025000945 arginine finger; other site 385025000946 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 385025000947 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 385025000948 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 385025000949 dimer interface [polypeptide binding]; other site 385025000950 phosphorylation site [posttranslational modification] 385025000951 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 385025000952 ATP binding site [chemical binding]; other site 385025000953 Mg2+ binding site [ion binding]; other site 385025000954 G-X-G motif; other site 385025000955 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 385025000956 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 385025000957 CoA-ligase; Region: Ligase_CoA; pfam00549 385025000958 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 385025000959 CoA binding domain; Region: CoA_binding; smart00881 385025000960 CoA-ligase; Region: Ligase_CoA; pfam00549 385025000961 NAD synthetase; Provisional; Region: PRK13981 385025000962 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 385025000963 multimer interface [polypeptide binding]; other site 385025000964 active site 385025000965 catalytic triad [active] 385025000966 protein interface 1 [polypeptide binding]; other site 385025000967 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 385025000968 homodimer interface [polypeptide binding]; other site 385025000969 NAD binding pocket [chemical binding]; other site 385025000970 ATP binding pocket [chemical binding]; other site 385025000971 Mg binding site [ion binding]; other site 385025000972 active-site loop [active] 385025000973 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 385025000974 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 385025000975 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 385025000976 RNA binding surface [nucleotide binding]; other site 385025000977 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 385025000978 active site 385025000979 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 385025000980 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 385025000981 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 385025000982 ZIP Zinc transporter; Region: Zip; pfam02535 385025000983 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 385025000984 Clp amino terminal domain; Region: Clp_N; pfam02861 385025000985 Clp amino terminal domain; Region: Clp_N; pfam02861 385025000986 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 385025000987 Walker A motif; other site 385025000988 ATP binding site [chemical binding]; other site 385025000989 Walker B motif; other site 385025000990 arginine finger; other site 385025000991 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 385025000992 Walker A motif; other site 385025000993 ATP binding site [chemical binding]; other site 385025000994 Walker B motif; other site 385025000995 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 385025000996 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 385025000997 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 385025000998 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025000999 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025001000 metal binding site [ion binding]; metal-binding site 385025001001 active site 385025001002 I-site; other site 385025001003 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 385025001004 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001005 active site 385025001006 phosphorylation site [posttranslational modification] 385025001007 intermolecular recognition site; other site 385025001008 dimerization interface [polypeptide binding]; other site 385025001009 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 385025001010 DNA binding site [nucleotide binding] 385025001011 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 385025001012 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 385025001013 dimer interface [polypeptide binding]; other site 385025001014 phosphorylation site [posttranslational modification] 385025001015 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 385025001016 ATP binding site [chemical binding]; other site 385025001017 Mg2+ binding site [ion binding]; other site 385025001018 G-X-G motif; other site 385025001019 PBP superfamily domain; Region: PBP_like_2; cl17296 385025001020 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 385025001021 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 385025001022 dimer interface [polypeptide binding]; other site 385025001023 conserved gate region; other site 385025001024 putative PBP binding loops; other site 385025001025 ABC-ATPase subunit interface; other site 385025001026 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 385025001027 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 385025001028 dimer interface [polypeptide binding]; other site 385025001029 conserved gate region; other site 385025001030 putative PBP binding loops; other site 385025001031 ABC-ATPase subunit interface; other site 385025001032 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 385025001033 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 385025001034 Walker A/P-loop; other site 385025001035 ATP binding site [chemical binding]; other site 385025001036 Q-loop/lid; other site 385025001037 ABC transporter signature motif; other site 385025001038 Walker B; other site 385025001039 D-loop; other site 385025001040 H-loop/switch region; other site 385025001041 transcriptional regulator PhoU; Provisional; Region: PRK11115 385025001042 PhoU domain; Region: PhoU; pfam01895 385025001043 PhoU domain; Region: PhoU; pfam01895 385025001044 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 385025001045 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 385025001046 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 385025001047 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 385025001048 flagellar motor protein MotB; Reviewed; Region: motB; PRK08944 385025001049 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 385025001050 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025001051 ligand binding site [chemical binding]; other site 385025001052 PilZ domain; Region: PilZ; pfam07238 385025001053 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 385025001054 Biotin operon repressor [Transcription]; Region: BirA; COG1654 385025001055 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 385025001056 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 385025001057 Type III pantothenate kinase; Region: Pan_kinase; cl17198 385025001058 Predicted membrane protein [Function unknown]; Region: COG2855 385025001059 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 385025001060 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 385025001061 Transcriptional regulator [Transcription]; Region: LysR; COG0583 385025001062 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 385025001063 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 385025001064 putative effector binding pocket; other site 385025001065 dimerization interface [polypeptide binding]; other site 385025001066 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 385025001067 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 385025001068 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 385025001069 PGAP1-like protein; Region: PGAP1; pfam07819 385025001070 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 385025001071 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025001072 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 385025001073 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 385025001074 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 385025001075 substrate binding site [chemical binding]; other site 385025001076 ligand binding site [chemical binding]; other site 385025001077 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 385025001078 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 385025001079 substrate binding site [chemical binding]; other site 385025001080 (R)-citramalate synthase; Provisional; Region: PRK09389 385025001081 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 385025001082 active site 385025001083 catalytic residues [active] 385025001084 metal binding site [ion binding]; metal-binding site 385025001085 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 385025001086 tartrate dehydrogenase; Region: TTC; TIGR02089 385025001087 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 385025001088 GTP-binding protein YchF; Reviewed; Region: PRK09601 385025001089 YchF GTPase; Region: YchF; cd01900 385025001090 G1 box; other site 385025001091 GTP/Mg2+ binding site [chemical binding]; other site 385025001092 Switch I region; other site 385025001093 G2 box; other site 385025001094 Switch II region; other site 385025001095 G3 box; other site 385025001096 G4 box; other site 385025001097 G5 box; other site 385025001098 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 385025001099 Domain of unknown function (DUF4405); Region: DUF4405; pfam14358 385025001100 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 385025001101 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 385025001102 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 385025001103 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 385025001104 active site 385025001105 metal binding site [ion binding]; metal-binding site 385025001106 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 385025001107 aromatic arch; other site 385025001108 DCoH dimer interaction site [polypeptide binding]; other site 385025001109 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 385025001110 DCoH tetramer interaction site [polypeptide binding]; other site 385025001111 substrate binding site [chemical binding]; other site 385025001112 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 385025001113 DNA-binding site [nucleotide binding]; DNA binding site 385025001114 RNA-binding motif; other site 385025001115 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 385025001116 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 385025001117 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 385025001118 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 385025001119 active site 385025001120 substrate binding site [chemical binding]; other site 385025001121 FMN binding site [chemical binding]; other site 385025001122 putative catalytic residues [active] 385025001123 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 385025001124 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 385025001125 N-terminal plug; other site 385025001126 ligand-binding site [chemical binding]; other site 385025001127 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 385025001128 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 385025001129 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 385025001130 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 385025001131 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 385025001132 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 385025001133 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 385025001134 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 385025001135 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 385025001136 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 385025001137 cell division protein MraZ; Reviewed; Region: PRK00326 385025001138 MraZ protein; Region: MraZ; pfam02381 385025001139 MraZ protein; Region: MraZ; pfam02381 385025001140 MraW methylase family; Region: Methyltransf_5; cl17771 385025001141 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 385025001142 Cell division protein FtsL; Region: FtsL; pfam04999 385025001143 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 385025001144 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 385025001145 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 385025001146 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 385025001147 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 385025001148 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 385025001149 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 385025001150 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 385025001151 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 385025001152 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 385025001153 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 385025001154 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 385025001155 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 385025001156 Mg++ binding site [ion binding]; other site 385025001157 putative catalytic motif [active] 385025001158 putative substrate binding site [chemical binding]; other site 385025001159 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03803 385025001160 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 385025001161 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 385025001162 cell division protein FtsW; Region: ftsW; TIGR02614 385025001163 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 385025001164 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 385025001165 active site 385025001166 homodimer interface [polypeptide binding]; other site 385025001167 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 385025001168 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 385025001169 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 385025001170 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 385025001171 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 385025001172 FAD binding domain; Region: FAD_binding_4; pfam01565 385025001173 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 385025001174 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 385025001175 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 385025001176 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025001177 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 385025001178 Cell division protein FtsQ; Region: FtsQ; pfam03799 385025001179 cell division protein FtsA; Region: ftsA; TIGR01174 385025001180 Cell division protein FtsA; Region: FtsA; smart00842 385025001181 Cell division protein FtsA; Region: FtsA; pfam14450 385025001182 cell division protein FtsZ; Validated; Region: PRK09330 385025001183 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 385025001184 nucleotide binding site [chemical binding]; other site 385025001185 SulA interaction site; other site 385025001186 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 385025001187 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 385025001188 Protein of unknown function (DUF721); Region: DUF721; pfam05258 385025001189 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 385025001190 Peptidase family M23; Region: Peptidase_M23; pfam01551 385025001191 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 385025001192 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 385025001193 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family; Region: SWIM_PBPRA1643; TIGR04102 385025001194 SEC-C motif; Region: SEC-C; pfam02810 385025001195 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 385025001196 heterotetramer interface [polypeptide binding]; other site 385025001197 active site pocket [active] 385025001198 cleavage site 385025001199 hypothetical protein; Provisional; Region: PRK08999 385025001200 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 385025001201 active site 385025001202 8-oxo-dGMP binding site [chemical binding]; other site 385025001203 nudix motif; other site 385025001204 metal binding site [ion binding]; metal-binding site 385025001205 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 385025001206 thiamine phosphate binding site [chemical binding]; other site 385025001207 active site 385025001208 pyrophosphate binding site [ion binding]; other site 385025001209 Domain of unknown function (DUF329); Region: DUF329; pfam03884 385025001210 hypothetical protein; Provisional; Region: PRK05287 385025001211 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 385025001212 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 385025001213 ATP-binding [chemical binding]; other site 385025001214 CoA-binding site [chemical binding]; other site 385025001215 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 385025001216 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 385025001217 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 385025001218 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 385025001219 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 385025001220 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 385025001221 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 385025001222 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 385025001223 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 385025001224 Walker A motif; other site 385025001225 ATP binding site [chemical binding]; other site 385025001226 Walker B motif; other site 385025001227 putative glycosyl transferase; Provisional; Region: PRK10063 385025001228 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 385025001229 metal-binding site 385025001230 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 385025001231 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 385025001232 This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis; Region: GT1_wcfI_like; cd03825 385025001233 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 385025001234 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 385025001235 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 385025001236 NADP-binding site; other site 385025001237 homotetramer interface [polypeptide binding]; other site 385025001238 substrate binding site [chemical binding]; other site 385025001239 homodimer interface [polypeptide binding]; other site 385025001240 active site 385025001241 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 385025001242 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 385025001243 NADP binding site [chemical binding]; other site 385025001244 active site 385025001245 putative substrate binding site [chemical binding]; other site 385025001246 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 385025001247 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 385025001248 active site 385025001249 Methyltransferase domain; Region: Methyltransf_31; pfam13847 385025001250 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 385025001251 S-adenosylmethionine binding site [chemical binding]; other site 385025001252 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 385025001253 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 385025001254 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 385025001255 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 385025001256 Ligand binding site; other site 385025001257 Putative Catalytic site; other site 385025001258 DXD motif; other site 385025001259 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 385025001260 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 385025001261 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 385025001262 HIGH motif; other site 385025001263 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 385025001264 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 385025001265 active site 385025001266 KMSKS motif; other site 385025001267 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 385025001268 tRNA binding surface [nucleotide binding]; other site 385025001269 anticodon binding site; other site 385025001270 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 385025001271 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 385025001272 multifunctional aminopeptidase A; Provisional; Region: PRK00913 385025001273 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 385025001274 interface (dimer of trimers) [polypeptide binding]; other site 385025001275 Substrate-binding/catalytic site; other site 385025001276 Zn-binding sites [ion binding]; other site 385025001277 Predicted permeases [General function prediction only]; Region: COG0795 385025001278 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 385025001279 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 385025001280 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 385025001281 RDD family; Region: RDD; pfam06271 385025001282 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 385025001283 Peptidase family M48; Region: Peptidase_M48; cl12018 385025001284 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 385025001285 binding surface 385025001286 TPR motif; other site 385025001287 sulfur relay protein TusD/DsrE; Region: sulf_tusD_dsrE; TIGR03012 385025001288 DsrE/DsrF-like family; Region: DrsE; cl00672 385025001289 DsrH like protein; Region: DsrH; pfam04077 385025001290 Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]; Region: DsrC; COG2920 385025001291 DsrC like protein; Region: DsrC; pfam04358 385025001292 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 385025001293 RNA binding surface [nucleotide binding]; other site 385025001294 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 385025001295 Cytochrome c553 [Energy production and conversion]; Region: COG2863 385025001296 Cytochrome c553 [Energy production and conversion]; Region: COG2863 385025001297 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 385025001298 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 385025001299 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 385025001300 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 385025001301 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 385025001302 TrkA-N domain; Region: TrkA_N; pfam02254 385025001303 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 385025001304 TrkA-N domain; Region: TrkA_N; pfam02254 385025001305 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025001306 beta-ketothiolase; Provisional; Region: PRK09051 385025001307 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 385025001308 dimer interface [polypeptide binding]; other site 385025001309 active site 385025001310 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 385025001311 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 385025001312 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 385025001313 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 385025001314 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 385025001315 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 385025001316 active site residue [active] 385025001317 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 385025001318 tetramerization interface [polypeptide binding]; other site 385025001319 active site 385025001320 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 385025001321 Mechanosensitive ion channel; Region: MS_channel; pfam00924 385025001322 pantoate--beta-alanine ligase; Region: panC; TIGR00018 385025001323 Pantoate-beta-alanine ligase; Region: PanC; cd00560 385025001324 active site 385025001325 ATP-binding site [chemical binding]; other site 385025001326 pantoate-binding site; other site 385025001327 HXXH motif; other site 385025001328 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 385025001329 oligomerization interface [polypeptide binding]; other site 385025001330 active site 385025001331 metal binding site [ion binding]; metal-binding site 385025001332 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 385025001333 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 385025001334 Substrate-binding site [chemical binding]; other site 385025001335 Substrate specificity [chemical binding]; other site 385025001336 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 385025001337 catalytic center binding site [active] 385025001338 ATP binding site [chemical binding]; other site 385025001339 poly(A) polymerase; Region: pcnB; TIGR01942 385025001340 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 385025001341 active site 385025001342 NTP binding site [chemical binding]; other site 385025001343 metal binding triad [ion binding]; metal-binding site 385025001344 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 385025001345 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 385025001346 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 385025001347 active site 385025001348 EamA-like transporter family; Region: EamA; pfam00892 385025001349 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 385025001350 EamA-like transporter family; Region: EamA; pfam00892 385025001351 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 385025001352 Cation efflux family; Region: Cation_efflux; pfam01545 385025001353 Domain of unknown function DUF20; Region: UPF0118; pfam01594 385025001354 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 385025001355 outer membrane lipoprotein; Provisional; Region: PRK11023 385025001356 BON domain; Region: BON; pfam04972 385025001357 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 385025001358 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 385025001359 catalytic triad [active] 385025001360 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 385025001361 dihydrodipicolinate synthase; Region: dapA; TIGR00674 385025001362 dimer interface [polypeptide binding]; other site 385025001363 active site 385025001364 catalytic residue [active] 385025001365 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 385025001366 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 385025001367 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 385025001368 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 385025001369 dimerization interface [polypeptide binding]; other site 385025001370 ATP binding site [chemical binding]; other site 385025001371 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 385025001372 dimerization interface [polypeptide binding]; other site 385025001373 ATP binding site [chemical binding]; other site 385025001374 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 385025001375 putative active site [active] 385025001376 catalytic triad [active] 385025001377 Short C-terminal domain; Region: SHOCT; pfam09851 385025001378 PAS fold; Region: PAS; pfam00989 385025001379 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 385025001380 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025001381 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025001382 metal binding site [ion binding]; metal-binding site 385025001383 active site 385025001384 I-site; other site 385025001385 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3012 385025001386 SEC-C motif; Region: SEC-C; pfam02810 385025001387 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 385025001388 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 385025001389 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 385025001390 benzoate transport; Region: 2A0115; TIGR00895 385025001391 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 385025001392 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 385025001393 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 385025001394 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 385025001395 putative dimer interface [polypeptide binding]; other site 385025001396 TMAO/DMSO reductase; Reviewed; Region: PRK05363 385025001397 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 385025001398 Moco binding site; other site 385025001399 metal coordination site [ion binding]; other site 385025001400 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 385025001401 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 385025001402 dimerization interface [polypeptide binding]; other site 385025001403 PAS domain S-box; Region: sensory_box; TIGR00229 385025001404 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 385025001405 putative active site [active] 385025001406 heme pocket [chemical binding]; other site 385025001407 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025001408 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 385025001409 dimer interface [polypeptide binding]; other site 385025001410 phosphorylation site [posttranslational modification] 385025001411 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 385025001412 ATP binding site [chemical binding]; other site 385025001413 Mg2+ binding site [ion binding]; other site 385025001414 G-X-G motif; other site 385025001415 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 385025001416 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001417 active site 385025001418 phosphorylation site [posttranslational modification] 385025001419 intermolecular recognition site; other site 385025001420 dimerization interface [polypeptide binding]; other site 385025001421 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 385025001422 Zn2+ binding site [ion binding]; other site 385025001423 Mg2+ binding site [ion binding]; other site 385025001424 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 385025001425 metal binding site 2 [ion binding]; metal-binding site 385025001426 putative DNA binding helix; other site 385025001427 metal binding site 1 [ion binding]; metal-binding site 385025001428 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 385025001429 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; cl17304 385025001430 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 385025001431 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 385025001432 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 385025001433 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 385025001434 substrate binding site [chemical binding]; other site 385025001435 catalytic Zn binding site [ion binding]; other site 385025001436 NAD binding site [chemical binding]; other site 385025001437 structural Zn binding site [ion binding]; other site 385025001438 dimer interface [polypeptide binding]; other site 385025001439 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 385025001440 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 385025001441 FeS/SAM binding site; other site 385025001442 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 385025001443 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; cl05126 385025001444 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 385025001445 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 385025001446 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 385025001447 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 385025001448 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 385025001449 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 385025001450 ATP binding site [chemical binding]; other site 385025001451 substrate interface [chemical binding]; other site 385025001452 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 385025001453 oligomerisation interface [polypeptide binding]; other site 385025001454 mobile loop; other site 385025001455 roof hairpin; other site 385025001456 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 385025001457 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 385025001458 ring oligomerisation interface [polypeptide binding]; other site 385025001459 ATP/Mg binding site [chemical binding]; other site 385025001460 stacking interactions; other site 385025001461 hinge regions; other site 385025001462 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 385025001463 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 385025001464 FMN binding site [chemical binding]; other site 385025001465 active site 385025001466 substrate binding site [chemical binding]; other site 385025001467 catalytic residue [active] 385025001468 hypothetical protein; Validated; Region: PRK00110 385025001469 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 385025001470 active site 385025001471 putative DNA-binding cleft [nucleotide binding]; other site 385025001472 dimer interface [polypeptide binding]; other site 385025001473 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 385025001474 RuvA N terminal domain; Region: RuvA_N; pfam01330 385025001475 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 385025001476 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 385025001477 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 385025001478 Walker A motif; other site 385025001479 ATP binding site [chemical binding]; other site 385025001480 Walker B motif; other site 385025001481 arginine finger; other site 385025001482 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 385025001483 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 385025001484 active site 385025001485 TolQ protein; Region: tolQ; TIGR02796 385025001486 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 385025001487 TolR protein; Region: tolR; TIGR02801 385025001488 TolA protein; Region: tolA_full; TIGR02794 385025001489 TolA protein; Region: tolA_full; TIGR02794 385025001490 TonB C terminal; Region: TonB_2; pfam13103 385025001491 translocation protein TolB; Provisional; Region: tolB; PRK04922 385025001492 TolB amino-terminal domain; Region: TolB_N; pfam04052 385025001493 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 385025001494 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 385025001495 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025001496 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 385025001497 ligand binding site [chemical binding]; other site 385025001498 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 385025001499 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 385025001500 TPR motif; other site 385025001501 binding surface 385025001502 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Region: rSAM_QueE_gams; TIGR04349 385025001503 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 385025001504 FeS/SAM binding site; other site 385025001505 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 385025001506 Ligand Binding Site [chemical binding]; other site 385025001507 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 385025001508 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 385025001509 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 385025001510 putative cation:proton antiport protein; Provisional; Region: PRK10669 385025001511 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 385025001512 TrkA-N domain; Region: TrkA_N; pfam02254 385025001513 Response regulator receiver domain; Region: Response_reg; pfam00072 385025001514 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001515 active site 385025001516 phosphorylation site [posttranslational modification] 385025001517 intermolecular recognition site; other site 385025001518 dimerization interface [polypeptide binding]; other site 385025001519 PAS domain S-box; Region: sensory_box; TIGR00229 385025001520 PAS domain; Region: PAS_8; pfam13188 385025001521 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 385025001522 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 385025001523 PAS domain; Region: PAS_9; pfam13426 385025001524 putative active site [active] 385025001525 heme pocket [chemical binding]; other site 385025001526 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025001527 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025001528 metal binding site [ion binding]; metal-binding site 385025001529 active site 385025001530 I-site; other site 385025001531 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 385025001532 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 385025001533 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001534 active site 385025001535 phosphorylation site [posttranslational modification] 385025001536 intermolecular recognition site; other site 385025001537 dimerization interface [polypeptide binding]; other site 385025001538 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 385025001539 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001540 active site 385025001541 phosphorylation site [posttranslational modification] 385025001542 intermolecular recognition site; other site 385025001543 dimerization interface [polypeptide binding]; other site 385025001544 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 385025001545 dimer interface [polypeptide binding]; other site 385025001546 phosphorylation site [posttranslational modification] 385025001547 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 385025001548 ATP binding site [chemical binding]; other site 385025001549 Mg2+ binding site [ion binding]; other site 385025001550 G-X-G motif; other site 385025001551 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001552 Response regulator receiver domain; Region: Response_reg; pfam00072 385025001553 active site 385025001554 phosphorylation site [posttranslational modification] 385025001555 intermolecular recognition site; other site 385025001556 dimerization interface [polypeptide binding]; other site 385025001557 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 385025001558 GAF domain; Region: GAF; pfam01590 385025001559 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 385025001560 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 385025001561 putative active site [active] 385025001562 heme pocket [chemical binding]; other site 385025001563 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 385025001564 dimer interface [polypeptide binding]; other site 385025001565 phosphorylation site [posttranslational modification] 385025001566 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 385025001567 ATP binding site [chemical binding]; other site 385025001568 Mg2+ binding site [ion binding]; other site 385025001569 G-X-G motif; other site 385025001570 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 385025001571 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001572 active site 385025001573 phosphorylation site [posttranslational modification] 385025001574 intermolecular recognition site; other site 385025001575 dimerization interface [polypeptide binding]; other site 385025001576 Response regulator receiver domain; Region: Response_reg; pfam00072 385025001577 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025001578 active site 385025001579 phosphorylation site [posttranslational modification] 385025001580 intermolecular recognition site; other site 385025001581 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 385025001582 active site residue [active] 385025001583 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 385025001584 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 385025001585 NAD(P) binding site [chemical binding]; other site 385025001586 catalytic residues [active] 385025001587 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 385025001588 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 385025001589 NAD(P) binding site [chemical binding]; other site 385025001590 catalytic residues [active] 385025001591 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 385025001592 FAD binding domain; Region: FAD_binding_4; pfam01565 385025001593 Protein of unknown function (DUF1062); Region: DUF1062; cl01786 385025001594 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; pfam01977 385025001595 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 385025001596 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 385025001597 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 385025001598 FAD binding domain; Region: FAD_binding_4; pfam01565 385025001599 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 385025001600 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 385025001601 Flavoprotein; Region: Flavoprotein; pfam02441 385025001602 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 385025001603 Helix-turn-helix domain; Region: HTH_18; pfam12833 385025001604 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 385025001605 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 385025001606 Fatty acid desaturase; Region: FA_desaturase; pfam00487 385025001607 putative di-iron ligands [ion binding]; other site 385025001608 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 385025001609 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 385025001610 iron-sulfur cluster [ion binding]; other site 385025001611 [2Fe-2S] cluster binding site [ion binding]; other site 385025001612 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 385025001613 putative alpha subunit interface [polypeptide binding]; other site 385025001614 putative active site [active] 385025001615 putative substrate binding site [chemical binding]; other site 385025001616 Fe binding site [ion binding]; other site 385025001617 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025001618 inter-subunit interface; other site 385025001619 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 385025001620 FAD binding pocket [chemical binding]; other site 385025001621 conserved FAD binding motif [chemical binding]; other site 385025001622 phosphate binding motif [ion binding]; other site 385025001623 beta-alpha-beta structure motif; other site 385025001624 NAD binding pocket [chemical binding]; other site 385025001625 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 385025001626 catalytic loop [active] 385025001627 iron binding site [ion binding]; other site 385025001628 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 385025001629 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 385025001630 tetramer interface [polypeptide binding]; other site 385025001631 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 385025001632 active site 385025001633 metal binding site [ion binding]; metal-binding site 385025001634 Domain of unknown function (DUF336); Region: DUF336; pfam03928 385025001635 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 385025001636 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 385025001637 NAD binding site [chemical binding]; other site 385025001638 catalytic residues [active] 385025001639 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 385025001640 acetaldehyde dehydrogenase; Validated; Region: PRK08300 385025001641 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 385025001642 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 385025001643 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 385025001644 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 385025001645 active site 385025001646 catalytic residues [active] 385025001647 metal binding site [ion binding]; metal-binding site 385025001648 DmpG-like communication domain; Region: DmpG_comm; pfam07836 385025001649 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 385025001650 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 385025001651 active site 1 [active] 385025001652 dimer interface [polypeptide binding]; other site 385025001653 hexamer interface [polypeptide binding]; other site 385025001654 active site 2 [active] 385025001655 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 385025001656 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 385025001657 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 385025001658 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025001659 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 385025001660 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 385025001661 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 385025001662 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 385025001663 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 385025001664 active site 1 [active] 385025001665 dimer interface [polypeptide binding]; other site 385025001666 active site 2 [active] 385025001667 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 385025001668 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 385025001669 dimer interface [polypeptide binding]; other site 385025001670 active site 385025001671 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 385025001672 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 385025001673 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 385025001674 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 385025001675 Malic enzyme, N-terminal domain; Region: malic; pfam00390 385025001676 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 385025001677 putative NAD(P) binding site [chemical binding]; other site 385025001678 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 385025001679 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 385025001680 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025001681 Walker A/P-loop; other site 385025001682 ATP binding site [chemical binding]; other site 385025001683 Q-loop/lid; other site 385025001684 ABC transporter signature motif; other site 385025001685 Walker B; other site 385025001686 D-loop; other site 385025001687 H-loop/switch region; other site 385025001688 inner membrane transport permease; Provisional; Region: PRK15066 385025001689 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 385025001690 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 385025001691 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 385025001692 E3 interaction surface; other site 385025001693 lipoyl attachment site [posttranslational modification]; other site 385025001694 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 385025001695 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 385025001696 Na(+)-translocating NADH-quinone reductase subunit C; Provisional; Region: PRK05346 385025001697 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 385025001698 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 385025001699 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 385025001700 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 385025001701 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 385025001702 catalytic loop [active] 385025001703 iron binding site [ion binding]; other site 385025001704 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 385025001705 FAD binding pocket [chemical binding]; other site 385025001706 FAD binding motif [chemical binding]; other site 385025001707 phosphate binding motif [ion binding]; other site 385025001708 beta-alpha-beta structure motif; other site 385025001709 NAD binding pocket [chemical binding]; other site 385025001710 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 385025001711 ApbE family; Region: ApbE; pfam02424 385025001712 Protein of unknown function (DUF539); Region: DUF539; cl01129 385025001713 FOG: CBS domain [General function prediction only]; Region: COG0517 385025001714 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_16; cd04629 385025001715 exonuclease I; Provisional; Region: sbcB; PRK11779 385025001716 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 385025001717 active site 385025001718 catalytic site [active] 385025001719 substrate binding site [chemical binding]; other site 385025001720 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 385025001721 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 385025001722 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025001723 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 385025001724 Walker A/P-loop; other site 385025001725 ATP binding site [chemical binding]; other site 385025001726 Q-loop/lid; other site 385025001727 ABC transporter signature motif; other site 385025001728 Walker B; other site 385025001729 D-loop; other site 385025001730 H-loop/switch region; other site 385025001731 Protein of unknown function (DUF1043); Region: DUF1043; cl11473 385025001732 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 385025001733 EamA-like transporter family; Region: EamA; pfam00892 385025001734 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 385025001735 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 385025001736 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 385025001737 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 385025001738 ATPase MipZ; Region: MipZ; pfam09140 385025001739 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 385025001740 P-loop; other site 385025001741 Magnesium ion binding site [ion binding]; other site 385025001742 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 385025001743 Magnesium ion binding site [ion binding]; other site 385025001744 hypothetical protein; Provisional; Region: PRK04860 385025001745 SprT homologues; Region: SprT; cl01182 385025001746 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 385025001747 GIY-YIG motif/motif A; other site 385025001748 putative active site [active] 385025001749 putative metal binding site [ion binding]; other site 385025001750 thioredoxin 2; Provisional; Region: PRK10996 385025001751 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 385025001752 catalytic residues [active] 385025001753 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 385025001754 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 385025001755 dimerization interface [polypeptide binding]; other site 385025001756 domain crossover interface; other site 385025001757 redox-dependent activation switch; other site 385025001758 methionine sulfoxide reductase A; Provisional; Region: PRK00058 385025001759 PAS domain; Region: PAS; smart00091 385025001760 PAS domain; Region: PAS_9; pfam13426 385025001761 putative active site [active] 385025001762 heme pocket [chemical binding]; other site 385025001763 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 385025001764 PAS domain; Region: PAS_9; pfam13426 385025001765 putative active site [active] 385025001766 heme pocket [chemical binding]; other site 385025001767 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025001768 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025001769 metal binding site [ion binding]; metal-binding site 385025001770 active site 385025001771 I-site; other site 385025001772 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 385025001773 ligand binding site [chemical binding]; other site 385025001774 active site 385025001775 UGI interface [polypeptide binding]; other site 385025001776 catalytic site [active] 385025001777 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 385025001778 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 385025001779 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 385025001780 Ligand Binding Site [chemical binding]; other site 385025001781 glycerol-3-phosphate O-acyltransferase; Region: plsB; TIGR03703 385025001782 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like; Region: LPLAT_DHAPAT-like; cd07993 385025001783 putative acyl-acceptor binding pocket; other site 385025001784 Uncharacterized homolog of PrgY (pheromone shutdown protein) [Function unknown]; Region: COG1916 385025001785 Domain of unknown function (DUF1853); Region: DUF1853; pfam08907 385025001786 Uncharacterized protein family (UPF0149); Region: UPF0149; pfam03695 385025001787 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 385025001788 amino acid carrier protein; Region: agcS; TIGR00835 385025001789 Protein of unknown function (DUF1249); Region: DUF1249; cl01223 385025001790 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 385025001791 active site 385025001792 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 385025001793 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 385025001794 NAD(P) binding site [chemical binding]; other site 385025001795 homotetramer interface [polypeptide binding]; other site 385025001796 homodimer interface [polypeptide binding]; other site 385025001797 active site 385025001798 acetyl-CoA synthetase; Provisional; Region: PRK00174 385025001799 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 385025001800 active site 385025001801 CoA binding site [chemical binding]; other site 385025001802 acyl-activating enzyme (AAE) consensus motif; other site 385025001803 AMP binding site [chemical binding]; other site 385025001804 acetate binding site [chemical binding]; other site 385025001805 glyceraldehyde-3-phosphate dehydrogenase; Reviewed; Region: PRK08289 385025001806 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 385025001807 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 385025001808 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 385025001809 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 385025001810 substrate binding pocket [chemical binding]; other site 385025001811 chain length determination region; other site 385025001812 substrate-Mg2+ binding site; other site 385025001813 catalytic residues [active] 385025001814 aspartate-rich region 1; other site 385025001815 active site lid residues [active] 385025001816 aspartate-rich region 2; other site 385025001817 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 385025001818 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 385025001819 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 385025001820 Obg family GTPase CgtA; Region: Obg_CgtA; TIGR02729 385025001821 GTP1/OBG; Region: GTP1_OBG; pfam01018 385025001822 Obg GTPase; Region: Obg; cd01898 385025001823 G1 box; other site 385025001824 GTP/Mg2+ binding site [chemical binding]; other site 385025001825 Switch I region; other site 385025001826 G2 box; other site 385025001827 G3 box; other site 385025001828 Switch II region; other site 385025001829 G4 box; other site 385025001830 G5 box; other site 385025001831 gamma-glutamyl kinase; Provisional; Region: PRK05429 385025001832 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 385025001833 nucleotide binding site [chemical binding]; other site 385025001834 homotetrameric interface [polypeptide binding]; other site 385025001835 putative phosphate binding site [ion binding]; other site 385025001836 putative allosteric binding site; other site 385025001837 PUA domain; Region: PUA; pfam01472 385025001838 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 385025001839 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 385025001840 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 385025001841 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 385025001842 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 385025001843 active site 385025001844 Riboflavin kinase; Region: Flavokinase; smart00904 385025001845 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 385025001846 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 385025001847 active site 385025001848 HIGH motif; other site 385025001849 nucleotide binding site [chemical binding]; other site 385025001850 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 385025001851 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 385025001852 active site 385025001853 KMSKS motif; other site 385025001854 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 385025001855 tRNA binding surface [nucleotide binding]; other site 385025001856 anticodon binding site; other site 385025001857 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 385025001858 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 385025001859 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 385025001860 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 385025001861 amidase catalytic site [active] 385025001862 Zn binding residues [ion binding]; other site 385025001863 substrate binding site [chemical binding]; other site 385025001864 Protein of unknown function (DUF1631); Region: DUF1631; pfam07793 385025001865 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05742 385025001866 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 385025001867 dimerization interface [polypeptide binding]; other site 385025001868 active site 385025001869 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 385025001870 Ligand Binding Site [chemical binding]; other site 385025001871 FAD binding domain; Region: FAD_binding_4; pfam01565 385025001872 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 385025001873 outer membrane lipoprotein; Provisional; Region: PRK11023 385025001874 BON domain; Region: BON; pfam04972 385025001875 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 385025001876 dimer interface [polypeptide binding]; other site 385025001877 active site 385025001878 hypothetical protein; Reviewed; Region: PRK12497 385025001879 LppC putative lipoprotein; Region: LppC; pfam04348 385025001880 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 385025001881 putative ligand binding site [chemical binding]; other site 385025001882 Predicted methyltransferases [General function prediction only]; Region: COG0313 385025001883 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 385025001884 putative SAM binding site [chemical binding]; other site 385025001885 putative homodimer interface [polypeptide binding]; other site 385025001886 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 385025001887 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 385025001888 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 385025001889 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 385025001890 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 385025001891 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025001892 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 385025001893 Protein export membrane protein; Region: SecD_SecF; cl14618 385025001894 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 385025001895 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 385025001896 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 385025001897 active site clefts [active] 385025001898 zinc binding site [ion binding]; other site 385025001899 dimer interface [polypeptide binding]; other site 385025001900 Dodecin; Region: Dodecin; pfam07311 385025001901 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 385025001902 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 385025001903 HSP70 interaction site [polypeptide binding]; other site 385025001904 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 385025001905 substrate binding site [polypeptide binding]; other site 385025001906 dimer interface [polypeptide binding]; other site 385025001907 MerR HTH family regulatory protein; Region: MerR_2; pfam13591 385025001908 chaperone-modulator protein CbpM; Provisional; Region: PRK10265 385025001909 Protein of unknown function, DUF393; Region: DUF393; pfam04134 385025001910 Uncharacterized conserved protein [Function unknown]; Region: COG1432 385025001911 LabA_like proteins; Region: LabA_like/DUF88; cl10034 385025001912 putative metal binding site [ion binding]; other site 385025001913 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 385025001914 active site 385025001915 oxyanion hole [active] 385025001916 switch loop; other site 385025001917 catalytic triad [active] 385025001918 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 385025001919 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 385025001920 Walker A/P-loop; other site 385025001921 ATP binding site [chemical binding]; other site 385025001922 Q-loop/lid; other site 385025001923 ABC transporter signature motif; other site 385025001924 Walker B; other site 385025001925 D-loop; other site 385025001926 H-loop/switch region; other site 385025001927 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 385025001928 FtsX-like permease family; Region: FtsX; pfam02687 385025001929 Uncharacterized protein conserved in bacteria (DUF2058); Region: DUF2058; pfam09831 385025001930 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 385025001931 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 385025001932 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025001933 Walker A/P-loop; other site 385025001934 ATP binding site [chemical binding]; other site 385025001935 Q-loop/lid; other site 385025001936 ABC transporter signature motif; other site 385025001937 Walker B; other site 385025001938 D-loop; other site 385025001939 H-loop/switch region; other site 385025001940 ABC transporter; Region: ABC_tran_2; pfam12848 385025001941 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025001942 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 385025001943 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 385025001944 ATP binding site [chemical binding]; other site 385025001945 Mg++ binding site [ion binding]; other site 385025001946 motif III; other site 385025001947 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 385025001948 nucleotide binding region [chemical binding]; other site 385025001949 ATP-binding site [chemical binding]; other site 385025001950 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 385025001951 DNA-binding site [nucleotide binding]; DNA binding site 385025001952 RNA-binding motif; other site 385025001953 Predicted permeases [General function prediction only]; Region: COG0679 385025001954 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 385025001955 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 385025001956 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 385025001957 active site 385025001958 multimer interface [polypeptide binding]; other site 385025001959 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 385025001960 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 385025001961 FeS/SAM binding site; other site 385025001962 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 385025001963 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 385025001964 binding surface 385025001965 TPR motif; other site 385025001966 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 385025001967 binding surface 385025001968 TPR motif; other site 385025001969 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 385025001970 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 385025001971 dimer interface [polypeptide binding]; other site 385025001972 motif 1; other site 385025001973 active site 385025001974 motif 2; other site 385025001975 motif 3; other site 385025001976 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 385025001977 anticodon binding site; other site 385025001978 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 385025001979 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 385025001980 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 385025001981 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 385025001982 Trp docking motif [polypeptide binding]; other site 385025001983 active site 385025001984 GTP-binding protein Der; Reviewed; Region: PRK00093 385025001985 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 385025001986 G1 box; other site 385025001987 GTP/Mg2+ binding site [chemical binding]; other site 385025001988 Switch I region; other site 385025001989 G2 box; other site 385025001990 Switch II region; other site 385025001991 G3 box; other site 385025001992 G4 box; other site 385025001993 G5 box; other site 385025001994 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 385025001995 G1 box; other site 385025001996 GTP/Mg2+ binding site [chemical binding]; other site 385025001997 Switch I region; other site 385025001998 G2 box; other site 385025001999 G3 box; other site 385025002000 Switch II region; other site 385025002001 G4 box; other site 385025002002 G5 box; other site 385025002003 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 385025002004 Peptidase family M23; Region: Peptidase_M23; pfam01551 385025002005 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 385025002006 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 385025002007 generic binding surface I; other site 385025002008 generic binding surface II; other site 385025002009 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 385025002010 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 385025002011 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 385025002012 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 385025002013 active site 385025002014 GMP synthase; Reviewed; Region: guaA; PRK00074 385025002015 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 385025002016 AMP/PPi binding site [chemical binding]; other site 385025002017 candidate oxyanion hole; other site 385025002018 catalytic triad [active] 385025002019 potential glutamine specificity residues [chemical binding]; other site 385025002020 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 385025002021 ATP Binding subdomain [chemical binding]; other site 385025002022 Ligand Binding sites [chemical binding]; other site 385025002023 Dimerization subdomain; other site 385025002024 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 385025002025 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 385025002026 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025002027 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 385025002028 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 385025002029 Walker A/P-loop; other site 385025002030 ATP binding site [chemical binding]; other site 385025002031 Q-loop/lid; other site 385025002032 ABC transporter signature motif; other site 385025002033 Walker B; other site 385025002034 D-loop; other site 385025002035 H-loop/switch region; other site 385025002036 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 385025002037 Walker A/P-loop; other site 385025002038 ATP binding site [chemical binding]; other site 385025002039 Q-loop/lid; other site 385025002040 ABC transporter signature motif; other site 385025002041 Walker B; other site 385025002042 D-loop; other site 385025002043 H-loop/switch region; other site 385025002044 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 385025002045 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 385025002046 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 385025002047 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 385025002048 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 385025002049 PAS domain S-box; Region: sensory_box; TIGR00229 385025002050 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 385025002051 putative active site [active] 385025002052 heme pocket [chemical binding]; other site 385025002053 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025002054 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025002055 metal binding site [ion binding]; metal-binding site 385025002056 active site 385025002057 I-site; other site 385025002058 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 385025002059 nucleoside/Zn binding site; other site 385025002060 dimer interface [polypeptide binding]; other site 385025002061 catalytic motif [active] 385025002062 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 385025002063 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 385025002064 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 385025002065 membrane-bound lytic transglycosylase F; Provisional; Region: PRK10859 385025002066 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 385025002067 substrate binding pocket [chemical binding]; other site 385025002068 membrane-bound complex binding site; other site 385025002069 hinge residues; other site 385025002070 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 385025002071 N-acetyl-D-glucosamine binding site [chemical binding]; other site 385025002072 catalytic residue [active] 385025002073 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 385025002074 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 385025002075 intersubunit interface [polypeptide binding]; other site 385025002076 active site 385025002077 zinc binding site [ion binding]; other site 385025002078 Na+ binding site [ion binding]; other site 385025002079 Phasin protein; Region: Phasin_2; cl11491 385025002080 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 385025002081 active site 385025002082 dimer interface [polypeptide binding]; other site 385025002083 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 385025002084 dimerization interface [polypeptide binding]; other site 385025002085 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 385025002086 dimer interface [polypeptide binding]; other site 385025002087 phosphorylation site [posttranslational modification] 385025002088 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 385025002089 ATP binding site [chemical binding]; other site 385025002090 Mg2+ binding site [ion binding]; other site 385025002091 G-X-G motif; other site 385025002092 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025002093 Response regulator receiver domain; Region: Response_reg; pfam00072 385025002094 active site 385025002095 phosphorylation site [posttranslational modification] 385025002096 intermolecular recognition site; other site 385025002097 dimerization interface [polypeptide binding]; other site 385025002098 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 385025002099 putative binding surface; other site 385025002100 active site 385025002101 Response regulator receiver domain; Region: Response_reg; pfam00072 385025002102 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025002103 active site 385025002104 phosphorylation site [posttranslational modification] 385025002105 intermolecular recognition site; other site 385025002106 dimerization interface [polypeptide binding]; other site 385025002107 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025002108 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025002109 metal binding site [ion binding]; metal-binding site 385025002110 active site 385025002111 I-site; other site 385025002112 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 385025002113 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 385025002114 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025002115 Protein of unknown function (DUF2797); Region: DUF2797; pfam10977 385025002116 hypothetical protein; Provisional; Region: PRK03673 385025002117 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 385025002118 putative MPT binding site; other site 385025002119 ABC transporter ATPase component; Reviewed; Region: PRK11147 385025002120 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025002121 Walker A/P-loop; other site 385025002122 ATP binding site [chemical binding]; other site 385025002123 Q-loop/lid; other site 385025002124 ABC transporter signature motif; other site 385025002125 Walker B; other site 385025002126 D-loop; other site 385025002127 H-loop/switch region; other site 385025002128 ABC transporter; Region: ABC_tran_2; pfam12848 385025002129 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025002130 multidrug resistance protein MdtN; Provisional; Region: PRK10476 385025002131 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 385025002132 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025002133 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 385025002134 Fusaric acid resistance protein family; Region: FUSC; pfam04632 385025002135 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 385025002136 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 385025002137 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 385025002138 MarR family; Region: MarR_2; cl17246 385025002139 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 385025002140 active site 385025002141 Zn binding site [ion binding]; other site 385025002142 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025002143 Protein of unknown function (DUF1643); Region: DUF1643; pfam07799 385025002144 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025002145 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 385025002146 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 385025002147 metal binding site [ion binding]; metal-binding site 385025002148 dimer interface [polypeptide binding]; other site 385025002149 Protein of unknown function (DUF432); Region: DUF432; cl01027 385025002150 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 385025002151 Mechanosensitive ion channel; Region: MS_channel; pfam00924 385025002152 Predicted membrane protein [Function unknown]; Region: COG3431 385025002153 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 385025002154 MgtE intracellular N domain; Region: MgtE_N; pfam03448 385025002155 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 385025002156 Divalent cation transporter; Region: MgtE; pfam01769 385025002157 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 385025002158 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 385025002159 Surface antigen; Region: Bac_surface_Ag; pfam01103 385025002160 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 385025002161 Family of unknown function (DUF490); Region: DUF490; pfam04357 385025002162 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 385025002163 Mechanosensitive ion channel; Region: MS_channel; pfam00924 385025002164 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup; Region: ZntB-like_1; cd12833 385025002165 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 385025002166 Cl binding site [ion binding]; other site 385025002167 oligomer interface [polypeptide binding]; other site 385025002168 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]; Region: COG4067 385025002169 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 385025002170 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025002171 Predicted deacylase [General function prediction only]; Region: COG3608 385025002172 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_1; cd06251 385025002173 putative active site [active] 385025002174 Zn binding site [ion binding]; other site 385025002175 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 385025002176 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025002177 TrkA-C domain; Region: TrkA_C; pfam02080 385025002178 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 385025002179 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 385025002180 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 385025002181 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025002182 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 385025002183 DNA binding residues [nucleotide binding] 385025002184 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 385025002185 Fatty acid desaturase; Region: FA_desaturase; pfam00487 385025002186 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 385025002187 Di-iron ligands [ion binding]; other site 385025002188 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 385025002189 SnoaL-like domain; Region: SnoaL_2; pfam12680 385025002190 short chain dehydrogenase; Provisional; Region: PRK06101 385025002191 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025002192 NAD(P) binding site [chemical binding]; other site 385025002193 active site 385025002194 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 385025002195 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 385025002196 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 385025002197 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 385025002198 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 385025002199 S-adenosylmethionine binding site [chemical binding]; other site 385025002200 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 385025002201 putative active site [active] 385025002202 Predicted membrane protein [Function unknown]; Region: COG3431 385025002203 Bacterial lipocalin [Cell envelope biogenesis, outer membrane]; Region: Blc; COG3040 385025002204 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 385025002205 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 385025002206 DNA photolyase; Region: DNA_photolyase; pfam00875 385025002207 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 385025002208 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 385025002209 DNA binding residues [nucleotide binding] 385025002210 Protein of unknown function (DUF523); Region: DUF523; pfam04463 385025002211 Uncharacterized conserved protein [Function unknown]; Region: COG3272 385025002212 Protein of unknown function (DUF1722); Region: DUF1722; pfam08349 385025002213 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025002214 Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]; Region: COG1090 385025002215 NAD(P) binding site [chemical binding]; other site 385025002216 active site 385025002217 ferrochelatase; Reviewed; Region: hemH; PRK00035 385025002218 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 385025002219 C-terminal domain interface [polypeptide binding]; other site 385025002220 active site 385025002221 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 385025002222 active site 385025002223 N-terminal domain interface [polypeptide binding]; other site 385025002224 succinic semialdehyde dehydrogenase; Region: PLN02278 385025002225 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 385025002226 tetramerization interface [polypeptide binding]; other site 385025002227 NAD(P) binding site [chemical binding]; other site 385025002228 catalytic residues [active] 385025002229 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 385025002230 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 385025002231 active site 385025002232 inhibitor site; inhibition site 385025002233 dimer interface [polypeptide binding]; other site 385025002234 catalytic residue [active] 385025002235 Ketopantoate reductase [Coenzyme metabolism]; Region: ApbA; COG1893 385025002236 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 385025002237 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 385025002238 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 385025002239 EamA-like transporter family; Region: EamA; pfam00892 385025002240 EamA-like transporter family; Region: EamA; pfam00892 385025002241 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 385025002242 Sodium Bile acid symporter family; Region: SBF; cl17470 385025002243 heat shock protein 90; Provisional; Region: PRK05218 385025002244 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 385025002245 ATP binding site [chemical binding]; other site 385025002246 Mg2+ binding site [ion binding]; other site 385025002247 G-X-G motif; other site 385025002248 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 385025002249 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 385025002250 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 385025002251 Walker A/P-loop; other site 385025002252 ATP binding site [chemical binding]; other site 385025002253 Q-loop/lid; other site 385025002254 CHDCT2 (NUC038) domain; Region: CHDCT2; pfam08074 385025002255 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 385025002256 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 385025002257 ABC transporter signature motif; other site 385025002258 Walker B; other site 385025002259 D-loop; other site 385025002260 H-loop/switch region; other site 385025002261 ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic...; Region: ZipA; cl12038 385025002262 FtsZ protein binding site [polypeptide binding]; other site 385025002263 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 385025002264 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 385025002265 nucleotide binding pocket [chemical binding]; other site 385025002266 K-X-D-G motif; other site 385025002267 catalytic site [active] 385025002268 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 385025002269 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 385025002270 Helix-hairpin-helix motif; Region: HHH; pfam00633 385025002271 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 385025002272 Dimer interface [polypeptide binding]; other site 385025002273 BRCT sequence motif; other site 385025002274 Protein of unknown function, DUF484; Region: DUF484; cl17449 385025002275 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025002276 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025002277 metal binding site [ion binding]; metal-binding site 385025002278 active site 385025002279 I-site; other site 385025002280 DNA gyrase subunit A; Validated; Region: PRK05560 385025002281 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 385025002282 CAP-like domain; other site 385025002283 active site 385025002284 primary dimer interface [polypeptide binding]; other site 385025002285 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025002286 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025002287 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025002288 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025002289 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025002290 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025002291 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 385025002292 homodimer interface [polypeptide binding]; other site 385025002293 substrate-cofactor binding pocket; other site 385025002294 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025002295 catalytic residue [active] 385025002296 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_3; cd12174 385025002297 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 385025002298 putative ligand binding site [chemical binding]; other site 385025002299 putative NAD binding site [chemical binding]; other site 385025002300 putative catalytic site [active] 385025002301 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 385025002302 L-serine binding site [chemical binding]; other site 385025002303 ACT domain interface; other site 385025002304 Chorismate mutase type II; Region: CM_2; cl00693 385025002305 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 385025002306 Prephenate dehydratase; Region: PDT; pfam00800 385025002307 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 385025002308 putative L-Phe binding site [chemical binding]; other site 385025002309 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 385025002310 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 385025002311 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025002312 homodimer interface [polypeptide binding]; other site 385025002313 catalytic residue [active] 385025002314 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 385025002315 prephenate dehydrogenase; Validated; Region: PRK08507 385025002316 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 385025002317 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 385025002318 hinge; other site 385025002319 active site 385025002320 cytidylate kinase; Provisional; Region: cmk; PRK00023 385025002321 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 385025002322 CMP-binding site; other site 385025002323 The sites determining sugar specificity; other site 385025002324 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 385025002325 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 385025002326 RNA binding site [nucleotide binding]; other site 385025002327 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 385025002328 RNA binding site [nucleotide binding]; other site 385025002329 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 385025002330 RNA binding site [nucleotide binding]; other site 385025002331 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 385025002332 RNA binding site [nucleotide binding]; other site 385025002333 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 385025002334 RNA binding site [nucleotide binding]; other site 385025002335 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 385025002336 RNA binding site [nucleotide binding]; other site 385025002337 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 385025002338 IHF dimer interface [polypeptide binding]; other site 385025002339 IHF - DNA interface [nucleotide binding]; other site 385025002340 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 385025002341 tetratricopeptide repeat protein; Provisional; Region: PRK11788 385025002342 StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been...; Region: StaR_like; cd05804 385025002343 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 385025002344 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 385025002345 helix-hairpin-helix signature motif; other site 385025002346 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 385025002347 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025002348 active site 385025002349 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 385025002350 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 385025002351 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 385025002352 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 385025002353 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 385025002354 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025002355 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 385025002356 substrate binding site [chemical binding]; other site 385025002357 oxyanion hole (OAH) forming residues; other site 385025002358 trimer interface [polypeptide binding]; other site 385025002359 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 385025002360 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 385025002361 dimer interface [polypeptide binding]; other site 385025002362 active site 385025002363 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 385025002364 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 385025002365 acyl-activating enzyme (AAE) consensus motif; other site 385025002366 putative AMP binding site [chemical binding]; other site 385025002367 putative active site [active] 385025002368 putative CoA binding site [chemical binding]; other site 385025002369 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 385025002370 enoyl-CoA hydratase; Provisional; Region: PRK06688 385025002371 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025002372 substrate binding site [chemical binding]; other site 385025002373 oxyanion hole (OAH) forming residues; other site 385025002374 trimer interface [polypeptide binding]; other site 385025002375 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 385025002376 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 385025002377 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 385025002378 ribonuclease R; Region: RNase_R; TIGR02063 385025002379 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 385025002380 RNB domain; Region: RNB; pfam00773 385025002381 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 385025002382 RNA binding site [nucleotide binding]; other site 385025002383 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 385025002384 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 385025002385 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 385025002386 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 385025002387 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 385025002388 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 385025002389 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 385025002390 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 385025002391 replicative DNA helicase; Region: DnaB; TIGR00665 385025002392 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 385025002393 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 385025002394 Walker A motif; other site 385025002395 ATP binding site [chemical binding]; other site 385025002396 Walker B motif; other site 385025002397 DNA binding loops [nucleotide binding] 385025002398 alanine racemase; Reviewed; Region: alr; PRK00053 385025002399 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 385025002400 active site 385025002401 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 385025002402 substrate binding site [chemical binding]; other site 385025002403 catalytic residues [active] 385025002404 dimer interface [polypeptide binding]; other site 385025002405 DNA repair protein RadA; Provisional; Region: PRK11823 385025002406 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 385025002407 Walker A motif/ATP binding site; other site 385025002408 ATP binding site [chemical binding]; other site 385025002409 Walker B motif; other site 385025002410 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 385025002411 FOG: FHA domain [Signal transduction mechanisms]; Region: COG1716 385025002412 FHA domain; Region: FHA; pfam00498 385025002413 phosphopeptide binding site; other site 385025002414 Domain of unknown function DUF21; Region: DUF21; pfam01595 385025002415 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 385025002416 Transporter associated domain; Region: CorC_HlyC; smart01091 385025002417 Flagellar regulatory protein FleQ; Region: FleQ; pfam06490 385025002418 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 385025002419 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 385025002420 Walker A motif; other site 385025002421 ATP binding site [chemical binding]; other site 385025002422 Walker B motif; other site 385025002423 arginine finger; other site 385025002424 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 385025002425 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 385025002426 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 385025002427 dimer interface [polypeptide binding]; other site 385025002428 phosphorylation site [posttranslational modification] 385025002429 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 385025002430 ATP binding site [chemical binding]; other site 385025002431 Mg2+ binding site [ion binding]; other site 385025002432 G-X-G motif; other site 385025002433 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 385025002434 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025002435 active site 385025002436 phosphorylation site [posttranslational modification] 385025002437 intermolecular recognition site; other site 385025002438 dimerization interface [polypeptide binding]; other site 385025002439 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 385025002440 Walker A motif; other site 385025002441 ATP binding site [chemical binding]; other site 385025002442 Walker B motif; other site 385025002443 arginine finger; other site 385025002444 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 385025002445 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 385025002446 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 385025002447 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 385025002448 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 385025002449 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 385025002450 MgtE intracellular N domain; Region: MgtE_N; smart00924 385025002451 FliG C-terminal domain; Region: FliG_C; pfam01706 385025002452 flagellar assembly protein H; Validated; Region: fliH; PRK05687 385025002453 Flagellar assembly protein FliH; Region: FliH; pfam02108 385025002454 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 385025002455 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 385025002456 Walker A motif/ATP binding site; other site 385025002457 Walker B motif; other site 385025002458 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 385025002459 flagellar export protein FliJ; Region: flagell_FliJ; TIGR02473 385025002460 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; pfam04277 385025002461 oxaloacetate decarboxylase; Provisional; Region: PRK14040 385025002462 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 385025002463 active site 385025002464 catalytic residues [active] 385025002465 metal binding site [ion binding]; metal-binding site 385025002466 homodimer binding site [polypeptide binding]; other site 385025002467 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 385025002468 carboxyltransferase (CT) interaction site; other site 385025002469 biotinylation site [posttranslational modification]; other site 385025002470 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 385025002471 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 385025002472 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 385025002473 FMN binding site [chemical binding]; other site 385025002474 active site 385025002475 catalytic residues [active] 385025002476 substrate binding site [chemical binding]; other site 385025002477 GTP cyclohydrolase I; Provisional; Region: PLN03044 385025002478 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 385025002479 homodecamer interface [polypeptide binding]; other site 385025002480 active site 385025002481 putative catalytic site residues [active] 385025002482 zinc binding site [ion binding]; other site 385025002483 GTP-CH-I/GFRP interaction surface; other site 385025002484 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 385025002485 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 385025002486 putative active site [active] 385025002487 putative dimer interface [polypeptide binding]; other site 385025002488 Glutamine amidotransferases class-II; Region: GATase_4; pfam13230 385025002489 HDOD domain; Region: HDOD; pfam08668 385025002490 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 385025002491 Zn2+ binding site [ion binding]; other site 385025002492 Mg2+ binding site [ion binding]; other site 385025002493 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 385025002494 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025002495 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025002496 metal binding site [ion binding]; metal-binding site 385025002497 active site 385025002498 I-site; other site 385025002499 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 385025002500 penicillin-binding protein 1B; Region: PBP_1b; TIGR02071 385025002501 Transglycosylase; Region: Transgly; pfam00912 385025002502 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 385025002503 TPR repeat; Region: TPR_11; pfam13414 385025002504 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 385025002505 binding surface 385025002506 TPR motif; other site 385025002507 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 385025002508 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 385025002509 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 385025002510 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 385025002511 Glycoprotease family; Region: Peptidase_M22; pfam00814 385025002512 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 385025002513 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 385025002514 Peptidase family M50; Region: Peptidase_M50; pfam02163 385025002515 active site 385025002516 putative substrate binding region [chemical binding]; other site 385025002517 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 385025002518 active site 385025002519 HIGH motif; other site 385025002520 dimer interface [polypeptide binding]; other site 385025002521 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 385025002522 active site 385025002523 KMSKS motif; other site 385025002524 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 385025002525 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 385025002526 pyruvate kinase; Provisional; Region: PRK05826 385025002527 domain interfaces; other site 385025002528 active site 385025002529 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 385025002530 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 385025002531 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 385025002532 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 385025002533 RNA binding surface [nucleotide binding]; other site 385025002534 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 385025002535 probable active site [active] 385025002536 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025002537 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025002538 metal binding site [ion binding]; metal-binding site 385025002539 active site 385025002540 I-site; other site 385025002541 FixH; Region: FixH; pfam05751 385025002542 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 385025002543 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 385025002544 4Fe-4S binding domain; Region: Fer4_5; pfam12801 385025002545 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 385025002546 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 385025002547 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 385025002548 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 385025002549 Cytochrome c; Region: Cytochrom_C; pfam00034 385025002550 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 385025002551 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 385025002552 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 385025002553 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 385025002554 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 385025002555 Low-spin heme binding site [chemical binding]; other site 385025002556 Putative water exit pathway; other site 385025002557 Binuclear center (active site) [active] 385025002558 Putative proton exit pathway; other site 385025002559 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 385025002560 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 385025002561 ligand binding site [chemical binding]; other site 385025002562 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 385025002563 non-specific DNA interactions [nucleotide binding]; other site 385025002564 DNA binding site [nucleotide binding] 385025002565 sequence specific DNA binding site [nucleotide binding]; other site 385025002566 putative cAMP binding site [chemical binding]; other site 385025002567 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 385025002568 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 385025002569 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 385025002570 metal-binding site [ion binding] 385025002571 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 385025002572 Soluble P-type ATPase [General function prediction only]; Region: COG4087 385025002573 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 385025002574 Family description; Region: DsbD_2; pfam13386 385025002575 Domain of unknown function DUF59; Region: DUF59; cl00941 385025002576 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 385025002577 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 385025002578 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 385025002579 active site 385025002580 HIGH motif; other site 385025002581 nucleotide binding site [chemical binding]; other site 385025002582 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 385025002583 KMSKS motif; other site 385025002584 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 385025002585 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 385025002586 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025002587 inter-subunit interface; other site 385025002588 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 385025002589 iron-sulfur cluster [ion binding]; other site 385025002590 [2Fe-2S] cluster binding site [ion binding]; other site 385025002591 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025002592 beta subunit interface [polypeptide binding]; other site 385025002593 alpha subunit interface [polypeptide binding]; other site 385025002594 active site 385025002595 substrate binding site [chemical binding]; other site 385025002596 Fe binding site [ion binding]; other site 385025002597 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 385025002598 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 385025002599 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 385025002600 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 385025002601 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 385025002602 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 385025002603 Walker A/P-loop; other site 385025002604 ATP binding site [chemical binding]; other site 385025002605 Q-loop/lid; other site 385025002606 ABC transporter signature motif; other site 385025002607 Walker B; other site 385025002608 D-loop; other site 385025002609 H-loop/switch region; other site 385025002610 50S ribosomal protein L37Ae; Reviewed; Region: rpl37ae; PRK03976 385025002611 aspartate aminotransferase; Provisional; Region: PRK05764 385025002612 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 385025002613 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025002614 homodimer interface [polypeptide binding]; other site 385025002615 catalytic residue [active] 385025002616 excinuclease ABC subunit B; Provisional; Region: PRK05298 385025002617 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 385025002618 ATP binding site [chemical binding]; other site 385025002619 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 385025002620 nucleotide binding region [chemical binding]; other site 385025002621 ATP-binding site [chemical binding]; other site 385025002622 Ultra-violet resistance protein B; Region: UvrB; pfam12344 385025002623 UvrB/uvrC motif; Region: UVR; pfam02151 385025002624 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 385025002625 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 385025002626 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 385025002627 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 385025002628 active site 385025002629 dimer interface [polypeptide binding]; other site 385025002630 motif 1; other site 385025002631 motif 2; other site 385025002632 motif 3; other site 385025002633 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 385025002634 anticodon binding site; other site 385025002635 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 385025002636 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 385025002637 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 385025002638 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 385025002639 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 385025002640 23S rRNA binding site [nucleotide binding]; other site 385025002641 L21 binding site [polypeptide binding]; other site 385025002642 L13 binding site [polypeptide binding]; other site 385025002643 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 385025002644 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 385025002645 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 385025002646 dimer interface [polypeptide binding]; other site 385025002647 motif 1; other site 385025002648 active site 385025002649 motif 2; other site 385025002650 motif 3; other site 385025002651 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 385025002652 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 385025002653 putative tRNA-binding site [nucleotide binding]; other site 385025002654 B3/4 domain; Region: B3_4; pfam03483 385025002655 tRNA synthetase B5 domain; Region: B5; smart00874 385025002656 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 385025002657 dimer interface [polypeptide binding]; other site 385025002658 motif 1; other site 385025002659 motif 3; other site 385025002660 motif 2; other site 385025002661 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 385025002662 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 385025002663 IHF dimer interface [polypeptide binding]; other site 385025002664 IHF - DNA interface [nucleotide binding]; other site 385025002665 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 385025002666 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 385025002667 DNA binding residues [nucleotide binding] 385025002668 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 385025002669 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025002670 NAD(P) binding site [chemical binding]; other site 385025002671 active site 385025002672 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 385025002673 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 385025002674 active site 385025002675 nucleophile elbow; other site 385025002676 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 385025002677 dimerization interface [polypeptide binding]; other site 385025002678 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 385025002679 ATP binding site [chemical binding]; other site 385025002680 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 385025002681 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 385025002682 HupF/HypC family; Region: HupF_HypC; pfam01455 385025002683 Acylphosphatase; Region: Acylphosphatase; pfam00708 385025002684 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 385025002685 HypF finger; Region: zf-HYPF; pfam07503 385025002686 HypF finger; Region: zf-HYPF; pfam07503 385025002687 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 385025002688 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 385025002689 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025002690 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 385025002691 SLBB domain; Region: SLBB; pfam10531 385025002692 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 385025002693 bidirectional hydrogenase complex protein HoxU; Validated; Region: PRK07569 385025002694 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 385025002695 catalytic loop [active] 385025002696 iron binding site [ion binding]; other site 385025002697 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 385025002698 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 385025002699 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 385025002700 Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]; Region: FrhA; COG3259 385025002701 Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit...; Region: H2MP_NAD-link-bidir; cd06066 385025002702 nickel binding site [ion binding]; other site 385025002703 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; COG0375 385025002704 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 385025002705 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 385025002706 Predicted membrane protein [Function unknown]; Region: COG3174 385025002707 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 385025002708 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 385025002709 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 385025002710 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 385025002711 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 385025002712 Soluble P-type ATPase [General function prediction only]; Region: COG4087 385025002713 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 385025002714 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 385025002715 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12599 385025002716 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 385025002717 Domain of unknown function (DUF4040); Region: DUF4040; pfam13244 385025002718 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 385025002719 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 385025002720 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 385025002721 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 385025002722 NADH dehydrogenase I, subunit N related protein; Region: NADHdeh_related; cl01688 385025002723 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 385025002724 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 385025002725 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 385025002726 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12668 385025002727 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 385025002728 cyanate hydratase; Validated; Region: PRK02866 385025002729 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 385025002730 oligomer interface [polypeptide binding]; other site 385025002731 active site 385025002732 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 385025002733 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 385025002734 active site 385025002735 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 385025002736 Catalytic domain of Protein Kinases; Region: PKc; cd00180 385025002737 active site 385025002738 ATP binding site [chemical binding]; other site 385025002739 substrate binding site [chemical binding]; other site 385025002740 activation loop (A-loop); other site 385025002741 NnrU protein; Region: NnrU; pfam07298 385025002742 Protein phosphatase 2C; Region: PP2C; pfam00481 385025002743 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 385025002744 active site 385025002745 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 385025002746 Catalytic domain of Protein Kinases; Region: PKc; cd00180 385025002747 active site 385025002748 ATP binding site [chemical binding]; other site 385025002749 substrate binding site [chemical binding]; other site 385025002750 activation loop (A-loop); other site 385025002751 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 385025002752 putative substrate translocation pore; other site 385025002753 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 385025002754 nitrite reductase subunit NirD; Provisional; Region: PRK14989 385025002755 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025002756 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025002757 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 385025002758 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 385025002759 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 385025002760 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 385025002761 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 385025002762 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 385025002763 [4Fe-4S] binding site [ion binding]; other site 385025002764 molybdopterin cofactor binding site; other site 385025002765 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 385025002766 molybdopterin cofactor binding site; other site 385025002767 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 385025002768 4Fe-4S binding domain; Region: Fer4; pfam00037 385025002769 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 385025002770 Thermostable hemolysin; Region: T_hemolysin; pfam12261 385025002771 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 385025002772 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 385025002773 acyl-activating enzyme (AAE) consensus motif; other site 385025002774 AMP binding site [chemical binding]; other site 385025002775 active site 385025002776 CoA binding site [chemical binding]; other site 385025002777 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 385025002778 heme binding pocket [chemical binding]; other site 385025002779 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 385025002780 TPR motif; other site 385025002781 binding surface 385025002782 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 385025002783 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025002784 active site 385025002785 phosphorylation site [posttranslational modification] 385025002786 intermolecular recognition site; other site 385025002787 dimerization interface [polypeptide binding]; other site 385025002788 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 385025002789 DNA binding site [nucleotide binding] 385025002790 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025002791 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 385025002792 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 385025002793 dimer interface [polypeptide binding]; other site 385025002794 phosphorylation site [posttranslational modification] 385025002795 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 385025002796 ATP binding site [chemical binding]; other site 385025002797 Mg2+ binding site [ion binding]; other site 385025002798 G-X-G motif; other site 385025002799 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 385025002800 Iron permease FTR1 family; Region: FTR1; cl00475 385025002801 HAMP domain; Region: HAMP; pfam00672 385025002802 dimerization interface [polypeptide binding]; other site 385025002803 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025002804 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 385025002805 dimer interface [polypeptide binding]; other site 385025002806 phosphorylation site [posttranslational modification] 385025002807 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 385025002808 ATP binding site [chemical binding]; other site 385025002809 Mg2+ binding site [ion binding]; other site 385025002810 G-X-G motif; other site 385025002811 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 385025002812 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025002813 active site 385025002814 phosphorylation site [posttranslational modification] 385025002815 intermolecular recognition site; other site 385025002816 dimerization interface [polypeptide binding]; other site 385025002817 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 385025002818 putative binding surface; other site 385025002819 active site 385025002820 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 385025002821 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 385025002822 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 385025002823 cysteine synthase B; Region: cysM; TIGR01138 385025002824 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 385025002825 dimer interface [polypeptide binding]; other site 385025002826 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025002827 catalytic residue [active] 385025002828 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 385025002829 TRAM domain; Region: TRAM; cl01282 385025002830 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 385025002831 S-adenosylmethionine binding site [chemical binding]; other site 385025002832 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 385025002833 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 385025002834 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 385025002835 beta-hexosaminidase; Provisional; Region: PRK05337 385025002836 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 385025002837 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 385025002838 active site 385025002839 5'-methylthioadenosine phosphorylase; Validated; Region: PRK09136 385025002840 Protein of unknown function (DUF3581); Region: DUF3581; pfam12119 385025002841 Protein of unknown function (DUF2803); Region: DUF2803; pfam10972 385025002842 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 385025002843 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 385025002844 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 385025002845 ATP binding site [chemical binding]; other site 385025002846 putative Mg++ binding site [ion binding]; other site 385025002847 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 385025002848 nucleotide binding region [chemical binding]; other site 385025002849 ATP-binding site [chemical binding]; other site 385025002850 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 385025002851 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 385025002852 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 385025002853 FtsX-like permease family; Region: FtsX; pfam02687 385025002854 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 385025002855 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 385025002856 Walker A/P-loop; other site 385025002857 ATP binding site [chemical binding]; other site 385025002858 Q-loop/lid; other site 385025002859 ABC transporter signature motif; other site 385025002860 Walker B; other site 385025002861 D-loop; other site 385025002862 H-loop/switch region; other site 385025002863 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 385025002864 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 385025002865 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 385025002866 Competence protein; Region: Competence; pfam03772 385025002867 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 385025002868 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 385025002869 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 385025002870 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 385025002871 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 385025002872 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 385025002873 Uncharacterized conserved protein [Function unknown]; Region: COG2835 385025002874 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 385025002875 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 385025002876 Ligand binding site; other site 385025002877 oligomer interface; other site 385025002878 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 385025002879 Low molecular weight phosphatase family; Region: LMWPc; cd00115 385025002880 active site 385025002881 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 385025002882 signal recognition particle protein; Provisional; Region: PRK10867 385025002883 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 385025002884 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 385025002885 P loop; other site 385025002886 GTP binding site [chemical binding]; other site 385025002887 Signal peptide binding domain; Region: SRP_SPB; pfam02978 385025002888 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 385025002889 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 385025002890 RimM N-terminal domain; Region: RimM; pfam01782 385025002891 PRC-barrel domain; Region: PRC; pfam05239 385025002892 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 385025002893 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 385025002894 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 385025002895 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 385025002896 active site 385025002897 Int/Topo IB signature motif; other site 385025002898 protein disulfide isomerase II DsbC; Provisional; Region: PRK10877 385025002899 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 385025002900 dimerization domain [polypeptide binding]; other site 385025002901 dimer interface [polypeptide binding]; other site 385025002902 catalytic residues [active] 385025002903 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 385025002904 MutS domain I; Region: MutS_I; pfam01624 385025002905 MutS domain II; Region: MutS_II; pfam05188 385025002906 MutS domain III; Region: MutS_III; pfam05192 385025002907 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 385025002908 Walker A/P-loop; other site 385025002909 ATP binding site [chemical binding]; other site 385025002910 Q-loop/lid; other site 385025002911 ABC transporter signature motif; other site 385025002912 Walker B; other site 385025002913 D-loop; other site 385025002914 H-loop/switch region; other site 385025002915 Competence-damaged protein; Region: CinA; pfam02464 385025002916 recombinase A; Provisional; Region: recA; PRK09354 385025002917 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 385025002918 hexamer interface [polypeptide binding]; other site 385025002919 Walker A motif; other site 385025002920 ATP binding site [chemical binding]; other site 385025002921 Walker B motif; other site 385025002922 recombination regulator RecX; Reviewed; Region: recX; PRK00117 385025002923 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 385025002924 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 385025002925 motif 1; other site 385025002926 active site 385025002927 motif 2; other site 385025002928 motif 3; other site 385025002929 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 385025002930 DHHA1 domain; Region: DHHA1; pfam02272 385025002931 aspartate kinase; Reviewed; Region: PRK06635 385025002932 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 385025002933 putative nucleotide binding site [chemical binding]; other site 385025002934 putative catalytic residues [active] 385025002935 putative Mg ion binding site [ion binding]; other site 385025002936 putative aspartate binding site [chemical binding]; other site 385025002937 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 385025002938 putative allosteric regulatory site; other site 385025002939 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 385025002940 carbon storage regulator; Provisional; Region: PRK01712 385025002941 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 385025002942 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 385025002943 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 385025002944 ligand binding site [chemical binding]; other site 385025002945 flexible hinge region; other site 385025002946 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 385025002947 non-specific DNA interactions [nucleotide binding]; other site 385025002948 DNA binding site [nucleotide binding] 385025002949 sequence specific DNA binding site [nucleotide binding]; other site 385025002950 putative cAMP binding site [chemical binding]; other site 385025002951 Transmembrane secretion effector; Region: MFS_3; pfam05977 385025002952 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 385025002953 putative substrate translocation pore; other site 385025002954 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 385025002955 iron-sulfur cluster [ion binding]; other site 385025002956 [2Fe-2S] cluster binding site [ion binding]; other site 385025002957 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025002958 beta subunit interface [polypeptide binding]; other site 385025002959 alpha subunit interface [polypeptide binding]; other site 385025002960 active site 385025002961 substrate binding site [chemical binding]; other site 385025002962 Fe binding site [ion binding]; other site 385025002963 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025002964 inter-subunit interface; other site 385025002965 Succinate dehydrogenase/fumarate reductase, flavoprotein subunit [Energy production and conversion]; Region: SdhA; COG1053 385025002966 L-aspartate oxidase; Provisional; Region: PRK06175 385025002967 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 385025002968 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 385025002969 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 385025002970 Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold...; Region: Sialidase; cl17698 385025002971 Asp-box motif; other site 385025002972 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 385025002973 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 385025002974 [2Fe-2S] cluster binding site [ion binding]; other site 385025002975 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 385025002976 hydrophobic ligand binding site; other site 385025002977 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 385025002978 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 385025002979 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 385025002980 NAD(P) binding site [chemical binding]; other site 385025002981 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 385025002982 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 385025002983 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 385025002984 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 385025002985 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 385025002986 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025002987 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025002988 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025002989 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 385025002990 dimer interface [polypeptide binding]; other site 385025002991 N-terminal domain interface [polypeptide binding]; other site 385025002992 substrate binding pocket (H-site) [chemical binding]; other site 385025002993 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 385025002994 active site 385025002995 catalytic residues [active] 385025002996 DNA binding site [nucleotide binding] 385025002997 Int/Topo IB signature motif; other site 385025002998 HTH domain; Region: HTH_11; cl17392 385025002999 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 385025003000 integrase; Provisional; Region: PRK09692 385025003001 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 385025003002 active site 385025003003 Int/Topo IB signature motif; other site 385025003004 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 385025003005 putative catalytic site [active] 385025003006 putative phosphate binding site [ion binding]; other site 385025003007 putative metal binding site [ion binding]; other site 385025003008 L-arabinose isomerase; Region: Arabinose_Isome; pfam02610 385025003009 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 385025003010 TPR motif; other site 385025003011 Tetratricopeptide repeat; Region: TPR_12; pfam13424 385025003012 binding surface 385025003013 aspartate kinase; Validated; Region: PRK09181 385025003014 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 385025003015 nucleotide binding site [chemical binding]; other site 385025003016 substrate binding site [chemical binding]; other site 385025003017 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway; Region: ACT_AK-Ectoine_1; cd04910 385025003018 allosteric regulatory residue; other site 385025003019 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 385025003020 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 385025003021 Ectoine synthase; Region: Ectoine_synth; pfam06339 385025003022 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 385025003023 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 385025003024 inhibitor-cofactor binding pocket; inhibition site 385025003025 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025003026 catalytic residue [active] 385025003027 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 385025003028 Coenzyme A binding pocket [chemical binding]; other site 385025003029 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 385025003030 MarR family; Region: MarR; pfam01047 385025003031 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 385025003032 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 385025003033 active site 385025003034 dimer interface [polypeptide binding]; other site 385025003035 effector binding site; other site 385025003036 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 385025003037 TSCPD domain; Region: TSCPD; pfam12637 385025003038 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N_2; pfam13588 385025003039 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 385025003040 Methyltransferase domain; Region: Methyltransf_26; pfam13659 385025003041 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 385025003042 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 385025003043 Outer membrane efflux protein; Region: OEP; pfam02321 385025003044 Outer membrane efflux protein; Region: OEP; pfam02321 385025003045 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 385025003046 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025003047 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 385025003048 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 385025003049 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 385025003050 TrkA-N domain; Region: TrkA_N; pfam02254 385025003051 Predicted membrane protein [Function unknown]; Region: COG4325 385025003052 Predicted membrane protein (DUF2254); Region: DUF2254; pfam10011 385025003053 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 385025003054 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 385025003055 ligand binding site [chemical binding]; other site 385025003056 flexible hinge region; other site 385025003057 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 385025003058 non-specific DNA interactions [nucleotide binding]; other site 385025003059 DNA binding site [nucleotide binding] 385025003060 sequence specific DNA binding site [nucleotide binding]; other site 385025003061 putative cAMP binding site [chemical binding]; other site 385025003062 Small integral membrane protein [Function unknown]; Region: COG5487; cl17674 385025003063 CsbD-like; Region: CsbD; cl17424 385025003064 Fatty acid cis/trans isomerase (CTI); Region: CTI; pfam06934 385025003065 Protein of unknown function (DUF502); Region: DUF502; cl01107 385025003066 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 385025003067 dimer interface [polypeptide binding]; other site 385025003068 putative radical transfer pathway; other site 385025003069 diiron center [ion binding]; other site 385025003070 tyrosyl radical; other site 385025003071 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 385025003072 ATP cone domain; Region: ATP-cone; pfam03477 385025003073 Class I ribonucleotide reductase; Region: RNR_I; cd01679 385025003074 active site 385025003075 dimer interface [polypeptide binding]; other site 385025003076 catalytic residues [active] 385025003077 effector binding site; other site 385025003078 R2 peptide binding site; other site 385025003079 Transcriptional regulator [Transcription]; Region: LysR; COG0583 385025003080 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 385025003081 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 385025003082 putative dimerization interface [polypeptide binding]; other site 385025003083 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 385025003084 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 385025003085 THF binding site; other site 385025003086 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 385025003087 substrate binding site [chemical binding]; other site 385025003088 THF binding site; other site 385025003089 zinc-binding site [ion binding]; other site 385025003090 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 385025003091 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 385025003092 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025003093 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025003094 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 385025003095 putative N-terminal domain interface [polypeptide binding]; other site 385025003096 putative dimer interface [polypeptide binding]; other site 385025003097 putative substrate binding pocket (H-site) [chemical binding]; other site 385025003098 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 385025003099 EamA-like transporter family; Region: EamA; pfam00892 385025003100 EamA-like transporter family; Region: EamA; pfam00892 385025003101 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 385025003102 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 385025003103 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 385025003104 putative acyl-acceptor binding pocket; other site 385025003105 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 385025003106 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 385025003107 Protein of unknown function, DUF606; Region: DUF606; pfam04657 385025003108 hypothetical protein; Provisional; Region: PRK10279 385025003109 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 385025003110 active site 385025003111 nucleophile elbow; other site 385025003112 hypothetical protein; Provisional; Region: PRK08317 385025003113 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 385025003114 S-adenosylmethionine binding site [chemical binding]; other site 385025003115 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 385025003116 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 385025003117 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 385025003118 active site 385025003119 Fe binding site [ion binding]; other site 385025003120 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025003121 inter-subunit interface; other site 385025003122 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 385025003123 iron-sulfur cluster [ion binding]; other site 385025003124 [2Fe-2S] cluster binding site [ion binding]; other site 385025003125 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025003126 beta subunit interface [polypeptide binding]; other site 385025003127 alpha subunit interface [polypeptide binding]; other site 385025003128 active site 385025003129 substrate binding site [chemical binding]; other site 385025003130 Fe binding site [ion binding]; other site 385025003131 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 385025003132 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 385025003133 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 385025003134 FeoC like transcriptional regulator; Region: FeoC; pfam09012 385025003135 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 385025003136 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 385025003137 G1 box; other site 385025003138 GTP/Mg2+ binding site [chemical binding]; other site 385025003139 Switch I region; other site 385025003140 G2 box; other site 385025003141 G3 box; other site 385025003142 Switch II region; other site 385025003143 G4 box; other site 385025003144 G5 box; other site 385025003145 Nucleoside recognition; Region: Gate; pfam07670 385025003146 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 385025003147 FeoA domain; Region: FeoA; pfam04023 385025003148 CAAX protease self-immunity; Region: Abi; pfam02517 385025003149 trigger factor; Provisional; Region: tig; PRK01490 385025003150 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 385025003151 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 385025003152 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 385025003153 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 385025003154 oligomer interface [polypeptide binding]; other site 385025003155 active site residues [active] 385025003156 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 385025003157 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 385025003158 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 385025003159 Walker A motif; other site 385025003160 ATP binding site [chemical binding]; other site 385025003161 Walker B motif; other site 385025003162 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 385025003163 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 385025003164 Found in ATP-dependent protease La (LON); Region: LON; smart00464 385025003165 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 385025003166 Walker A motif; other site 385025003167 ATP binding site [chemical binding]; other site 385025003168 Walker B motif; other site 385025003169 arginine finger; other site 385025003170 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 385025003171 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 385025003172 IHF dimer interface [polypeptide binding]; other site 385025003173 IHF - DNA interface [nucleotide binding]; other site 385025003174 periplasmic folding chaperone; Provisional; Region: PRK10788 385025003175 SurA N-terminal domain; Region: SurA_N_3; cl07813 385025003176 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 385025003177 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 385025003178 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 385025003179 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_18; cd08505 385025003180 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 385025003181 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 385025003182 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 385025003183 dimer interface [polypeptide binding]; other site 385025003184 conserved gate region; other site 385025003185 putative PBP binding loops; other site 385025003186 ABC-ATPase subunit interface; other site 385025003187 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 385025003188 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 385025003189 dimer interface [polypeptide binding]; other site 385025003190 conserved gate region; other site 385025003191 putative PBP binding loops; other site 385025003192 ABC-ATPase subunit interface; other site 385025003193 phosphoserine phosphatase SerB; Region: serB; TIGR00338 385025003194 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 385025003195 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 385025003196 motif II; other site 385025003197 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 385025003198 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 385025003199 Walker A/P-loop; other site 385025003200 ATP binding site [chemical binding]; other site 385025003201 Q-loop/lid; other site 385025003202 ABC transporter signature motif; other site 385025003203 Walker B; other site 385025003204 D-loop; other site 385025003205 H-loop/switch region; other site 385025003206 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 385025003207 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 385025003208 Walker A/P-loop; other site 385025003209 ATP binding site [chemical binding]; other site 385025003210 Q-loop/lid; other site 385025003211 ABC transporter signature motif; other site 385025003212 Walker B; other site 385025003213 D-loop; other site 385025003214 H-loop/switch region; other site 385025003215 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 385025003216 membrane-bound lytic murein transglycosylase D; Provisional; Region: mltD; PRK10783 385025003217 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 385025003218 N-acetyl-D-glucosamine binding site [chemical binding]; other site 385025003219 catalytic residue [active] 385025003220 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025003221 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025003222 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025003223 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 385025003224 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 385025003225 RNA/DNA hybrid binding site [nucleotide binding]; other site 385025003226 active site 385025003227 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 385025003228 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 385025003229 active site 385025003230 catalytic site [active] 385025003231 substrate binding site [chemical binding]; other site 385025003232 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 385025003233 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 385025003234 active site 385025003235 HIGH motif; other site 385025003236 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 385025003237 active site 385025003238 KMSKS motif; other site 385025003239 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 385025003240 active site 385025003241 DNA polymerase IV; Validated; Region: PRK02406 385025003242 DNA binding site [nucleotide binding] 385025003243 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 385025003244 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 385025003245 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 385025003246 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025003247 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 385025003248 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 385025003249 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 385025003250 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 385025003251 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 385025003252 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 385025003253 active site 385025003254 Fe binding site [ion binding]; other site 385025003255 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 385025003256 iron-sulfur cluster [ion binding]; other site 385025003257 [2Fe-2S] cluster binding site [ion binding]; other site 385025003258 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 385025003259 putative alpha subunit interface [polypeptide binding]; other site 385025003260 putative active site [active] 385025003261 putative substrate binding site [chemical binding]; other site 385025003262 Fe binding site [ion binding]; other site 385025003263 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 385025003264 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025003265 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025003266 inter-subunit interface; other site 385025003267 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 385025003268 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 385025003269 iron-sulfur cluster [ion binding]; other site 385025003270 [2Fe-2S] cluster binding site [ion binding]; other site 385025003271 C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_DMO-like; cd08878 385025003272 alpha subunit interface [polypeptide binding]; other site 385025003273 active site 385025003274 substrate binding site [chemical binding]; other site 385025003275 Fe binding site [ion binding]; other site 385025003276 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 385025003277 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 385025003278 iron-sulfur cluster [ion binding]; other site 385025003279 [2Fe-2S] cluster binding site [ion binding]; other site 385025003280 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 385025003281 putative alpha subunit interface [polypeptide binding]; other site 385025003282 putative active site [active] 385025003283 putative substrate binding site [chemical binding]; other site 385025003284 Fe binding site [ion binding]; other site 385025003285 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025003286 inter-subunit interface; other site 385025003287 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 385025003288 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 385025003289 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 385025003290 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 385025003291 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 385025003292 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 385025003293 ligand binding site [chemical binding]; other site 385025003294 flexible hinge region; other site 385025003295 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 385025003296 hybrid cluster protein; Provisional; Region: PRK05290 385025003297 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 385025003298 ACS interaction site; other site 385025003299 CODH interaction site; other site 385025003300 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 385025003301 ACS interaction site; other site 385025003302 CODH interaction site; other site 385025003303 metal cluster binding site [ion binding]; other site 385025003304 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 385025003305 iron-sulfur cluster [ion binding]; other site 385025003306 [2Fe-2S] cluster binding site [ion binding]; other site 385025003307 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025003308 beta subunit interface [polypeptide binding]; other site 385025003309 alpha subunit interface [polypeptide binding]; other site 385025003310 active site 385025003311 substrate binding site [chemical binding]; other site 385025003312 Fe binding site [ion binding]; other site 385025003313 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025003314 inter-subunit interface; other site 385025003315 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 385025003316 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 385025003317 ligand binding site [chemical binding]; other site 385025003318 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 385025003319 putative switch regulator; other site 385025003320 non-specific DNA interactions [nucleotide binding]; other site 385025003321 DNA binding site [nucleotide binding] 385025003322 sequence specific DNA binding site [nucleotide binding]; other site 385025003323 putative cAMP binding site [chemical binding]; other site 385025003324 Predicted metal-binding protein [General function prediction only]; Region: COG3019 385025003325 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 385025003326 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 385025003327 catalytic residues [active] 385025003328 Protein of unknown function (DUF3010); Region: DUF3010; pfam11215 385025003329 Protein of unknown function, DUF481; Region: DUF481; pfam04338 385025003330 GDP-mannose pyrophosphatase NudK; Provisional; Region: PRK15009 385025003331 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 385025003332 dimer interface [polypeptide binding]; other site 385025003333 ADP-ribose binding site [chemical binding]; other site 385025003334 active site 385025003335 nudix motif; other site 385025003336 metal binding site [ion binding]; metal-binding site 385025003337 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 385025003338 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 385025003339 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 385025003340 putative active site [active] 385025003341 catalytic site [active] 385025003342 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 385025003343 putative active site [active] 385025003344 catalytic site [active] 385025003345 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 385025003346 Methyltransferase domain; Region: Methyltransf_23; pfam13489 385025003347 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 385025003348 S-adenosylmethionine binding site [chemical binding]; other site 385025003349 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 385025003350 HI0933-like protein; Region: HI0933_like; pfam03486 385025003351 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025003352 MoxR-like ATPases [General function prediction only]; Region: COG0714 385025003353 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 385025003354 Walker A motif; other site 385025003355 ATP binding site [chemical binding]; other site 385025003356 Walker B motif; other site 385025003357 arginine finger; other site 385025003358 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 385025003359 Protein of unknown function DUF58; Region: DUF58; pfam01882 385025003360 Domain of unknown function (DUF4381); Region: DUF4381; pfam14316 385025003361 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 385025003362 metal ion-dependent adhesion site (MIDAS); other site 385025003363 von Willebrand factor type A domain; Region: VWA_2; pfam13519 385025003364 metal ion-dependent adhesion site (MIDAS); other site 385025003365 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 385025003366 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 385025003367 TPR motif; other site 385025003368 binding surface 385025003369 Oxygen tolerance; Region: BatD; pfam13584 385025003370 nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2; Region: Nitrilotriacetate_monoxgenase; cd01095 385025003371 FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family; Region: FMN_nitrolo; TIGR03860 385025003372 active site 385025003373 non-prolyl cis peptide bond; other site 385025003374 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 385025003375 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 385025003376 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025003377 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 385025003378 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 385025003379 Predicted membrane protein [Function unknown]; Region: COG3671 385025003380 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 385025003381 PAS domain; Region: PAS_9; pfam13426 385025003382 putative active site [active] 385025003383 heme pocket [chemical binding]; other site 385025003384 GAF domain; Region: GAF; cl17456 385025003385 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025003386 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025003387 metal binding site [ion binding]; metal-binding site 385025003388 active site 385025003389 I-site; other site 385025003390 probable DNA repair protein; Region: TIGR03623 385025003391 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 385025003392 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 385025003393 Part of AAA domain; Region: AAA_19; pfam13245 385025003394 Family description; Region: UvrD_C_2; pfam13538 385025003395 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 385025003396 Uncharacterized conserved protein [Function unknown]; Region: COG0398 385025003397 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 385025003398 mercuric reductase; Validated; Region: PRK06370 385025003399 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025003400 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025003401 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 385025003402 radical SAM/Cys-rich domain protein; Region: rSAM_SeCys; TIGR04167 385025003403 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 385025003404 FeS/SAM binding site; other site 385025003405 Protein of unknown function (DUF3641); Region: DUF3641; pfam12345 385025003406 GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function; Region: GT_2_like_a; cd02522 385025003407 transferase 2, rSAM/selenodomain-associated; Region: glyco_like_mftF; TIGR04283 385025003408 Probable Catalytic site; other site 385025003409 PII uridylyl-transferase; Provisional; Region: glnD; PRK00275 385025003410 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 385025003411 metal binding triad; other site 385025003412 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 385025003413 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 385025003414 Zn2+ binding site [ion binding]; other site 385025003415 Mg2+ binding site [ion binding]; other site 385025003416 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 385025003417 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 385025003418 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 385025003419 active site 385025003420 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 385025003421 rRNA interaction site [nucleotide binding]; other site 385025003422 S8 interaction site; other site 385025003423 putative laminin-1 binding site; other site 385025003424 elongation factor Ts; Provisional; Region: tsf; PRK09377 385025003425 UBA/TS-N domain; Region: UBA; pfam00627 385025003426 Elongation factor TS; Region: EF_TS; pfam00889 385025003427 Elongation factor TS; Region: EF_TS; pfam00889 385025003428 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 385025003429 putative nucleotide binding site [chemical binding]; other site 385025003430 uridine monophosphate binding site [chemical binding]; other site 385025003431 homohexameric interface [polypeptide binding]; other site 385025003432 ribosome recycling factor; Reviewed; Region: frr; PRK00083 385025003433 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 385025003434 hinge region; other site 385025003435 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 385025003436 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 385025003437 catalytic residue [active] 385025003438 putative FPP diphosphate binding site; other site 385025003439 putative FPP binding hydrophobic cleft; other site 385025003440 dimer interface [polypeptide binding]; other site 385025003441 putative IPP diphosphate binding site; other site 385025003442 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 385025003443 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 385025003444 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 385025003445 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 385025003446 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 385025003447 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 385025003448 zinc metallopeptidase RseP; Provisional; Region: PRK10779 385025003449 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 385025003450 active site 385025003451 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 385025003452 protein binding site [polypeptide binding]; other site 385025003453 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 385025003454 protein binding site [polypeptide binding]; other site 385025003455 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 385025003456 putative substrate binding region [chemical binding]; other site 385025003457 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 385025003458 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 385025003459 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 385025003460 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 385025003461 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 385025003462 Surface antigen; Region: Bac_surface_Ag; pfam01103 385025003463 periplasmic chaperone; Provisional; Region: PRK10780 385025003464 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 385025003465 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 385025003466 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 385025003467 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 385025003468 trimer interface [polypeptide binding]; other site 385025003469 active site 385025003470 UDP-GlcNAc binding site [chemical binding]; other site 385025003471 lipid binding site [chemical binding]; lipid-binding site 385025003472 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 385025003473 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 385025003474 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 385025003475 active site 385025003476 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 385025003477 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 385025003478 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 385025003479 RNA/DNA hybrid binding site [nucleotide binding]; other site 385025003480 active site 385025003481 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 385025003482 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 385025003483 putative active site [active] 385025003484 putative PHP Thumb interface [polypeptide binding]; other site 385025003485 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 385025003486 generic binding surface II; other site 385025003487 generic binding surface I; other site 385025003488 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 385025003489 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 385025003490 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 385025003491 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 385025003492 Ligand Binding Site [chemical binding]; other site 385025003493 TilS substrate binding domain; Region: TilS; pfam09179 385025003494 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 385025003495 CTP synthetase; Validated; Region: pyrG; PRK05380 385025003496 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 385025003497 Catalytic site [active] 385025003498 active site 385025003499 UTP binding site [chemical binding]; other site 385025003500 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 385025003501 active site 385025003502 putative oxyanion hole; other site 385025003503 catalytic triad [active] 385025003504 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 385025003505 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 385025003506 enolase; Provisional; Region: eno; PRK00077 385025003507 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 385025003508 dimer interface [polypeptide binding]; other site 385025003509 metal binding site [ion binding]; metal-binding site 385025003510 substrate binding pocket [chemical binding]; other site 385025003511 Septum formation initiator; Region: DivIC; cl17659 385025003512 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 385025003513 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 385025003514 substrate binding site; other site 385025003515 dimer interface; other site 385025003516 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 385025003517 homotrimer interaction site [polypeptide binding]; other site 385025003518 zinc binding site [ion binding]; other site 385025003519 CDP-binding sites; other site 385025003520 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 385025003521 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 385025003522 Permutation of conserved domain; other site 385025003523 active site 385025003524 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 385025003525 Bacitracin resistance protein BacA; Region: BacA; pfam02673 385025003526 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 385025003527 Smr domain; Region: Smr; pfam01713 385025003528 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 385025003529 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 385025003530 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 385025003531 S-adenosylmethionine binding site [chemical binding]; other site 385025003532 Predicted membrane protein [Function unknown]; Region: COG1238 385025003533 lipoprotein NlpD; Provisional; Region: nlpD; PRK10871 385025003534 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025003535 Peptidase family M23; Region: Peptidase_M23; pfam01551 385025003536 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 385025003537 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 385025003538 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025003539 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 385025003540 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 385025003541 DNA binding residues [nucleotide binding] 385025003542 aminotransferase; Validated; Region: PRK08175 385025003543 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 385025003544 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025003545 homodimer interface [polypeptide binding]; other site 385025003546 catalytic residue [active] 385025003547 homoserine dehydrogenase; Provisional; Region: PRK06349 385025003548 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 385025003549 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 385025003550 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 385025003551 threonine synthase; Reviewed; Region: PRK06721 385025003552 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 385025003553 homodimer interface [polypeptide binding]; other site 385025003554 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025003555 catalytic residue [active] 385025003556 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 385025003557 DHH family; Region: DHH; pfam01368 385025003558 DHHA1 domain; Region: DHHA1; pfam02272 385025003559 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 385025003560 aromatic arch; other site 385025003561 DCoH dimer interaction site [polypeptide binding]; other site 385025003562 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 385025003563 DCoH tetramer interaction site [polypeptide binding]; other site 385025003564 substrate binding site [chemical binding]; other site 385025003565 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 385025003566 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 385025003567 RNA binding surface [nucleotide binding]; other site 385025003568 FeS assembly SUF system regulator, gammaproteobacterial; Region: suf_reg_Xantho; TIGR02944 385025003569 Transcriptional regulator; Region: Rrf2; pfam02082 385025003570 Transcriptional regulator; Region: Rrf2; cl17282 385025003571 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 385025003572 putative ABC transporter; Region: ycf24; CHL00085 385025003573 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 385025003574 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 385025003575 Walker A/P-loop; other site 385025003576 ATP binding site [chemical binding]; other site 385025003577 Q-loop/lid; other site 385025003578 ABC transporter signature motif; other site 385025003579 Walker B; other site 385025003580 D-loop; other site 385025003581 H-loop/switch region; other site 385025003582 FeS assembly protein SufD; Region: sufD; TIGR01981 385025003583 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 385025003584 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 385025003585 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 385025003586 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 385025003587 catalytic residue [active] 385025003588 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 385025003589 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 385025003590 trimerization site [polypeptide binding]; other site 385025003591 active site 385025003592 This domain is found in peptide chain release factors; Region: PCRF; smart00937 385025003593 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 385025003594 RF-1 domain; Region: RF-1; pfam00472 385025003595 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 385025003596 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 385025003597 dimer interface [polypeptide binding]; other site 385025003598 putative anticodon binding site; other site 385025003599 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 385025003600 motif 1; other site 385025003601 active site 385025003602 motif 2; other site 385025003603 motif 3; other site 385025003604 Protein of unknown function (DUF1282); Region: DUF1282; pfam06930 385025003605 Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG); Region: Caa3_CtaG; pfam09678 385025003606 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 385025003607 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 385025003608 Cu(I) binding site [ion binding]; other site 385025003609 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 385025003610 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 385025003611 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 385025003612 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 385025003613 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 385025003614 SdhD (CybS) interface [polypeptide binding]; other site 385025003615 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 385025003616 putative SdhC subunit interface [polypeptide binding]; other site 385025003617 putative proximal heme binding site [chemical binding]; other site 385025003618 putative Iron-sulfur protein interface [polypeptide binding]; other site 385025003619 putative proximal quinone binding site; other site 385025003620 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 385025003621 L-aspartate oxidase; Provisional; Region: PRK06175 385025003622 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 385025003623 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 385025003624 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 385025003625 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 385025003626 L-aspartate oxidase; Provisional; Region: PRK09077 385025003627 L-aspartate oxidase; Provisional; Region: PRK06175 385025003628 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 385025003629 RNA polymerase sigma factor AlgU; Provisional; Region: algU; PRK11923 385025003630 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025003631 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 385025003632 DNA binding residues [nucleotide binding] 385025003633 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 385025003634 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 385025003635 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 385025003636 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 385025003637 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 385025003638 protein binding site [polypeptide binding]; other site 385025003639 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 385025003640 protein binding site [polypeptide binding]; other site 385025003641 GTP-binding protein LepA; Provisional; Region: PRK05433 385025003642 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 385025003643 G1 box; other site 385025003644 putative GEF interaction site [polypeptide binding]; other site 385025003645 GTP/Mg2+ binding site [chemical binding]; other site 385025003646 Switch I region; other site 385025003647 G2 box; other site 385025003648 G3 box; other site 385025003649 Switch II region; other site 385025003650 G4 box; other site 385025003651 G5 box; other site 385025003652 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 385025003653 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 385025003654 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 385025003655 signal peptidase I; Provisional; Region: PRK10861 385025003656 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 385025003657 Catalytic site [active] 385025003658 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 385025003659 ribonuclease III; Reviewed; Region: rnc; PRK00102 385025003660 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 385025003661 dimerization interface [polypeptide binding]; other site 385025003662 active site 385025003663 metal binding site [ion binding]; metal-binding site 385025003664 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 385025003665 dsRNA binding site [nucleotide binding]; other site 385025003666 GTPase Era; Reviewed; Region: era; PRK00089 385025003667 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 385025003668 G1 box; other site 385025003669 GTP/Mg2+ binding site [chemical binding]; other site 385025003670 Switch I region; other site 385025003671 G2 box; other site 385025003672 Switch II region; other site 385025003673 G3 box; other site 385025003674 G4 box; other site 385025003675 G5 box; other site 385025003676 KH domain; Region: KH_2; pfam07650 385025003677 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 385025003678 Recombination protein O N terminal; Region: RecO_N; pfam11967 385025003679 Recombination protein O C terminal; Region: RecO_C; pfam02565 385025003680 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 385025003681 active site 385025003682 hydrophilic channel; other site 385025003683 dimerization interface [polypeptide binding]; other site 385025003684 catalytic residues [active] 385025003685 active site lid [active] 385025003686 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 385025003687 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 385025003688 dimerization interface 3.5A [polypeptide binding]; other site 385025003689 active site 385025003690 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 385025003691 active site 385025003692 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 385025003693 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 385025003694 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025003695 catalytic residue [active] 385025003696 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 385025003697 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 385025003698 substrate binding site [chemical binding]; other site 385025003699 active site 385025003700 catalytic residues [active] 385025003701 heterodimer interface [polypeptide binding]; other site 385025003702 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 385025003703 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 385025003704 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 385025003705 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 385025003706 Uncharacterized protein conserved in bacteria [Function unknown]; Region: DedD; COG3147 385025003707 Sporulation related domain; Region: SPOR; pfam05036 385025003708 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 385025003709 Colicin V production protein; Region: Colicin_V; cl00567 385025003710 amidophosphoribosyltransferase; Provisional; Region: PRK09246 385025003711 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 385025003712 active site 385025003713 tetramer interface [polypeptide binding]; other site 385025003714 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 385025003715 active site 385025003716 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 385025003717 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 385025003718 homodimer interface [polypeptide binding]; other site 385025003719 substrate-cofactor binding pocket; other site 385025003720 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025003721 catalytic residue [active] 385025003722 hypothetical protein; Provisional; Region: PRK12378 385025003723 NRDE protein; Region: NRDE; cl01315 385025003724 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 385025003725 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 385025003726 substrate binding site [chemical binding]; other site 385025003727 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 385025003728 substrate binding site [chemical binding]; other site 385025003729 ligand binding site [chemical binding]; other site 385025003730 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 385025003731 PAS domain; Region: PAS_9; pfam13426 385025003732 putative active site [active] 385025003733 heme pocket [chemical binding]; other site 385025003734 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 385025003735 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 385025003736 putative active site [active] 385025003737 heme pocket [chemical binding]; other site 385025003738 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 385025003739 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 385025003740 putative active site [active] 385025003741 heme pocket [chemical binding]; other site 385025003742 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 385025003743 dimer interface [polypeptide binding]; other site 385025003744 phosphorylation site [posttranslational modification] 385025003745 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 385025003746 ATP binding site [chemical binding]; other site 385025003747 Mg2+ binding site [ion binding]; other site 385025003748 G-X-G motif; other site 385025003749 Response regulator receiver domain; Region: Response_reg; pfam00072 385025003750 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025003751 active site 385025003752 phosphorylation site [posttranslational modification] 385025003753 intermolecular recognition site; other site 385025003754 dimerization interface [polypeptide binding]; other site 385025003755 Hemerythrin family; Region: Hemerythrin-like; cl15774 385025003756 Fe binding site [ion binding]; other site 385025003757 Response regulator receiver domain; Region: Response_reg; pfam00072 385025003758 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025003759 active site 385025003760 phosphorylation site [posttranslational modification] 385025003761 intermolecular recognition site; other site 385025003762 dimerization interface [polypeptide binding]; other site 385025003763 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 385025003764 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 385025003765 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 385025003766 Walker A/P-loop; other site 385025003767 ATP binding site [chemical binding]; other site 385025003768 Q-loop/lid; other site 385025003769 ABC transporter signature motif; other site 385025003770 Walker B; other site 385025003771 D-loop; other site 385025003772 H-loop/switch region; other site 385025003773 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 385025003774 nitrate transport ATP-binding subunits C and D; Region: ntrCD; TIGR01184 385025003775 Walker A/P-loop; other site 385025003776 ATP binding site [chemical binding]; other site 385025003777 Q-loop/lid; other site 385025003778 ABC transporter signature motif; other site 385025003779 Walker B; other site 385025003780 D-loop; other site 385025003781 H-loop/switch region; other site 385025003782 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 385025003783 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 385025003784 dimer interface [polypeptide binding]; other site 385025003785 conserved gate region; other site 385025003786 putative PBP binding loops; other site 385025003787 ABC-ATPase subunit interface; other site 385025003788 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 385025003789 NMT1-like family; Region: NMT1_2; pfam13379 385025003790 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 385025003791 ANTAR domain; Region: ANTAR; pfam03861 385025003792 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 385025003793 soluble pyridine nucleotide transhydrogenase; Provisional; Region: PRK05249 385025003794 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025003795 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025003796 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 385025003797 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 385025003798 dinuclear metal binding motif [ion binding]; other site 385025003799 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 385025003800 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 385025003801 putative active site [active] 385025003802 putative metal binding site [ion binding]; other site 385025003803 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 385025003804 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 385025003805 substrate binding site [chemical binding]; other site 385025003806 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 385025003807 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 385025003808 active site 385025003809 HIGH motif; other site 385025003810 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 385025003811 KMSKS motif; other site 385025003812 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 385025003813 tRNA binding surface [nucleotide binding]; other site 385025003814 anticodon binding site; other site 385025003815 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 385025003816 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 385025003817 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 385025003818 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 385025003819 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 385025003820 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 385025003821 recombination factor protein RarA; Reviewed; Region: PRK13342 385025003822 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 385025003823 Walker A motif; other site 385025003824 ATP binding site [chemical binding]; other site 385025003825 Walker B motif; other site 385025003826 arginine finger; other site 385025003827 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 385025003828 BON domain; Region: BON; pfam04972 385025003829 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 385025003830 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 385025003831 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 385025003832 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 385025003833 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 385025003834 Substrate binding site; other site 385025003835 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 385025003836 Dicarboxylate transport; Region: DctA-YdbH; cl14674 385025003837 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 385025003838 Putative ATP-dependant zinc protease; Region: Zn_protease; cl01682 385025003839 Inactive transglutaminase fused to 7 transmembrane helices; Region: Transglut_i_TM; pfam14400 385025003840 7 transmembrane helices usually fused to an inactive transglutaminase; Region: 7TM_transglut; pfam14402 385025003841 alpha-L-glutamate ligase-related protein; Region: rimK_rel_E_lig; TIGR02291 385025003842 CHASE domain; Region: CHASE; pfam03924 385025003843 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025003844 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 385025003845 ATP binding site [chemical binding]; other site 385025003846 Mg2+ binding site [ion binding]; other site 385025003847 G-X-G motif; other site 385025003848 Response regulator receiver domain; Region: Response_reg; pfam00072 385025003849 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025003850 active site 385025003851 phosphorylation site [posttranslational modification] 385025003852 intermolecular recognition site; other site 385025003853 dimerization interface [polypeptide binding]; other site 385025003854 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025003855 short chain dehydrogenase; Provisional; Region: PRK07890 385025003856 NAD(P) binding site [chemical binding]; other site 385025003857 active site 385025003858 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 385025003859 active site 1 [active] 385025003860 dimer interface [polypeptide binding]; other site 385025003861 hexamer interface [polypeptide binding]; other site 385025003862 active site 2 [active] 385025003863 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 385025003864 active site 1 [active] 385025003865 dimer interface [polypeptide binding]; other site 385025003866 hexamer interface [polypeptide binding]; other site 385025003867 active site 2 [active] 385025003868 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 385025003869 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 385025003870 Transposase zinc-binding domain; Region: Zn_Tnp_IS91; pfam14319 385025003871 Putative transposase; Region: Y2_Tnp; pfam04986 385025003872 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 385025003873 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 385025003874 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 385025003875 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 385025003876 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 385025003877 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 385025003878 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 385025003879 Response regulator receiver domain; Region: Response_reg; pfam00072 385025003880 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025003881 active site 385025003882 phosphorylation site [posttranslational modification] 385025003883 intermolecular recognition site; other site 385025003884 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025003885 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025003886 metal binding site [ion binding]; metal-binding site 385025003887 active site 385025003888 I-site; other site 385025003889 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 385025003890 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 385025003891 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 385025003892 DNA phosphorothioation system restriction enzyme; Region: dnd_restrict_1; TIGR04095 385025003893 ATP binding site [chemical binding]; other site 385025003894 putative Mg++ binding site [ion binding]; other site 385025003895 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 385025003896 EcoEI R protein C-terminal; Region: EcoEI_R_C; pfam08463 385025003897 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 385025003898 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 385025003899 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 385025003900 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 385025003901 ATP binding site [chemical binding]; other site 385025003902 putative Mg++ binding site [ion binding]; other site 385025003903 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 385025003904 nucleotide binding region [chemical binding]; other site 385025003905 ATP-binding site [chemical binding]; other site 385025003906 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 385025003907 HsdM N-terminal domain; Region: HsdM_N; pfam12161 385025003908 Methyltransferase domain; Region: Methyltransf_26; pfam13659 385025003909 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea; Region: GIY-YIG_unchar_2; cd10447 385025003910 GIY-YIG motif/motif A; other site 385025003911 putative active site [active] 385025003912 putative metal binding site [ion binding]; other site 385025003913 Domain of unknown function (DUF4357); Region: DUF4357; pfam14267 385025003914 response regulator; Provisional; Region: PRK09483 385025003915 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025003916 active site 385025003917 phosphorylation site [posttranslational modification] 385025003918 intermolecular recognition site; other site 385025003919 dimerization interface [polypeptide binding]; other site 385025003920 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 385025003921 DNA binding residues [nucleotide binding] 385025003922 dimerization interface [polypeptide binding]; other site 385025003923 TonB-dependent vitamin B12 receptor; Region: TonB-B12; TIGR01779 385025003924 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 385025003925 N-terminal plug; other site 385025003926 ligand-binding site [chemical binding]; other site 385025003927 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 385025003928 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 385025003929 Walker A/P-loop; other site 385025003930 ATP binding site [chemical binding]; other site 385025003931 Q-loop/lid; other site 385025003932 ABC transporter signature motif; other site 385025003933 Walker B; other site 385025003934 D-loop; other site 385025003935 H-loop/switch region; other site 385025003936 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 385025003937 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 385025003938 ABC-ATPase subunit interface; other site 385025003939 dimer interface [polypeptide binding]; other site 385025003940 putative PBP binding regions; other site 385025003941 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 385025003942 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 385025003943 intersubunit interface [polypeptide binding]; other site 385025003944 MAPEG family; Region: MAPEG; pfam01124 385025003945 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 385025003946 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 385025003947 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 385025003948 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 385025003949 Catalytic site [active] 385025003950 DNA polymerase V subunit UmuC; Reviewed; Region: umuC; PRK03609 385025003951 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 385025003952 active site 385025003953 DNA binding site [nucleotide binding] 385025003954 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 385025003955 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 385025003956 FtsX-like permease family; Region: FtsX; pfam02687 385025003957 ABC-type arginine transport system, ATPase component [Amino acid transport and metabolism]; Region: ArtP; COG4161 385025003958 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 385025003959 Walker A/P-loop; other site 385025003960 ATP binding site [chemical binding]; other site 385025003961 Q-loop/lid; other site 385025003962 ABC transporter signature motif; other site 385025003963 Walker B; other site 385025003964 D-loop; other site 385025003965 H-loop/switch region; other site 385025003966 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 385025003967 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 385025003968 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 385025003969 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 385025003970 MerC mercury resistance protein; Region: MerC; pfam03203 385025003971 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 385025003972 metal binding site 2 [ion binding]; metal-binding site 385025003973 putative DNA binding helix; other site 385025003974 metal binding site 1 [ion binding]; metal-binding site 385025003975 dimer interface [polypeptide binding]; other site 385025003976 structural Zn2+ binding site [ion binding]; other site 385025003977 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 385025003978 FOG: CBS domain [General function prediction only]; Region: COG0517 385025003979 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_27; cd04640 385025003980 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 385025003981 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 385025003982 Class I aldolases; Region: Aldolase_Class_I; cl17187 385025003983 catalytic residue [active] 385025003984 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 385025003985 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 385025003986 hexamer interface [polypeptide binding]; other site 385025003987 ligand binding site [chemical binding]; other site 385025003988 putative active site [active] 385025003989 NAD(P) binding site [chemical binding]; other site 385025003990 thioredoxin reductase; Provisional; Region: PRK10262 385025003991 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025003992 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025003993 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 385025003994 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 385025003995 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 385025003996 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 385025003997 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 385025003998 rRNA binding site [nucleotide binding]; other site 385025003999 predicted 30S ribosome binding site; other site 385025004000 ATP-dependent Clp protease ATP-binding subunit; Provisional; Region: clpA; PRK11034 385025004001 Clp amino terminal domain; Region: Clp_N; pfam02861 385025004002 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 385025004003 Walker A motif; other site 385025004004 ATP binding site [chemical binding]; other site 385025004005 Walker B motif; other site 385025004006 arginine finger; other site 385025004007 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 385025004008 Walker A motif; other site 385025004009 ATP binding site [chemical binding]; other site 385025004010 Walker B motif; other site 385025004011 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 385025004012 Uncharacterized conserved protein [Function unknown]; Region: COG2127 385025004013 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 385025004014 tetramer interface [polypeptide binding]; other site 385025004015 active site 385025004016 Mg2+/Mn2+ binding site [ion binding]; other site 385025004017 isocitrate lyase; Region: PLN02892 385025004018 malate synthase A; Region: malate_syn_A; TIGR01344 385025004019 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 385025004020 active site 385025004021 Transcriptional regulator [Transcription]; Region: LysR; COG0583 385025004022 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 385025004023 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 385025004024 dimerization interface [polypeptide binding]; other site 385025004025 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 385025004026 nudix motif; other site 385025004027 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 385025004028 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 385025004029 Ligand Binding Site [chemical binding]; other site 385025004030 adenylosuccinate lyase; Provisional; Region: PRK09285 385025004031 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 385025004032 tetramer interface [polypeptide binding]; other site 385025004033 active site 385025004034 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 385025004035 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 385025004036 sensor protein PhoQ; Provisional; Region: PRK10815 385025004037 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 385025004038 ATP binding site [chemical binding]; other site 385025004039 Mg2+ binding site [ion binding]; other site 385025004040 G-X-G motif; other site 385025004041 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 385025004042 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025004043 active site 385025004044 phosphorylation site [posttranslational modification] 385025004045 intermolecular recognition site; other site 385025004046 dimerization interface [polypeptide binding]; other site 385025004047 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 385025004048 DNA binding site [nucleotide binding] 385025004049 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 385025004050 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 385025004051 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 385025004052 tandem repeat interface [polypeptide binding]; other site 385025004053 oligomer interface [polypeptide binding]; other site 385025004054 active site residues [active] 385025004055 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 385025004056 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 385025004057 motif II; other site 385025004058 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 385025004059 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 385025004060 RNA binding surface [nucleotide binding]; other site 385025004061 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 385025004062 active site 385025004063 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 385025004064 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 385025004065 homodimer interface [polypeptide binding]; other site 385025004066 oligonucleotide binding site [chemical binding]; other site 385025004067 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 385025004068 CoenzymeA binding site [chemical binding]; other site 385025004069 subunit interaction site [polypeptide binding]; other site 385025004070 PHB binding site; other site 385025004071 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 385025004072 DUF35 OB-fold domain; Region: DUF35; pfam01796 385025004073 thiolase; Provisional; Region: PRK06158 385025004074 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 385025004075 active site 385025004076 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 385025004077 CoA-transferase family III; Region: CoA_transf_3; pfam02515 385025004078 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 385025004079 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 385025004080 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004081 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004082 active site 385025004083 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 385025004084 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 385025004085 active site 385025004086 oxalacetate binding site [chemical binding]; other site 385025004087 citrylCoA binding site [chemical binding]; other site 385025004088 coenzyme A binding site [chemical binding]; other site 385025004089 catalytic triad [active] 385025004090 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 385025004091 active site 385025004092 catalytic site [active] 385025004093 (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel...; Region: R_hydratase_like; cd03441 385025004094 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 385025004095 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 385025004096 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 385025004097 active site 385025004098 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 385025004099 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004100 active site 385025004101 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 385025004102 2-methylcitrate dehydratase; Region: prpD; TIGR02330 385025004103 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 385025004104 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 385025004105 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 385025004106 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 385025004107 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 385025004108 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 385025004109 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 385025004110 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 385025004111 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 385025004112 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 385025004113 Ligand binding site [chemical binding]; other site 385025004114 Electron transfer flavoprotein domain; Region: ETF; pfam01012 385025004115 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 385025004116 putative FMN binding site [chemical binding]; other site 385025004117 NnrS protein; Region: NnrS; pfam05940 385025004118 MAPEG family; Region: MAPEG; cl09190 385025004119 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 385025004120 CoA-transferase family III; Region: CoA_transf_3; pfam02515 385025004121 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 385025004122 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 385025004123 NAD(P) binding site [chemical binding]; other site 385025004124 substrate binding site [chemical binding]; other site 385025004125 homotetramer interface [polypeptide binding]; other site 385025004126 active site 385025004127 homodimer interface [polypeptide binding]; other site 385025004128 enoyl-CoA hydratase; Provisional; Region: PRK05862 385025004129 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025004130 substrate binding site [chemical binding]; other site 385025004131 oxyanion hole (OAH) forming residues; other site 385025004132 trimer interface [polypeptide binding]; other site 385025004133 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 385025004134 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 385025004135 NAD binding site [chemical binding]; other site 385025004136 homodimer interface [polypeptide binding]; other site 385025004137 homotetramer interface [polypeptide binding]; other site 385025004138 active site 385025004139 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 385025004140 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 385025004141 dimer interface [polypeptide binding]; other site 385025004142 active site 385025004143 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 385025004144 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 385025004145 dimer interface [polypeptide binding]; other site 385025004146 acyl-activating enzyme (AAE) consensus motif; other site 385025004147 putative active site [active] 385025004148 AMP binding site [chemical binding]; other site 385025004149 putative CoA binding site [chemical binding]; other site 385025004150 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 385025004151 Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; Region: NT_2-5OAS_ClassI-CCAase; cd05400 385025004152 active site 385025004153 NTP binding site [chemical binding]; other site 385025004154 metal binding triad [ion binding]; metal-binding site 385025004155 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 385025004156 putative active site [active] 385025004157 putative catalytic site [active] 385025004158 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 385025004159 active site 2 [active] 385025004160 active site 1 [active] 385025004161 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 385025004162 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 385025004163 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 385025004164 active site 385025004165 FMN binding site [chemical binding]; other site 385025004166 2,4-decadienoyl-CoA binding site; other site 385025004167 catalytic residue [active] 385025004168 4Fe-4S cluster binding site [ion binding]; other site 385025004169 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025004170 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 385025004171 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 385025004172 dimer interface [polypeptide binding]; other site 385025004173 active site 385025004174 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 385025004175 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 385025004176 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 385025004177 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025004178 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 385025004179 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 385025004180 carboxyltransferase (CT) interaction site; other site 385025004181 biotinylation site [posttranslational modification]; other site 385025004182 enoyl-CoA hydratase; Provisional; Region: PRK05995 385025004183 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025004184 substrate binding site [chemical binding]; other site 385025004185 oxyanion hole (OAH) forming residues; other site 385025004186 trimer interface [polypeptide binding]; other site 385025004187 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 385025004188 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004189 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004190 active site 385025004191 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 385025004192 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 385025004193 tetramerization interface [polypeptide binding]; other site 385025004194 NAD(P) binding site [chemical binding]; other site 385025004195 catalytic residues [active] 385025004196 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 385025004197 CoA binding domain; Region: CoA_binding_2; pfam13380 385025004198 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 385025004199 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 385025004200 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025004201 enoyl-CoA hydratase; Provisional; Region: PRK09245 385025004202 substrate binding site [chemical binding]; other site 385025004203 oxyanion hole (OAH) forming residues; other site 385025004204 trimer interface [polypeptide binding]; other site 385025004205 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 385025004206 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 385025004207 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 385025004208 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 385025004209 dimer interaction site [polypeptide binding]; other site 385025004210 substrate-binding tunnel; other site 385025004211 active site 385025004212 catalytic site [active] 385025004213 substrate binding site [chemical binding]; other site 385025004214 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004215 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004216 active site 385025004217 enoyl-CoA hydratase; Provisional; Region: PRK07468 385025004218 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025004219 substrate binding site [chemical binding]; other site 385025004220 oxyanion hole (OAH) forming residues; other site 385025004221 trimer interface [polypeptide binding]; other site 385025004222 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 385025004223 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 385025004224 isovaleryl-CoA dehydrogenase; Region: PLN02519 385025004225 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 385025004226 substrate binding site [chemical binding]; other site 385025004227 FAD binding site [chemical binding]; other site 385025004228 catalytic base [active] 385025004229 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 385025004230 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 385025004231 dimer interface [polypeptide binding]; other site 385025004232 active site 385025004233 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 385025004234 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 385025004235 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 385025004236 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 385025004237 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025004238 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 385025004239 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 385025004240 carboxyltransferase (CT) interaction site; other site 385025004241 biotinylation site [posttranslational modification]; other site 385025004242 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 385025004243 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 385025004244 active site 385025004245 catalytic residues [active] 385025004246 metal binding site [ion binding]; metal-binding site 385025004247 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 385025004248 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 385025004249 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 385025004250 nudix motif; other site 385025004251 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004252 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004253 active site 385025004254 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 385025004255 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 385025004256 Walker A motif; other site 385025004257 ATP binding site [chemical binding]; other site 385025004258 Walker B motif; other site 385025004259 arginine finger; other site 385025004260 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 385025004261 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 385025004262 short chain dehydrogenase; Provisional; Region: PRK07791 385025004263 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025004264 NAD(P) binding site [chemical binding]; other site 385025004265 active site 385025004266 enoyl-CoA hydratase; Provisional; Region: PRK09245 385025004267 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 385025004268 substrate binding site [chemical binding]; other site 385025004269 oxyanion hole (OAH) forming residues; other site 385025004270 trimer interface [polypeptide binding]; other site 385025004271 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004272 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004273 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004274 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004275 active site 385025004276 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 385025004277 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 385025004278 active site 385025004279 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 385025004280 CoA-transferase family III; Region: CoA_transf_3; pfam02515 385025004281 ammonium transporter; Region: amt; TIGR00836 385025004282 PAS domain S-box; Region: sensory_box; TIGR00229 385025004283 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 385025004284 putative active site [active] 385025004285 heme pocket [chemical binding]; other site 385025004286 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025004287 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025004288 metal binding site [ion binding]; metal-binding site 385025004289 active site 385025004290 I-site; other site 385025004291 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 385025004292 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 385025004293 YccA-like proteins; Region: YccA_like; cd10433 385025004294 seryl-tRNA synthetase; Provisional; Region: PRK05431 385025004295 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 385025004296 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 385025004297 dimer interface [polypeptide binding]; other site 385025004298 active site 385025004299 motif 1; other site 385025004300 motif 2; other site 385025004301 motif 3; other site 385025004302 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 385025004303 CrcB-like protein; Region: CRCB; cl09114 385025004304 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 385025004305 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 385025004306 active site 385025004307 putative substrate binding pocket [chemical binding]; other site 385025004308 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 385025004309 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 385025004310 S-adenosylmethionine binding site [chemical binding]; other site 385025004311 phosphoglycolate phosphatase; Provisional; Region: PRK13222 385025004312 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 385025004313 motif II; other site 385025004314 RmuC family; Region: RmuC; pfam02646 385025004315 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 385025004316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025004317 NAD(P) binding site [chemical binding]; other site 385025004318 active site 385025004319 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 385025004320 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 385025004321 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 385025004322 catalytic residue [active] 385025004323 serine O-acetyltransferase; Region: cysE; TIGR01172 385025004324 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 385025004325 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 385025004326 trimer interface [polypeptide binding]; other site 385025004327 active site 385025004328 substrate binding site [chemical binding]; other site 385025004329 CoA binding site [chemical binding]; other site 385025004330 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 385025004331 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 385025004332 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 385025004333 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 385025004334 active site 385025004335 dimerization interface [polypeptide binding]; other site 385025004336 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 385025004337 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 385025004338 Protein export membrane protein; Region: SecD_SecF; pfam02355 385025004339 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 385025004340 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 385025004341 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 385025004342 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 385025004343 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 385025004344 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 385025004345 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 385025004346 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 385025004347 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 385025004348 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 385025004349 metal-binding site [ion binding] 385025004350 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 385025004351 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 385025004352 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 385025004353 Ion channel; Region: Ion_trans_2; pfam07885 385025004354 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 385025004355 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 385025004356 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025004357 Outer membrane efflux protein; Region: OEP; pfam02321 385025004358 Outer membrane efflux protein; Region: OEP; pfam02321 385025004359 Herpesvirus BLRF2 protein; Region: Herpes_BLRF2; cl17417 385025004360 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 385025004361 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 385025004362 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 385025004363 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 385025004364 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 385025004365 metal-binding site [ion binding] 385025004366 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 385025004367 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 385025004368 motif II; other site 385025004369 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 385025004370 DNA binding residues [nucleotide binding] 385025004371 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 385025004372 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 385025004373 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 385025004374 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 385025004375 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 385025004376 Multicopper oxidase; Region: Cu-oxidase; pfam00394 385025004377 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 385025004378 Predicted metal-binding protein [General function prediction only]; Region: COG3019 385025004379 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 385025004380 Domain of unknown function (DUF4177); Region: DUF4177; pfam13783 385025004381 hypothetical protein; Reviewed; Region: PRK00024 385025004382 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 385025004383 MPN+ (JAMM) motif; other site 385025004384 Zinc-binding site [ion binding]; other site 385025004385 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 385025004386 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 385025004387 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 385025004388 Histone acetyltransferases subunit 3; Region: Ada3; pfam10198 385025004389 TraU protein; Region: TraU; cl06067 385025004390 Protein of unknown function (DUF1525); Region: DUF1525; cl06515 385025004391 Cytochrome c; Region: Cytochrom_C; pfam00034 385025004392 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 385025004393 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 385025004394 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 385025004395 DNA binding residues [nucleotide binding] 385025004396 dimer interface [polypeptide binding]; other site 385025004397 putative metal binding site [ion binding]; other site 385025004398 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 385025004399 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 385025004400 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 385025004401 Outer membrane efflux protein; Region: OEP; pfam02321 385025004402 Outer membrane efflux protein; Region: OEP; pfam02321 385025004403 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 385025004404 carboxyltransferase (CT) interaction site; other site 385025004405 biotinylation site [posttranslational modification]; other site 385025004406 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025004407 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 385025004408 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 385025004409 active site 385025004410 catalytic residues [active] 385025004411 DNA binding site [nucleotide binding] 385025004412 Int/Topo IB signature motif; other site 385025004413 Protein with unknown function (DUF469); Region: DUF469; cl01237 385025004414 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 385025004415 active site 385025004416 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 385025004417 active site 385025004418 metal binding site [ion binding]; metal-binding site 385025004419 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 385025004420 active site 385025004421 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 385025004422 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025004423 inter-subunit interface; other site 385025004424 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 385025004425 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 385025004426 iron-sulfur cluster [ion binding]; other site 385025004427 [2Fe-2S] cluster binding site [ion binding]; other site 385025004428 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 385025004429 hydrophobic ligand binding site; other site 385025004430 MAPEG family; Region: MAPEG; pfam01124 385025004431 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 385025004432 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 385025004433 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 385025004434 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025004435 active site 385025004436 phosphorylation site [posttranslational modification] 385025004437 intermolecular recognition site; other site 385025004438 dimerization interface [polypeptide binding]; other site 385025004439 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 385025004440 DNA binding site [nucleotide binding] 385025004441 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025004442 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 385025004443 dimerization interface [polypeptide binding]; other site 385025004444 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 385025004445 dimer interface [polypeptide binding]; other site 385025004446 phosphorylation site [posttranslational modification] 385025004447 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 385025004448 ATP binding site [chemical binding]; other site 385025004449 Mg2+ binding site [ion binding]; other site 385025004450 G-X-G motif; other site 385025004451 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025004452 Transcriptional activator [Transcription]; Region: ChrR; COG3806 385025004453 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 385025004454 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 385025004455 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025004456 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 385025004457 nucleophilic elbow; other site 385025004458 catalytic triad; other site 385025004459 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 385025004460 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025004461 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025004462 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 385025004463 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 385025004464 Uncharacterized conserved protein [Function unknown]; Region: COG1479 385025004465 Protein of unknown function DUF262; Region: DUF262; pfam03235 385025004466 Protein of unknown function DUF262; Region: DUF262; pfam03235 385025004467 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 385025004468 AAA domain; Region: AAA_17; pfam13207 385025004469 AAA domain; Region: AAA_33; pfam13671 385025004470 Major Facilitator Superfamily; Region: MFS_1; pfam07690 385025004471 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 385025004472 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK08955 385025004473 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 385025004474 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 385025004475 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 385025004476 putative DNA binding site [nucleotide binding]; other site 385025004477 putative Zn2+ binding site [ion binding]; other site 385025004478 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 385025004479 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 385025004480 dimer interface [polypeptide binding]; other site 385025004481 PYR/PP interface [polypeptide binding]; other site 385025004482 TPP binding site [chemical binding]; other site 385025004483 substrate binding site [chemical binding]; other site 385025004484 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 385025004485 TPP-binding site [chemical binding]; other site 385025004486 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 385025004487 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 385025004488 dimer interaction site [polypeptide binding]; other site 385025004489 substrate-binding tunnel; other site 385025004490 active site 385025004491 catalytic site [active] 385025004492 substrate binding site [chemical binding]; other site 385025004493 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 385025004494 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 385025004495 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 385025004496 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 385025004497 active site 385025004498 catalytic site [active] 385025004499 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 385025004500 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 385025004501 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 385025004502 catalytic residue [active] 385025004503 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 385025004504 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 385025004505 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 385025004506 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 385025004507 DNA-binding site [nucleotide binding]; DNA binding site 385025004508 RNA-binding motif; other site 385025004509 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 385025004510 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 385025004511 homodimer interface [polypeptide binding]; other site 385025004512 metal binding site [ion binding]; metal-binding site 385025004513 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 385025004514 homodimer interface [polypeptide binding]; other site 385025004515 active site 385025004516 putative chemical substrate binding site [chemical binding]; other site 385025004517 metal binding site [ion binding]; metal-binding site 385025004518 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 385025004519 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 385025004520 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 385025004521 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 385025004522 putative acyl-acceptor binding pocket; other site 385025004523 acyl-CoA synthetase; Validated; Region: PRK09192 385025004524 The adenylation domain of nonribosomal peptide synthetases (NRPS) similar to mycosubtilin synthase subunit A (MycA); Region: A_NRPS_MycA_like; cd05908 385025004525 acyl-activating enzyme (AAE) consensus motif; other site 385025004526 putative AMP binding site [chemical binding]; other site 385025004527 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 385025004528 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 385025004529 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 385025004530 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 385025004531 putative acyl-acceptor binding pocket; other site 385025004532 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025004533 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 385025004534 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 385025004535 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 385025004536 FeS/SAM binding site; other site 385025004537 putative sulfate transport protein CysZ; Validated; Region: PRK04949 385025004538 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 385025004539 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 385025004540 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 385025004541 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 385025004542 active site 385025004543 PilZ domain; Region: PilZ; cl01260 385025004544 DNA polymerase III subunit delta'; Validated; Region: PRK05707 385025004545 DNA polymerase III subunit delta'; Validated; Region: PRK08485 385025004546 DNA polymerase III, delta subunit, C terminal; Region: DNApol3-delta_C; pfam09115 385025004547 thymidylate kinase; Validated; Region: tmk; PRK00698 385025004548 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 385025004549 TMP-binding site; other site 385025004550 ATP-binding site [chemical binding]; other site 385025004551 YceG-like family; Region: YceG; pfam02618 385025004552 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 385025004553 dimerization interface [polypeptide binding]; other site 385025004554 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 385025004555 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 385025004556 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025004557 catalytic residue [active] 385025004558 hypothetical protein; Validated; Region: PRK09070 385025004559 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 385025004560 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 385025004561 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 385025004562 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 385025004563 dimer interface [polypeptide binding]; other site 385025004564 active site 385025004565 acyl carrier protein; Provisional; Region: acpP; PRK00982 385025004566 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 385025004567 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 385025004568 NAD(P) binding site [chemical binding]; other site 385025004569 homotetramer interface [polypeptide binding]; other site 385025004570 homodimer interface [polypeptide binding]; other site 385025004571 active site 385025004572 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 385025004573 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 385025004574 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 385025004575 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 385025004576 dimer interface [polypeptide binding]; other site 385025004577 active site 385025004578 CoA binding pocket [chemical binding]; other site 385025004579 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 385025004580 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 385025004581 Maf-like protein; Region: Maf; pfam02545 385025004582 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 385025004583 active site 385025004584 dimer interface [polypeptide binding]; other site 385025004585 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 385025004586 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 385025004587 dimer interface [polypeptide binding]; other site 385025004588 active site 385025004589 metal binding site [ion binding]; metal-binding site 385025004590 glutathione binding site [chemical binding]; other site 385025004591 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 385025004592 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 385025004593 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 385025004594 N-acetyl-D-glucosamine binding site [chemical binding]; other site 385025004595 catalytic residue [active] 385025004596 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025004597 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025004598 metal binding site [ion binding]; metal-binding site 385025004599 active site 385025004600 I-site; other site 385025004601 ABC-2 type transporter; Region: ABC2_membrane; cl17235 385025004602 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 385025004603 nodulation ABC transporter NodI; Provisional; Region: PRK13537 385025004604 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 385025004605 Walker A/P-loop; other site 385025004606 ATP binding site [chemical binding]; other site 385025004607 Q-loop/lid; other site 385025004608 ABC transporter signature motif; other site 385025004609 Walker B; other site 385025004610 D-loop; other site 385025004611 H-loop/switch region; other site 385025004612 transferase 1, rSAM/selenodomain-associated; Region: glyco_like_cofC; TIGR04282 385025004613 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 385025004614 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 385025004615 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025004616 homodimer interface [polypeptide binding]; other site 385025004617 catalytic residue [active] 385025004618 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 385025004619 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 385025004620 trimer interface [polypeptide binding]; other site 385025004621 active site 385025004622 substrate binding site [chemical binding]; other site 385025004623 CoA binding site [chemical binding]; other site 385025004624 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 385025004625 ArsC family; Region: ArsC; pfam03960 385025004626 putative catalytic residues [active] 385025004627 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 385025004628 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 385025004629 metal binding site [ion binding]; metal-binding site 385025004630 dimer interface [polypeptide binding]; other site 385025004631 glutathione reductase; Validated; Region: PRK06116 385025004632 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 385025004633 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025004634 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 385025004635 Protein of unknown function (DUF1244); Region: DUF1244; pfam06844 385025004636 Predicted ATPase [General function prediction only]; Region: COG1485 385025004637 intracellular septation protein A; Reviewed; Region: PRK00259 385025004638 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 385025004639 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 385025004640 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 385025004641 adenylate kinase; Reviewed; Region: adk; PRK00279 385025004642 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 385025004643 AMP-binding site [chemical binding]; other site 385025004644 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 385025004645 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 385025004646 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 385025004647 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 385025004648 FimV N-terminal domain; Region: FimV_core; TIGR03505 385025004649 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 385025004650 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 385025004651 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 385025004652 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 385025004653 Flagellar protein FliT; Region: FliT; pfam05400 385025004654 flagellar protein FliS; Validated; Region: fliS; PRK05685 385025004655 flagellar capping protein; Reviewed; Region: fliD; PRK08032 385025004656 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 385025004657 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 385025004658 FlaG protein; Region: FlaG; pfam03646 385025004659 flagellin; Validated; Region: PRK08026 385025004660 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 385025004661 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 385025004662 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK08870 385025004663 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 385025004664 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 385025004665 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 385025004666 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 385025004667 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 385025004668 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 385025004669 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 385025004670 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 385025004671 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 385025004672 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12698 385025004673 Flagellar L-ring protein; Region: FlgH; pfam02107 385025004674 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 385025004675 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 385025004676 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 385025004677 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 385025004678 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 385025004679 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 385025004680 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 385025004681 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 385025004682 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 385025004683 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 385025004684 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 385025004685 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 385025004686 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 385025004687 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 385025004688 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 385025004689 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 385025004690 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 385025004691 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 385025004692 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 385025004693 SAF-like; Region: SAF_2; pfam13144 385025004694 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 385025004695 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 385025004696 FlgN protein; Region: FlgN; pfam05130 385025004697 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 385025004698 PilZ domain; Region: PilZ; pfam07238 385025004699 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 385025004700 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 385025004701 TPP-binding site [chemical binding]; other site 385025004702 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 385025004703 PYR/PP interface [polypeptide binding]; other site 385025004704 dimer interface [polypeptide binding]; other site 385025004705 TPP binding site [chemical binding]; other site 385025004706 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 385025004707 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 385025004708 E3 interaction surface; other site 385025004709 lipoyl attachment site [posttranslational modification]; other site 385025004710 e3 binding domain; Region: E3_binding; pfam02817 385025004711 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 385025004712 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 385025004713 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025004714 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 385025004715 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvB; COG0028 385025004716 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 385025004717 PYR/PP interface [polypeptide binding]; other site 385025004718 dimer interface [polypeptide binding]; other site 385025004719 TPP binding site [chemical binding]; other site 385025004720 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 385025004721 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 385025004722 TPP-binding site [chemical binding]; other site 385025004723 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 385025004724 active site 385025004725 oxalacetate binding site [chemical binding]; other site 385025004726 citrylCoA binding site [chemical binding]; other site 385025004727 coenzyme A binding site [chemical binding]; other site 385025004728 catalytic triad [active] 385025004729 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 385025004730 citrylCoA binding site [chemical binding]; other site 385025004731 oxalacetate binding site [chemical binding]; other site 385025004732 coenzyme A binding site [chemical binding]; other site 385025004733 catalytic triad [active] 385025004734 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 385025004735 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 385025004736 N-terminal plug; other site 385025004737 ligand-binding site [chemical binding]; other site 385025004738 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 385025004739 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 385025004740 dimer interface [polypeptide binding]; other site 385025004741 phosphorylation site [posttranslational modification] 385025004742 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 385025004743 ATP binding site [chemical binding]; other site 385025004744 Mg2+ binding site [ion binding]; other site 385025004745 G-X-G motif; other site 385025004746 Response regulator receiver domain; Region: Response_reg; pfam00072 385025004747 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025004748 active site 385025004749 phosphorylation site [posttranslational modification] 385025004750 intermolecular recognition site; other site 385025004751 dimerization interface [polypeptide binding]; other site 385025004752 Response regulator receiver domain; Region: Response_reg; pfam00072 385025004753 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025004754 active site 385025004755 phosphorylation site [posttranslational modification] 385025004756 intermolecular recognition site; other site 385025004757 Response regulator receiver domain; Region: Response_reg; pfam00072 385025004758 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025004759 active site 385025004760 phosphorylation site [posttranslational modification] 385025004761 intermolecular recognition site; other site 385025004762 dimerization interface [polypeptide binding]; other site 385025004763 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025004764 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025004765 metal binding site [ion binding]; metal-binding site 385025004766 active site 385025004767 I-site; other site 385025004768 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 385025004769 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 385025004770 Fumarase C-terminus; Region: Fumerase_C; pfam05683 385025004771 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 385025004772 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 385025004773 CAP-like domain; other site 385025004774 active site 385025004775 primary dimer interface [polypeptide binding]; other site 385025004776 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025004777 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 385025004778 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 385025004779 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 385025004780 ATP binding site [chemical binding]; other site 385025004781 Mg2+ binding site [ion binding]; other site 385025004782 G-X-G motif; other site 385025004783 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 385025004784 anchoring element; other site 385025004785 dimer interface [polypeptide binding]; other site 385025004786 ATP binding site [chemical binding]; other site 385025004787 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 385025004788 active site 385025004789 metal binding site [ion binding]; metal-binding site 385025004790 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 385025004791 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 385025004792 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025004793 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025004794 metal binding site [ion binding]; metal-binding site 385025004795 active site 385025004796 I-site; other site 385025004797 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 385025004798 Protein of unknown function (DUF3501); Region: DUF3501; pfam12007 385025004799 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 385025004800 Cysteine-rich domain; Region: CCG; pfam02754 385025004801 Rubrerythrin [Energy production and conversion]; Region: COG1592 385025004802 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 385025004803 binuclear metal center [ion binding]; other site 385025004804 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 385025004805 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 385025004806 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 385025004807 substrate binding pocket [chemical binding]; other site 385025004808 chain length determination region; other site 385025004809 substrate-Mg2+ binding site; other site 385025004810 catalytic residues [active] 385025004811 aspartate-rich region 1; other site 385025004812 active site lid residues [active] 385025004813 aspartate-rich region 2; other site 385025004814 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 385025004815 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 385025004816 TPP-binding site; other site 385025004817 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 385025004818 PYR/PP interface [polypeptide binding]; other site 385025004819 dimer interface [polypeptide binding]; other site 385025004820 TPP binding site [chemical binding]; other site 385025004821 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 385025004822 putative GTP cyclohydrolase; Provisional; Region: PRK13674 385025004823 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 385025004824 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 385025004825 active site 385025004826 substrate-binding site [chemical binding]; other site 385025004827 metal-binding site [ion binding] 385025004828 ATP binding site [chemical binding]; other site 385025004829 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 385025004830 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH...; Region: TRX_Fd_NuoE_W_FDH_beta; cd03082 385025004831 putative dimer interface [polypeptide binding]; other site 385025004832 [2Fe-2S] cluster binding site [ion binding]; other site 385025004833 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 385025004834 SLBB domain; Region: SLBB; pfam10531 385025004835 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 385025004836 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 385025004837 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 385025004838 catalytic loop [active] 385025004839 iron binding site [ion binding]; other site 385025004840 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 385025004841 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 385025004842 [4Fe-4S] binding site [ion binding]; other site 385025004843 molybdopterin cofactor binding site; other site 385025004844 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_CT_Formate-Dh_H; cd02790 385025004845 molybdopterin cofactor binding site; other site 385025004846 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 385025004847 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 385025004848 GTP binding site; other site 385025004849 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 385025004850 malate dehydrogenase; Provisional; Region: PRK05442 385025004851 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 385025004852 NAD(P) binding site [chemical binding]; other site 385025004853 dimer interface [polypeptide binding]; other site 385025004854 malate binding site [chemical binding]; other site 385025004855 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 385025004856 Preprotein translocase SecG subunit; Region: SecG; pfam03840 385025004857 triosephosphate isomerase; Provisional; Region: PRK14567 385025004858 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 385025004859 substrate binding site [chemical binding]; other site 385025004860 dimer interface [polypeptide binding]; other site 385025004861 catalytic triad [active] 385025004862 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 385025004863 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 385025004864 active site 385025004865 substrate binding site [chemical binding]; other site 385025004866 metal binding site [ion binding]; metal-binding site 385025004867 dihydropteroate synthase; Region: DHPS; TIGR01496 385025004868 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 385025004869 substrate binding pocket [chemical binding]; other site 385025004870 dimer interface [polypeptide binding]; other site 385025004871 inhibitor binding site; inhibition site 385025004872 ATP-dependent metalloprotease; Reviewed; Region: hflB; PRK10733 385025004873 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 385025004874 Walker A motif; other site 385025004875 ATP binding site [chemical binding]; other site 385025004876 Walker B motif; other site 385025004877 arginine finger; other site 385025004878 Peptidase family M41; Region: Peptidase_M41; pfam01434 385025004879 FtsJ-like methyltransferase; Region: FtsJ; cl17430 385025004880 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 385025004881 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; pfam01985 385025004882 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 385025004883 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 385025004884 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 385025004885 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 385025004886 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 385025004887 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 385025004888 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 385025004889 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 385025004890 ATP-grasp domain; Region: ATP-grasp_4; cl17255 385025004891 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 385025004892 IMP binding site; other site 385025004893 dimer interface [polypeptide binding]; other site 385025004894 interdomain contacts; other site 385025004895 partial ornithine binding site; other site 385025004896 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 385025004897 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 385025004898 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 385025004899 catalytic site [active] 385025004900 subunit interface [polypeptide binding]; other site 385025004901 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 385025004902 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025004903 dihydrodipicolinate reductase; Provisional; Region: PRK00048 385025004904 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 385025004905 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 385025004906 chaperone protein DnaJ; Provisional; Region: PRK10767 385025004907 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 385025004908 HSP70 interaction site [polypeptide binding]; other site 385025004909 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 385025004910 substrate binding site [polypeptide binding]; other site 385025004911 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 385025004912 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 385025004913 dimer interface [polypeptide binding]; other site 385025004914 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 385025004915 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 385025004916 nucleotide binding site [chemical binding]; other site 385025004917 GrpE; Region: GrpE; pfam01025 385025004918 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 385025004919 dimer interface [polypeptide binding]; other site 385025004920 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 385025004921 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 385025004922 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 385025004923 recombination and repair protein; Provisional; Region: PRK10869 385025004924 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 385025004925 Walker A/P-loop; other site 385025004926 ATP binding site [chemical binding]; other site 385025004927 Q-loop/lid; other site 385025004928 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 385025004929 ABC transporter signature motif; other site 385025004930 Walker B; other site 385025004931 D-loop; other site 385025004932 H-loop/switch region; other site 385025004933 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 385025004934 metal binding site 2 [ion binding]; metal-binding site 385025004935 putative DNA binding helix; other site 385025004936 metal binding site 1 [ion binding]; metal-binding site 385025004937 dimer interface [polypeptide binding]; other site 385025004938 structural Zn2+ binding site [ion binding]; other site 385025004939 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 385025004940 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 385025004941 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 385025004942 CoenzymeA binding site [chemical binding]; other site 385025004943 subunit interaction site [polypeptide binding]; other site 385025004944 PHB binding site; other site 385025004945 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 385025004946 CoenzymeA binding site [chemical binding]; other site 385025004947 subunit interaction site [polypeptide binding]; other site 385025004948 PHB binding site; other site 385025004949 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 385025004950 iron-sulfur cluster [ion binding]; other site 385025004951 [2Fe-2S] cluster binding site [ion binding]; other site 385025004952 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 385025004953 putative alpha subunit interface [polypeptide binding]; other site 385025004954 putative active site [active] 385025004955 putative substrate binding site [chemical binding]; other site 385025004956 Fe binding site [ion binding]; other site 385025004957 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025004958 inter-subunit interface; other site 385025004959 2-isopropylmalate synthase; Validated; Region: PRK00915 385025004960 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 385025004961 active site 385025004962 catalytic residues [active] 385025004963 metal binding site [ion binding]; metal-binding site 385025004964 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 385025004965 hypothetical protein; Validated; Region: PRK01777 385025004966 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 385025004967 putative coenzyme Q binding site [chemical binding]; other site 385025004968 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 385025004969 Na2 binding site [ion binding]; other site 385025004970 putative substrate binding site 1 [chemical binding]; other site 385025004971 Na binding site 1 [ion binding]; other site 385025004972 putative substrate binding site 2 [chemical binding]; other site 385025004973 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 385025004974 SmpB-tmRNA interface; other site 385025004975 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 385025004976 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 385025004977 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 385025004978 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 385025004979 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 385025004980 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 385025004981 FAD binding pocket [chemical binding]; other site 385025004982 FAD binding motif [chemical binding]; other site 385025004983 phosphate binding motif [ion binding]; other site 385025004984 beta-alpha-beta structure motif; other site 385025004985 NAD binding pocket [chemical binding]; other site 385025004986 Heme binding pocket [chemical binding]; other site 385025004987 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 385025004988 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 385025004989 catalytic loop [active] 385025004990 iron binding site [ion binding]; other site 385025004991 MAPEG family; Region: MAPEG; cl09190 385025004992 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025004993 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 385025004994 putative C-terminal domain interface [polypeptide binding]; other site 385025004995 putative GSH binding site (G-site) [chemical binding]; other site 385025004996 putative dimer interface [polypeptide binding]; other site 385025004997 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases; Region: GST_C_7; cd03206 385025004998 putative N-terminal domain interface [polypeptide binding]; other site 385025004999 putative dimer interface [polypeptide binding]; other site 385025005000 putative substrate binding pocket (H-site) [chemical binding]; other site 385025005001 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 385025005002 GSH binding site [chemical binding]; other site 385025005003 catalytic residues [active] 385025005004 Transcriptional regulator [Transcription]; Region: LysR; COG0583 385025005005 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 385025005006 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 385025005007 putative effector binding pocket; other site 385025005008 dimerization interface [polypeptide binding]; other site 385025005009 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 385025005010 Uncharacterized protein family (UPF0156); Region: RHH_2; pfam03693 385025005011 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 385025005012 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 385025005013 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025005014 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 385025005015 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 385025005016 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025005017 active site 385025005018 phosphorylation site [posttranslational modification] 385025005019 intermolecular recognition site; other site 385025005020 dimerization interface [polypeptide binding]; other site 385025005021 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 385025005022 DNA binding site [nucleotide binding] 385025005023 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 385025005024 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025005025 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 385025005026 dimer interface [polypeptide binding]; other site 385025005027 phosphorylation site [posttranslational modification] 385025005028 acetaldehyde dehydrogenase; Validated; Region: PRK08300 385025005029 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 385025005030 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 385025005031 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 385025005032 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 385025005033 active site 385025005034 catalytic residues [active] 385025005035 metal binding site [ion binding]; metal-binding site 385025005036 DmpG-like communication domain; Region: DmpG_comm; pfam07836 385025005037 helicase 45; Provisional; Region: PTZ00424 385025005038 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 385025005039 ATP binding site [chemical binding]; other site 385025005040 Mg++ binding site [ion binding]; other site 385025005041 motif III; other site 385025005042 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 385025005043 nucleotide binding region [chemical binding]; other site 385025005044 ATP-binding site [chemical binding]; other site 385025005045 RNA recognition motif in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; Region: RRM_EcCsdA_like; cd12499 385025005046 putative RNA binding site [nucleotide binding]; other site 385025005047 SlyX; Region: SlyX; pfam04102 385025005048 GTPase YlqF; Reviewed; Region: rbgA; PRK09563 385025005049 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 385025005050 GTP/Mg2+ binding site [chemical binding]; other site 385025005051 G4 box; other site 385025005052 G5 box; other site 385025005053 G1 box; other site 385025005054 Switch I region; other site 385025005055 G2 box; other site 385025005056 G3 box; other site 385025005057 Switch II region; other site 385025005058 NHAD transporter family protein; Provisional; Region: PLN00137; cl17324 385025005059 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 385025005060 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 385025005061 Walker A motif; other site 385025005062 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 385025005063 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 385025005064 dimer interface [polypeptide binding]; other site 385025005065 putative functional site; other site 385025005066 putative MPT binding site; other site 385025005067 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 385025005068 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 385025005069 NAD binding site [chemical binding]; other site 385025005070 homodimer interface [polypeptide binding]; other site 385025005071 active site 385025005072 substrate binding site [chemical binding]; other site 385025005073 hypothetical protein; Provisional; Region: PRK08960 385025005074 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 385025005075 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025005076 homodimer interface [polypeptide binding]; other site 385025005077 catalytic residue [active] 385025005078 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 385025005079 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 385025005080 active site 385025005081 nucleotide binding site [chemical binding]; other site 385025005082 HIGH motif; other site 385025005083 KMSKS motif; other site 385025005084 Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E); Region: PHA_synth_III_E; cl09914 385025005085 poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; Region: PHA_synth_III_C; TIGR01836 385025005086 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 385025005087 Phasin protein; Region: Phasin_2; pfam09361 385025005088 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 385025005089 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 385025005090 NAD(P) binding site [chemical binding]; other site 385025005091 homotetramer interface [polypeptide binding]; other site 385025005092 homodimer interface [polypeptide binding]; other site 385025005093 active site 385025005094 hypothetical protein; Validated; Region: PRK02101 385025005095 ATP-dependent helicase HepA; Validated; Region: PRK04914 385025005096 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 385025005097 ATP binding site [chemical binding]; other site 385025005098 putative Mg++ binding site [ion binding]; other site 385025005099 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 385025005100 nucleotide binding region [chemical binding]; other site 385025005101 ATP-binding site [chemical binding]; other site 385025005102 PEP synthetase regulatory protein; Provisional; Region: PRK05339 385025005103 phosphoenolpyruvate synthase; Validated; Region: PRK06464 385025005104 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 385025005105 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 385025005106 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 385025005107 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 385025005108 homodimer interface [polypeptide binding]; other site 385025005109 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025005110 catalytic residue [active] 385025005111 phosphatidylserine decarboxylase; Reviewed; Region: psd; PRK00044 385025005112 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 385025005113 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 385025005114 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 385025005115 motif 1; other site 385025005116 dimer interface [polypeptide binding]; other site 385025005117 active site 385025005118 motif 2; other site 385025005119 motif 3; other site 385025005120 elongation factor P; Validated; Region: PRK00529 385025005121 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 385025005122 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 385025005123 RNA binding site [nucleotide binding]; other site 385025005124 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 385025005125 RNA binding site [nucleotide binding]; other site 385025005126 Radical SAM superfamily; Region: Radical_SAM; pfam04055 385025005127 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 385025005128 FeS/SAM binding site; other site 385025005129 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025005130 active site 385025005131 I-site; other site 385025005132 metal binding site [ion binding]; metal-binding site 385025005133 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 385025005134 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 385025005135 putative 3-phenylpropionic acid transporter; Provisional; Region: PRK11128 385025005136 MFS_1 like family; Region: MFS_1_like; pfam12832 385025005137 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 385025005138 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 385025005139 Tetramer interface [polypeptide binding]; other site 385025005140 active site 385025005141 FMN-binding site [chemical binding]; other site 385025005142 HemK family putative methylases; Region: hemK_fam; TIGR00536 385025005143 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 385025005144 S-adenosylmethionine binding site [chemical binding]; other site 385025005145 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 385025005146 ligand binding site [chemical binding]; other site 385025005147 HDOD domain; Region: HDOD; pfam08668 385025005148 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 385025005149 Zn2+ binding site [ion binding]; other site 385025005150 Mg2+ binding site [ion binding]; other site 385025005151 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 385025005152 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 385025005153 Protein of unknown function (DUF2802); Region: DUF2802; pfam10975 385025005154 flagellar motor protein MotD; Reviewed; Region: PRK09038 385025005155 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 385025005156 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025005157 ligand binding site [chemical binding]; other site 385025005158 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 385025005159 flagellar motor protein; Reviewed; Region: motC; PRK09109 385025005160 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 385025005161 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025005162 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 385025005163 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 385025005164 DNA binding residues [nucleotide binding] 385025005165 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 385025005166 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 385025005167 P-loop; other site 385025005168 ADP binding residues [chemical binding]; other site 385025005169 Switch I; other site 385025005170 Switch II; other site 385025005171 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 385025005172 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 385025005173 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 385025005174 FHIPEP family; Region: FHIPEP; pfam00771 385025005175 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 385025005176 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 385025005177 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 385025005178 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 385025005179 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 385025005180 Flagellar biosynthesis protein, FliO; Region: FliO; pfam04347 385025005181 flagellar motor switch protein; Validated; Region: fliN; PRK05698 385025005182 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 385025005183 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 385025005184 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 385025005185 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 385025005186 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07718 385025005187 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 385025005188 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 385025005189 B12 binding site [chemical binding]; other site 385025005190 cobalt ligand [ion binding]; other site 385025005191 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 385025005192 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 385025005193 Walker A; other site 385025005194 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 385025005195 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 385025005196 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 385025005197 GDP-binding site [chemical binding]; other site 385025005198 ACT binding site; other site 385025005199 IMP binding site; other site 385025005200 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 385025005201 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 385025005202 dimer interface [polypeptide binding]; other site 385025005203 motif 1; other site 385025005204 active site 385025005205 motif 2; other site 385025005206 motif 3; other site 385025005207 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 385025005208 FtsH protease regulator HflC; Provisional; Region: PRK11029 385025005209 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 385025005210 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 385025005211 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 385025005212 HflK protein; Region: hflK; TIGR01933 385025005213 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 385025005214 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 385025005215 HflX GTPase family; Region: HflX; cd01878 385025005216 G1 box; other site 385025005217 GTP/Mg2+ binding site [chemical binding]; other site 385025005218 Switch I region; other site 385025005219 G2 box; other site 385025005220 G3 box; other site 385025005221 Switch II region; other site 385025005222 G4 box; other site 385025005223 G5 box; other site 385025005224 bacterial Hfq-like; Region: Hfq; cd01716 385025005225 hexamer interface [polypeptide binding]; other site 385025005226 Sm1 motif; other site 385025005227 RNA binding site [nucleotide binding]; other site 385025005228 Sm2 motif; other site 385025005229 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 385025005230 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 385025005231 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 385025005232 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 385025005233 ATP binding site [chemical binding]; other site 385025005234 Mg2+ binding site [ion binding]; other site 385025005235 G-X-G motif; other site 385025005236 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 385025005237 ATP binding site [chemical binding]; other site 385025005238 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 385025005239 AMIN domain; Region: AMIN; pfam11741 385025005240 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 385025005241 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 385025005242 active site 385025005243 metal binding site [ion binding]; metal-binding site 385025005244 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025005245 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 385025005246 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 385025005247 putative substrate binding site [chemical binding]; other site 385025005248 putative ATP binding site [chemical binding]; other site 385025005249 epoxyqueuosine reductase; Region: TIGR00276 385025005250 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 385025005251 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 385025005252 catalytic site [active] 385025005253 putative active site [active] 385025005254 putative substrate binding site [chemical binding]; other site 385025005255 dimer interface [polypeptide binding]; other site 385025005256 Peptidase family M48; Region: Peptidase_M48; pfam01435 385025005257 GTPase RsgA; Reviewed; Region: PRK00098 385025005258 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 385025005259 RNA binding site [nucleotide binding]; other site 385025005260 homodimer interface [polypeptide binding]; other site 385025005261 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 385025005262 GTPase/Zn-binding domain interface [polypeptide binding]; other site 385025005263 GTP/Mg2+ binding site [chemical binding]; other site 385025005264 G4 box; other site 385025005265 G5 box; other site 385025005266 G1 box; other site 385025005267 Switch I region; other site 385025005268 G2 box; other site 385025005269 G3 box; other site 385025005270 Switch II region; other site 385025005271 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 385025005272 nucleotide binding site/active site [active] 385025005273 HIT family signature motif; other site 385025005274 catalytic residue [active] 385025005275 recombination protein RecR; Reviewed; Region: recR; PRK00076 385025005276 RecR protein; Region: RecR; pfam02132 385025005277 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 385025005278 putative active site [active] 385025005279 putative metal-binding site [ion binding]; other site 385025005280 tetramer interface [polypeptide binding]; other site 385025005281 hypothetical protein; Validated; Region: PRK00153 385025005282 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07994 385025005283 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 385025005284 Walker A motif; other site 385025005285 ATP binding site [chemical binding]; other site 385025005286 Walker B motif; other site 385025005287 arginine finger; other site 385025005288 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 385025005289 DNA polymerase III tau subunit V interacting with alpha; Region: DNA_pol3_tau_5; pfam12170 385025005290 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 385025005291 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025005292 active site 385025005293 phosphorylation site [posttranslational modification] 385025005294 intermolecular recognition site; other site 385025005295 dimerization interface [polypeptide binding]; other site 385025005296 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 385025005297 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 385025005298 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 385025005299 ATP binding site [chemical binding]; other site 385025005300 Mg2+ binding site [ion binding]; other site 385025005301 G-X-G motif; other site 385025005302 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025005303 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025005304 active site 385025005305 I-site; other site 385025005306 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 385025005307 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 385025005308 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 385025005309 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 385025005310 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 385025005311 GIY-YIG motif/motif A; other site 385025005312 active site 385025005313 catalytic site [active] 385025005314 putative DNA binding site [nucleotide binding]; other site 385025005315 metal binding site [ion binding]; metal-binding site 385025005316 UvrB/uvrC motif; Region: UVR; pfam02151 385025005317 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 385025005318 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 385025005319 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 385025005320 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 385025005321 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 385025005322 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 385025005323 RNase E interface [polypeptide binding]; other site 385025005324 trimer interface [polypeptide binding]; other site 385025005325 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 385025005326 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 385025005327 RNase E interface [polypeptide binding]; other site 385025005328 trimer interface [polypeptide binding]; other site 385025005329 active site 385025005330 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 385025005331 putative nucleic acid binding region [nucleotide binding]; other site 385025005332 G-X-X-G motif; other site 385025005333 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 385025005334 RNA binding site [nucleotide binding]; other site 385025005335 domain interface; other site 385025005336 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 385025005337 16S/18S rRNA binding site [nucleotide binding]; other site 385025005338 S13e-L30e interaction site [polypeptide binding]; other site 385025005339 25S rRNA binding site [nucleotide binding]; other site 385025005340 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 385025005341 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 385025005342 RNA binding site [nucleotide binding]; other site 385025005343 active site 385025005344 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 385025005345 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 385025005346 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 385025005347 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 385025005348 translation initiation factor IF-2; Region: IF-2; TIGR00487 385025005349 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 385025005350 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 385025005351 G1 box; other site 385025005352 putative GEF interaction site [polypeptide binding]; other site 385025005353 GTP/Mg2+ binding site [chemical binding]; other site 385025005354 Switch I region; other site 385025005355 G2 box; other site 385025005356 G3 box; other site 385025005357 Switch II region; other site 385025005358 G4 box; other site 385025005359 G5 box; other site 385025005360 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 385025005361 Translation-initiation factor 2; Region: IF-2; pfam11987 385025005362 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 385025005363 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 385025005364 NusA N-terminal domain; Region: NusA_N; pfam08529 385025005365 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 385025005366 RNA binding site [nucleotide binding]; other site 385025005367 homodimer interface [polypeptide binding]; other site 385025005368 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 385025005369 G-X-X-G motif; other site 385025005370 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 385025005371 G-X-X-G motif; other site 385025005372 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 385025005373 ribosome maturation protein RimP; Reviewed; Region: PRK00092 385025005374 Sm and related proteins; Region: Sm_like; cl00259 385025005375 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 385025005376 putative oligomer interface [polypeptide binding]; other site 385025005377 putative RNA binding site [nucleotide binding]; other site 385025005378 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 385025005379 tetramer interfaces [polypeptide binding]; other site 385025005380 binuclear metal-binding site [ion binding]; other site 385025005381 thiamine monophosphate kinase; Provisional; Region: PRK05731 385025005382 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 385025005383 ATP binding site [chemical binding]; other site 385025005384 dimerization interface [polypeptide binding]; other site 385025005385 transcription antitermination factor NusB; Region: nusB; TIGR01951 385025005386 putative RNA binding site [nucleotide binding]; other site 385025005387 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 385025005388 homopentamer interface [polypeptide binding]; other site 385025005389 active site 385025005390 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 385025005391 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 385025005392 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 385025005393 dimerization interface [polypeptide binding]; other site 385025005394 active site 385025005395 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 385025005396 Lumazine binding domain; Region: Lum_binding; pfam00677 385025005397 Lumazine binding domain; Region: Lum_binding; pfam00677 385025005398 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 385025005399 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 385025005400 catalytic motif [active] 385025005401 Zn binding site [ion binding]; other site 385025005402 RibD C-terminal domain; Region: RibD_C; cl17279 385025005403 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 385025005404 ATP cone domain; Region: ATP-cone; pfam03477 385025005405 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 385025005406 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 385025005407 dimer interface [polypeptide binding]; other site 385025005408 active site 385025005409 glycine-pyridoxal phosphate binding site [chemical binding]; other site 385025005410 folate binding site [chemical binding]; other site 385025005411 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 385025005412 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 385025005413 putative active site [active] 385025005414 Zn binding site [ion binding]; other site 385025005415 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 385025005416 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025005417 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025005418 ABC transporter; Region: ABC_tran_2; pfam12848 385025005419 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025005420 Protein of unknown function (DUF2834); Region: DUF2834; pfam11196 385025005421 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 385025005422 Plasmid encoded toxin Txe; Region: Plasmid_Txe; cl17389 385025005423 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 385025005424 catalytic residues [active] 385025005425 dimer interface [polypeptide binding]; other site 385025005426 SdiA-regulated; Region: SdiA-regulated; pfam06977 385025005427 SdiA-regulated; Region: SdiA-regulated; cd09971 385025005428 putative active site [active] 385025005429 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 385025005430 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 385025005431 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 385025005432 Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C1_like; cd09164 385025005433 domain interface [polypeptide binding]; other site 385025005434 active site 385025005435 catalytic site [active] 385025005436 Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins; Region: PLDc_EcPPK1_C2_like; cd09167 385025005437 domain interface [polypeptide binding]; other site 385025005438 active site 385025005439 catalytic site [active] 385025005440 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 385025005441 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 385025005442 nucleotide binding site [chemical binding]; other site 385025005443 heat shock protein HtpX; Provisional; Region: PRK05457 385025005444 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 385025005445 iron-sulfur cluster [ion binding]; other site 385025005446 [2Fe-2S] cluster binding site [ion binding]; other site 385025005447 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 385025005448 FMN-binding domain; Region: FMN_bind; pfam04205 385025005449 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 385025005450 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 385025005451 Peptidase family U32; Region: Peptidase_U32; pfam01136 385025005452 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 385025005453 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 385025005454 dimer interface [polypeptide binding]; other site 385025005455 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025005456 catalytic residue [active] 385025005457 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 385025005458 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 385025005459 catalytic residue [active] 385025005460 sodium or proton efflux -- potassium uptake antiporter, P-type ATPase, alpha subunit; Region: ATPase-IIC_X-K; TIGR01106 385025005461 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 385025005462 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 385025005463 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 385025005464 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 385025005465 active site 385025005466 motif I; other site 385025005467 motif II; other site 385025005468 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 385025005469 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 385025005470 S-adenosylmethionine binding site [chemical binding]; other site 385025005471 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 385025005472 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 385025005473 active site residue [active] 385025005474 YaeQ protein; Region: YaeQ; pfam07152 385025005475 amino acid transporter; Region: 2A0306; TIGR00909 385025005476 Uncharacterized conserved protein [Function unknown]; Region: COG0397 385025005477 hypothetical protein; Validated; Region: PRK00029 385025005478 Predicted ATPases of PP-loop superfamily [General function prediction only]; Region: COG2102 385025005479 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_IV; cd01994 385025005480 Ligand Binding Site [chemical binding]; other site 385025005481 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 385025005482 active site 385025005483 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07656 385025005484 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 385025005485 acyl-activating enzyme (AAE) consensus motif; other site 385025005486 putative AMP binding site [chemical binding]; other site 385025005487 putative active site [active] 385025005488 putative CoA binding site [chemical binding]; other site 385025005489 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 385025005490 stringent starvation protein A; Provisional; Region: sspA; PRK09481 385025005491 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025005492 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 385025005493 dimer interface [polypeptide binding]; other site 385025005494 N-terminal domain interface [polypeptide binding]; other site 385025005495 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 385025005496 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 385025005497 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 385025005498 Qi binding site; other site 385025005499 intrachain domain interface; other site 385025005500 interchain domain interface [polypeptide binding]; other site 385025005501 heme bH binding site [chemical binding]; other site 385025005502 heme bL binding site [chemical binding]; other site 385025005503 Qo binding site; other site 385025005504 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 385025005505 interchain domain interface [polypeptide binding]; other site 385025005506 intrachain domain interface; other site 385025005507 Qi binding site; other site 385025005508 Qo binding site; other site 385025005509 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 385025005510 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 385025005511 [2Fe-2S] cluster binding site [ion binding]; other site 385025005512 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 385025005513 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 385025005514 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025005515 homodimer interface [polypeptide binding]; other site 385025005516 catalytic residue [active] 385025005517 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 385025005518 histidinol dehydrogenase; Region: hisD; TIGR00069 385025005519 NAD binding site [chemical binding]; other site 385025005520 dimerization interface [polypeptide binding]; other site 385025005521 product binding site; other site 385025005522 substrate binding site [chemical binding]; other site 385025005523 zinc binding site [ion binding]; other site 385025005524 catalytic residues [active] 385025005525 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 385025005526 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 385025005527 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 385025005528 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 385025005529 hinge; other site 385025005530 active site 385025005531 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 385025005532 anti sigma factor interaction site; other site 385025005533 regulatory phosphorylation site [posttranslational modification]; other site 385025005534 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 385025005535 mce related protein; Region: MCE; pfam02470 385025005536 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 385025005537 Permease; Region: Permease; pfam02405 385025005538 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 385025005539 ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]; Region: ThiQ; COG3840 385025005540 Walker A/P-loop; other site 385025005541 ATP binding site [chemical binding]; other site 385025005542 Q-loop/lid; other site 385025005543 ABC transporter signature motif; other site 385025005544 Walker B; other site 385025005545 D-loop; other site 385025005546 H-loop/switch region; other site 385025005547 putative calcium/sodium:proton antiporter; Provisional; Region: PRK10734 385025005548 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 385025005549 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 385025005550 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 385025005551 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 385025005552 putative active site [active] 385025005553 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 385025005554 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 385025005555 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 385025005556 active site 385025005557 motif I; other site 385025005558 motif II; other site 385025005559 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 385025005560 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 385025005561 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 385025005562 OstA-like protein; Region: OstA; pfam03968 385025005563 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 385025005564 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 385025005565 Walker A/P-loop; other site 385025005566 ATP binding site [chemical binding]; other site 385025005567 Q-loop/lid; other site 385025005568 ABC transporter signature motif; other site 385025005569 Walker B; other site 385025005570 D-loop; other site 385025005571 H-loop/switch region; other site 385025005572 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 385025005573 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 385025005574 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 385025005575 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 385025005576 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 385025005577 30S subunit binding site; other site 385025005578 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 385025005579 AAA domain; Region: AAA_18; pfam13238 385025005580 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 385025005581 MgtE intracellular N domain; Region: MgtE_N; smart00924 385025005582 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 385025005583 Divalent cation transporter; Region: MgtE; cl00786 385025005584 peptidase PmbA; Provisional; Region: PRK11040 385025005585 protease TldD; Provisional; Region: tldD; PRK10735 385025005586 nitrilase; Region: PLN02798 385025005587 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 385025005588 putative active site [active] 385025005589 catalytic triad [active] 385025005590 dimer interface [polypeptide binding]; other site 385025005591 TIGR02099 family protein; Region: TIGR02099 385025005592 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 385025005593 ribonuclease G; Provisional; Region: PRK11712 385025005594 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 385025005595 homodimer interface [polypeptide binding]; other site 385025005596 oligonucleotide binding site [chemical binding]; other site 385025005597 Maf-like protein; Region: Maf; pfam02545 385025005598 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 385025005599 active site 385025005600 dimer interface [polypeptide binding]; other site 385025005601 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 385025005602 putative outer membrane lipoprotein; Provisional; Region: PRK10510 385025005603 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025005604 ligand binding site [chemical binding]; other site 385025005605 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 385025005606 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 385025005607 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 385025005608 active site 385025005609 (T/H)XGH motif; other site 385025005610 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 385025005611 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 385025005612 putative catalytic cysteine [active] 385025005613 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 385025005614 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 385025005615 Lipopolysaccharide-assembly; Region: LptE; cl01125 385025005616 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 385025005617 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 385025005618 HIGH motif; other site 385025005619 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 385025005620 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 385025005621 active site 385025005622 KMSKS motif; other site 385025005623 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 385025005624 tRNA binding surface [nucleotide binding]; other site 385025005625 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 385025005626 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 385025005627 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 385025005628 P-loop; other site 385025005629 Magnesium ion binding site [ion binding]; other site 385025005630 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 385025005631 Magnesium ion binding site [ion binding]; other site 385025005632 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 385025005633 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 385025005634 catalytic loop [active] 385025005635 iron binding site [ion binding]; other site 385025005636 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 385025005637 FAD binding pocket [chemical binding]; other site 385025005638 conserved FAD binding motif [chemical binding]; other site 385025005639 phosphate binding motif [ion binding]; other site 385025005640 beta-alpha-beta structure motif; other site 385025005641 NAD binding pocket [chemical binding]; other site 385025005642 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 385025005643 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 385025005644 putative active site [active] 385025005645 catalytic triad [active] 385025005646 putative dimer interface [polypeptide binding]; other site 385025005647 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 385025005648 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 385025005649 Transporter associated domain; Region: CorC_HlyC; smart01091 385025005650 metal-binding heat shock protein; Provisional; Region: PRK00016 385025005651 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 385025005652 PhoH-like protein; Region: PhoH; pfam02562 385025005653 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 385025005654 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 385025005655 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 385025005656 FeS/SAM binding site; other site 385025005657 TRAM domain; Region: TRAM; pfam01938 385025005658 ABC-2 type transporter; Region: ABC2_membrane; cl17235 385025005659 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 385025005660 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 385025005661 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025005662 Walker A/P-loop; other site 385025005663 ATP binding site [chemical binding]; other site 385025005664 Q-loop/lid; other site 385025005665 ABC transporter signature motif; other site 385025005666 Walker B; other site 385025005667 D-loop; other site 385025005668 H-loop/switch region; other site 385025005669 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 385025005670 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 385025005671 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 385025005672 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 385025005673 Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily; Region: PBP1_ABC_transporter_LIVBP_like; cd06268 385025005674 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 385025005675 ligand binding site [chemical binding]; other site 385025005676 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 385025005677 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025005678 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 385025005679 PilZ domain; Region: PilZ; pfam07238 385025005680 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 385025005681 PBP superfamily domain; Region: PBP_like_2; pfam12849 385025005682 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 385025005683 dimer interface [polypeptide binding]; other site 385025005684 conserved gate region; other site 385025005685 ABC-ATPase subunit interface; other site 385025005686 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 385025005687 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 385025005688 Walker A/P-loop; other site 385025005689 ATP binding site [chemical binding]; other site 385025005690 Q-loop/lid; other site 385025005691 ABC transporter signature motif; other site 385025005692 Walker B; other site 385025005693 D-loop; other site 385025005694 H-loop/switch region; other site 385025005695 molybdopterin biosynthesis protein MoeA; Provisional; Region: PRK10680 385025005696 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 385025005697 dimer interface [polypeptide binding]; other site 385025005698 putative functional site; other site 385025005699 putative MPT binding site; other site 385025005700 Staphylococcal nuclease homologues; Region: SNc; smart00318 385025005701 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 385025005702 Catalytic site; other site 385025005703 Glutamate-cysteine ligase; Region: Glu_cys_ligase; cl17352 385025005704 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 385025005705 Active Sites [active] 385025005706 transcriptional regulator CysB; Reviewed; Region: cysB; PRK12681 385025005707 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 385025005708 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 385025005709 substrate binding site [chemical binding]; other site 385025005710 dimerization interface [polypeptide binding]; other site 385025005711 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 385025005712 Ferredoxin [Energy production and conversion]; Region: COG1146 385025005713 4Fe-4S binding domain; Region: Fer4; cl02805 385025005714 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 385025005715 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 385025005716 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 385025005717 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 385025005718 alphaNTD homodimer interface [polypeptide binding]; other site 385025005719 alphaNTD - beta interaction site [polypeptide binding]; other site 385025005720 alphaNTD - beta' interaction site [polypeptide binding]; other site 385025005721 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 385025005722 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 385025005723 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 385025005724 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 385025005725 RNA binding surface [nucleotide binding]; other site 385025005726 30S ribosomal protein S11; Validated; Region: PRK05309 385025005727 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 385025005728 30S ribosomal protein S13; Region: bact_S13; TIGR03631 385025005729 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 385025005730 SecY translocase; Region: SecY; pfam00344 385025005731 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 385025005732 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 385025005733 23S rRNA binding site [nucleotide binding]; other site 385025005734 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 385025005735 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 385025005736 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 385025005737 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 385025005738 5S rRNA interface [nucleotide binding]; other site 385025005739 L27 interface [polypeptide binding]; other site 385025005740 23S rRNA interface [nucleotide binding]; other site 385025005741 L5 interface [polypeptide binding]; other site 385025005742 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 385025005743 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 385025005744 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 385025005745 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 385025005746 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 385025005747 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 385025005748 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 385025005749 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 385025005750 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 385025005751 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 385025005752 RNA binding site [nucleotide binding]; other site 385025005753 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 385025005754 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 385025005755 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 385025005756 putative translocon interaction site; other site 385025005757 23S rRNA interface [nucleotide binding]; other site 385025005758 signal recognition particle (SRP54) interaction site; other site 385025005759 L23 interface [polypeptide binding]; other site 385025005760 trigger factor interaction site; other site 385025005761 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 385025005762 23S rRNA interface [nucleotide binding]; other site 385025005763 5S rRNA interface [nucleotide binding]; other site 385025005764 putative antibiotic binding site [chemical binding]; other site 385025005765 L25 interface [polypeptide binding]; other site 385025005766 L27 interface [polypeptide binding]; other site 385025005767 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 385025005768 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 385025005769 G-X-X-G motif; other site 385025005770 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 385025005771 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 385025005772 putative translocon binding site; other site 385025005773 protein-rRNA interface [nucleotide binding]; other site 385025005774 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 385025005775 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 385025005776 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 385025005777 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 385025005778 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 385025005779 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 385025005780 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 385025005781 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 385025005782 elongation factor Tu; Reviewed; Region: PRK00049 385025005783 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 385025005784 G1 box; other site 385025005785 GEF interaction site [polypeptide binding]; other site 385025005786 GTP/Mg2+ binding site [chemical binding]; other site 385025005787 Switch I region; other site 385025005788 G2 box; other site 385025005789 G3 box; other site 385025005790 Switch II region; other site 385025005791 G4 box; other site 385025005792 G5 box; other site 385025005793 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 385025005794 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 385025005795 Antibiotic Binding Site [chemical binding]; other site 385025005796 elongation factor G; Reviewed; Region: PRK00007 385025005797 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 385025005798 G1 box; other site 385025005799 putative GEF interaction site [polypeptide binding]; other site 385025005800 GTP/Mg2+ binding site [chemical binding]; other site 385025005801 Switch I region; other site 385025005802 G2 box; other site 385025005803 G3 box; other site 385025005804 Switch II region; other site 385025005805 G4 box; other site 385025005806 G5 box; other site 385025005807 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 385025005808 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 385025005809 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 385025005810 30S ribosomal protein S7; Validated; Region: PRK05302 385025005811 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 385025005812 S17 interaction site [polypeptide binding]; other site 385025005813 S8 interaction site; other site 385025005814 16S rRNA interaction site [nucleotide binding]; other site 385025005815 streptomycin interaction site [chemical binding]; other site 385025005816 23S rRNA interaction site [nucleotide binding]; other site 385025005817 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 385025005818 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 385025005819 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 385025005820 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 385025005821 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 385025005822 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 385025005823 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 385025005824 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 385025005825 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 385025005826 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 385025005827 DNA binding site [nucleotide binding] 385025005828 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 385025005829 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 385025005830 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 385025005831 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 385025005832 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 385025005833 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 385025005834 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 385025005835 RPB3 interaction site [polypeptide binding]; other site 385025005836 RPB1 interaction site [polypeptide binding]; other site 385025005837 RPB11 interaction site [polypeptide binding]; other site 385025005838 RPB10 interaction site [polypeptide binding]; other site 385025005839 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 385025005840 peripheral dimer interface [polypeptide binding]; other site 385025005841 core dimer interface [polypeptide binding]; other site 385025005842 L10 interface [polypeptide binding]; other site 385025005843 L11 interface [polypeptide binding]; other site 385025005844 putative EF-Tu interaction site [polypeptide binding]; other site 385025005845 putative EF-G interaction site [polypeptide binding]; other site 385025005846 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 385025005847 23S rRNA interface [nucleotide binding]; other site 385025005848 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 385025005849 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 385025005850 mRNA/rRNA interface [nucleotide binding]; other site 385025005851 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 385025005852 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 385025005853 23S rRNA interface [nucleotide binding]; other site 385025005854 L7/L12 interface [polypeptide binding]; other site 385025005855 putative thiostrepton binding site; other site 385025005856 L25 interface [polypeptide binding]; other site 385025005857 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 385025005858 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 385025005859 putative homodimer interface [polypeptide binding]; other site 385025005860 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 385025005861 heterodimer interface [polypeptide binding]; other site 385025005862 homodimer interface [polypeptide binding]; other site 385025005863 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 385025005864 elongation factor Tu; Reviewed; Region: PRK00049 385025005865 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 385025005866 G1 box; other site 385025005867 GEF interaction site [polypeptide binding]; other site 385025005868 GTP/Mg2+ binding site [chemical binding]; other site 385025005869 Switch I region; other site 385025005870 G2 box; other site 385025005871 G3 box; other site 385025005872 Switch II region; other site 385025005873 G4 box; other site 385025005874 G5 box; other site 385025005875 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 385025005876 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 385025005877 Antibiotic Binding Site [chemical binding]; other site 385025005878 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 385025005879 putative active site [active] 385025005880 catalytic residue [active] 385025005881 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 385025005882 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 385025005883 5S rRNA interface [nucleotide binding]; other site 385025005884 CTC domain interface [polypeptide binding]; other site 385025005885 L16 interface [polypeptide binding]; other site 385025005886 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 385025005887 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 385025005888 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 385025005889 active site 385025005890 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 385025005891 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 385025005892 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 385025005893 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 385025005894 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 385025005895 binding surface 385025005896 TPR motif; other site 385025005897 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 385025005898 binding surface 385025005899 TPR motif; other site 385025005900 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 385025005901 binding surface 385025005902 TPR motif; other site 385025005903 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 385025005904 binding surface 385025005905 TPR motif; other site 385025005906 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 385025005907 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 385025005908 tRNA; other site 385025005909 putative tRNA binding site [nucleotide binding]; other site 385025005910 putative NADP binding site [chemical binding]; other site 385025005911 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 385025005912 peptide chain release factor 1; Validated; Region: prfA; PRK00591 385025005913 This domain is found in peptide chain release factors; Region: PCRF; smart00937 385025005914 RF-1 domain; Region: RF-1; pfam00472 385025005915 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 385025005916 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 385025005917 S-adenosylmethionine binding site [chemical binding]; other site 385025005918 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); Region: MPN_like; cd08070 385025005919 MPN+ (JAMM) motif; other site 385025005920 Zinc-binding site [ion binding]; other site 385025005921 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 385025005922 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 385025005923 GatB domain; Region: GatB_Yqey; smart00845 385025005924 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 385025005925 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 385025005926 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 385025005927 rod shape-determining protein MreB; Provisional; Region: PRK13927 385025005928 MreB and similar proteins; Region: MreB_like; cd10225 385025005929 nucleotide binding site [chemical binding]; other site 385025005930 Mg binding site [ion binding]; other site 385025005931 putative protofilament interaction site [polypeptide binding]; other site 385025005932 RodZ interaction site [polypeptide binding]; other site 385025005933 rod shape-determining protein MreC; Provisional; Region: PRK13922 385025005934 rod shape-determining protein MreC; Region: MreC; pfam04085 385025005935 rod shape-determining protein MreD; Region: MreD; cl01087 385025005936 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 385025005937 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 385025005938 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 385025005939 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 385025005940 Transglycosylase SLT domain; Region: SLT_2; pfam13406 385025005941 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 385025005942 N-acetyl-D-glucosamine binding site [chemical binding]; other site 385025005943 catalytic residue [active] 385025005944 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 385025005945 rare lipoprotein A; Region: rlpA; TIGR00413 385025005946 Sporulation related domain; Region: SPOR; pfam05036 385025005947 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 385025005948 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 385025005949 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 385025005950 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 385025005951 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 385025005952 homodimer interface [polypeptide binding]; other site 385025005953 substrate-cofactor binding pocket; other site 385025005954 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025005955 catalytic residue [active] 385025005956 Protein of unknown function (DUF493); Region: DUF493; pfam04359 385025005957 lipoate-protein ligase B; Provisional; Region: PRK14342 385025005958 lipoyl synthase; Provisional; Region: PRK05481 385025005959 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 385025005960 FeS/SAM binding site; other site 385025005961 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 385025005962 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 385025005963 Substrate binding site; other site 385025005964 metal-binding site 385025005965 Phosphotransferase enzyme family; Region: APH; pfam01636 385025005966 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 385025005967 substrate binding site [chemical binding]; other site 385025005968 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 385025005969 OstA-like protein; Region: OstA; cl00844 385025005970 Organic solvent tolerance protein; Region: OstA_C; pfam04453 385025005971 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 385025005972 SurA N-terminal domain; Region: SurA_N; pfam09312 385025005973 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 385025005974 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 385025005975 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 385025005976 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 385025005977 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 385025005978 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 385025005979 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 385025005980 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 385025005981 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 385025005982 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 385025005983 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 385025005984 Lipopolysaccharide kinase (Kdo/WaaP) family; Region: Kdo; cl17488 385025005985 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 385025005986 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 385025005987 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 385025005988 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 385025005989 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 385025005990 Walker A/P-loop; other site 385025005991 ATP binding site [chemical binding]; other site 385025005992 Q-loop/lid; other site 385025005993 ABC transporter signature motif; other site 385025005994 Walker B; other site 385025005995 D-loop; other site 385025005996 H-loop/switch region; other site 385025005997 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 385025005998 Sulfotransferase family; Region: Sulfotransfer_2; pfam03567 385025005999 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 385025006000 active site 385025006001 ATP binding site [chemical binding]; other site 385025006002 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 385025006003 active site 385025006004 substrate binding site [chemical binding]; other site 385025006005 ATP binding site [chemical binding]; other site 385025006006 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 385025006007 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 385025006008 putative active site [active] 385025006009 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 385025006010 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 385025006011 putative active site [active] 385025006012 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 385025006013 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 385025006014 homodimer interface [polypeptide binding]; other site 385025006015 substrate-cofactor binding pocket; other site 385025006016 catalytic residue [active] 385025006017 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 385025006018 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 385025006019 metal binding triad; other site 385025006020 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 385025006021 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 385025006022 metal binding triad; other site 385025006023 PAS fold; Region: PAS; pfam00989 385025006024 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 385025006025 putative active site [active] 385025006026 heme pocket [chemical binding]; other site 385025006027 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025006028 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025006029 metal binding site [ion binding]; metal-binding site 385025006030 active site 385025006031 I-site; other site 385025006032 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 385025006033 YHS domain; Region: YHS; pfam04945 385025006034 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 385025006035 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 385025006036 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 385025006037 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 385025006038 motif II; other site 385025006039 BphX-like; Region: BphX; pfam06139 385025006040 glutathionine S-transferase; Provisional; Region: PRK10542 385025006041 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 385025006042 C-terminal domain interface [polypeptide binding]; other site 385025006043 GSH binding site (G-site) [chemical binding]; other site 385025006044 dimer interface [polypeptide binding]; other site 385025006045 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 385025006046 dimer interface [polypeptide binding]; other site 385025006047 N-terminal domain interface [polypeptide binding]; other site 385025006048 substrate binding pocket (H-site) [chemical binding]; other site 385025006049 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 385025006050 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 385025006051 NAD binding site [chemical binding]; other site 385025006052 catalytic residues [active] 385025006053 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 385025006054 Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO); Region: Rieske_RO_Alpha_BPDO_like; cd03472 385025006055 beta subunit interaction site [polypeptide binding]; other site 385025006056 alpha subunit interaction site [polypeptide binding]; other site 385025006057 iron-sulfur cluster [ion binding]; other site 385025006058 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025006059 beta subunit interface [polypeptide binding]; other site 385025006060 alpha subunit interface [polypeptide binding]; other site 385025006061 active site 385025006062 substrate binding site [chemical binding]; other site 385025006063 Fe binding site [ion binding]; other site 385025006064 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025006065 inter-subunit interface; other site 385025006066 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 385025006067 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 385025006068 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 385025006069 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025006070 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 385025006071 SnoaL-like domain; Region: SnoaL_3; pfam13474 385025006072 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 385025006073 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 385025006074 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 385025006075 gliding motility-associated ABC transporter ATP-binding subunit GldA; Region: GldA_ABC_ATP; TIGR03522 385025006076 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 385025006077 Walker A/P-loop; other site 385025006078 ATP binding site [chemical binding]; other site 385025006079 Q-loop/lid; other site 385025006080 ABC transporter signature motif; other site 385025006081 Walker B; other site 385025006082 D-loop; other site 385025006083 H-loop/switch region; other site 385025006084 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 385025006085 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 385025006086 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 385025006087 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 385025006088 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 385025006089 DNA binding site [nucleotide binding] 385025006090 catalytic residue [active] 385025006091 H2TH interface [polypeptide binding]; other site 385025006092 putative catalytic residues [active] 385025006093 turnover-facilitating residue; other site 385025006094 intercalation triad [nucleotide binding]; other site 385025006095 8OG recognition residue [nucleotide binding]; other site 385025006096 putative reading head residues; other site 385025006097 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 385025006098 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 385025006099 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 385025006100 Protein of unknown function (DUF1538); Region: DUF1538; pfam07556 385025006101 Nitrogen regulatory protein P-II; Region: P-II; smart00938 385025006102 FOG: CBS domain [General function prediction only]; Region: COG0517 385025006103 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_17; cd04630 385025006104 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 385025006105 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 385025006106 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 385025006107 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 385025006108 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 385025006109 active site 385025006110 (T/H)XGH motif; other site 385025006111 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 385025006112 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 385025006113 S-adenosylmethionine binding site [chemical binding]; other site 385025006114 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 385025006115 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 385025006116 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 385025006117 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 385025006118 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 385025006119 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 385025006120 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 385025006121 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 385025006122 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 385025006123 P loop; other site 385025006124 GTP binding site [chemical binding]; other site 385025006125 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 385025006126 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025006127 Walker A/P-loop; other site 385025006128 ATP binding site [chemical binding]; other site 385025006129 Q-loop/lid; other site 385025006130 ABC transporter signature motif; other site 385025006131 Walker B; other site 385025006132 D-loop; other site 385025006133 H-loop/switch region; other site 385025006134 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 385025006135 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 385025006136 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 385025006137 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025006138 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 385025006139 DNA binding residues [nucleotide binding] 385025006140 Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly...; Region: Peptidase_C19; cl02553 385025006141 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 385025006142 catalytic motif [active] 385025006143 Catalytic residue [active] 385025006144 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 385025006145 UbiA prenyltransferase family; Region: UbiA; pfam01040 385025006146 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 385025006147 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 385025006148 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 385025006149 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 385025006150 Subunit III/VIIa interface [polypeptide binding]; other site 385025006151 Phospholipid binding site [chemical binding]; other site 385025006152 Subunit I/III interface [polypeptide binding]; other site 385025006153 Subunit III/VIb interface [polypeptide binding]; other site 385025006154 Subunit III/VIa interface; other site 385025006155 Subunit III/Vb interface [polypeptide binding]; other site 385025006156 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 385025006157 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 385025006158 Subunit I/III interface [polypeptide binding]; other site 385025006159 D-pathway; other site 385025006160 Subunit I/VIIc interface [polypeptide binding]; other site 385025006161 Subunit I/IV interface [polypeptide binding]; other site 385025006162 Subunit I/II interface [polypeptide binding]; other site 385025006163 Low-spin heme (heme a) binding site [chemical binding]; other site 385025006164 Subunit I/VIIa interface [polypeptide binding]; other site 385025006165 Subunit I/VIa interface [polypeptide binding]; other site 385025006166 Dimer interface; other site 385025006167 Putative water exit pathway; other site 385025006168 Binuclear center (heme a3/CuB) [ion binding]; other site 385025006169 K-pathway; other site 385025006170 Subunit I/Vb interface [polypeptide binding]; other site 385025006171 Putative proton exit pathway; other site 385025006172 Subunit I/VIb interface; other site 385025006173 Subunit I/VIc interface [polypeptide binding]; other site 385025006174 Electron transfer pathway; other site 385025006175 Subunit I/VIIIb interface [polypeptide binding]; other site 385025006176 Subunit I/VIIb interface [polypeptide binding]; other site 385025006177 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 385025006178 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 385025006179 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 385025006180 AAA domain; Region: AAA_26; pfam13500 385025006181 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 385025006182 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 385025006183 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 385025006184 S-adenosylmethionine binding site [chemical binding]; other site 385025006185 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 385025006186 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025006187 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 385025006188 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 385025006189 substrate-cofactor binding pocket; other site 385025006190 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025006191 catalytic residue [active] 385025006192 biotin synthase; Region: bioB; TIGR00433 385025006193 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 385025006194 FeS/SAM binding site; other site 385025006195 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 385025006196 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 385025006197 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 385025006198 active site 385025006199 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 385025006200 UbiA prenyltransferase family; Region: UbiA; pfam01040 385025006201 Chorismate lyase; Region: Chor_lyase; cl01230 385025006202 Y-family of DNA polymerases; Region: PolY; cl12025 385025006203 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 385025006204 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 385025006205 ssDNA binding site; other site 385025006206 generic binding surface II; other site 385025006207 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 385025006208 ATP binding site [chemical binding]; other site 385025006209 putative Mg++ binding site [ion binding]; other site 385025006210 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 385025006211 nucleotide binding region [chemical binding]; other site 385025006212 ATP-binding site [chemical binding]; other site 385025006213 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 385025006214 homotrimer interaction site [polypeptide binding]; other site 385025006215 putative active site [active] 385025006216 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional; Region: PRK11092 385025006217 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 385025006218 Zn2+ binding site [ion binding]; other site 385025006219 Mg2+ binding site [ion binding]; other site 385025006220 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 385025006221 synthetase active site [active] 385025006222 NTP binding site [chemical binding]; other site 385025006223 metal binding site [ion binding]; metal-binding site 385025006224 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 385025006225 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 385025006226 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 385025006227 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 385025006228 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 385025006229 catalytic site [active] 385025006230 G-X2-G-X-G-K; other site 385025006231 hypothetical protein; Provisional; Region: PRK11820 385025006232 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 385025006233 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 385025006234 Protein kinase domain; Region: Pkinase; pfam00069 385025006235 Catalytic domain of Protein Kinases; Region: PKc; cd00180 385025006236 active site 385025006237 ATP binding site [chemical binding]; other site 385025006238 substrate binding site [chemical binding]; other site 385025006239 activation loop (A-loop); other site 385025006240 ribonuclease PH; Reviewed; Region: rph; PRK00173 385025006241 Ribonuclease PH; Region: RNase_PH_bact; cd11362 385025006242 hexamer interface [polypeptide binding]; other site 385025006243 active site 385025006244 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 385025006245 active site 385025006246 dimerization interface [polypeptide binding]; other site 385025006247 HemN family oxidoreductase; Provisional; Region: PRK05660 385025006248 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 385025006249 FeS/SAM binding site; other site 385025006250 HemN C-terminal domain; Region: HemN_C; pfam06969 385025006251 Cysteine-rich CPXCG; Region: Cys_rich_CPXG; pfam14255 385025006252 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 385025006253 active site 385025006254 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 385025006255 4Fe-4S dicluster domain; Region: Fer4_11; pfam13247 385025006256 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 385025006257 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 385025006258 FeS/SAM binding site; other site 385025006259 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 385025006260 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 385025006261 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 385025006262 substrate binding pocket [chemical binding]; other site 385025006263 membrane-bound complex binding site; other site 385025006264 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 385025006265 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 385025006266 dimer interface [polypeptide binding]; other site 385025006267 conserved gate region; other site 385025006268 putative PBP binding loops; other site 385025006269 ABC-ATPase subunit interface; other site 385025006270 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 385025006271 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 385025006272 Walker A/P-loop; other site 385025006273 ATP binding site [chemical binding]; other site 385025006274 Q-loop/lid; other site 385025006275 ABC transporter signature motif; other site 385025006276 Walker B; other site 385025006277 D-loop; other site 385025006278 H-loop/switch region; other site 385025006279 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 385025006280 phage T7 F exclusion suppressor FxsA; Reviewed; Region: fxsA; PRK11463 385025006281 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 385025006282 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 385025006283 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 385025006284 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 385025006285 DsbD alpha interface [polypeptide binding]; other site 385025006286 catalytic residues [active] 385025006287 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 385025006288 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 385025006289 catalytic residues [active] 385025006290 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 385025006291 Dehydroquinase class II; Region: DHquinase_II; pfam01220 385025006292 trimer interface [polypeptide binding]; other site 385025006293 active site 385025006294 dimer interface [polypeptide binding]; other site 385025006295 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 385025006296 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 385025006297 carboxyltransferase (CT) interaction site; other site 385025006298 biotinylation site [posttranslational modification]; other site 385025006299 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 385025006300 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 385025006301 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 385025006302 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 385025006303 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 385025006304 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 385025006305 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 385025006306 tRNA-dihydrouridine synthase B; Provisional; Region: PRK10415 385025006307 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 385025006308 FMN binding site [chemical binding]; other site 385025006309 active site 385025006310 catalytic residues [active] 385025006311 substrate binding site [chemical binding]; other site 385025006312 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 385025006313 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 385025006314 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 385025006315 purine monophosphate binding site [chemical binding]; other site 385025006316 dimer interface [polypeptide binding]; other site 385025006317 putative catalytic residues [active] 385025006318 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 385025006319 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 385025006320 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 385025006321 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 385025006322 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 385025006323 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 385025006324 transcription termination factor Rho; Provisional; Region: rho; PRK09376 385025006325 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 385025006326 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 385025006327 RNA binding site [nucleotide binding]; other site 385025006328 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 385025006329 multimer interface [polypeptide binding]; other site 385025006330 Walker A motif; other site 385025006331 ATP binding site [chemical binding]; other site 385025006332 Walker B motif; other site 385025006333 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 385025006334 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 385025006335 catalytic residues [active] 385025006336 ATP-dependent RNA helicase RhlB; Provisional; Region: PRK04837 385025006337 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 385025006338 ATP binding site [chemical binding]; other site 385025006339 Mg++ binding site [ion binding]; other site 385025006340 motif III; other site 385025006341 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 385025006342 nucleotide binding region [chemical binding]; other site 385025006343 ATP-binding site [chemical binding]; other site 385025006344 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 385025006345 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 385025006346 motif II; other site 385025006347 endonuclease III; Provisional; Region: PRK10702 385025006348 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 385025006349 minor groove reading motif; other site 385025006350 helix-hairpin-helix signature motif; other site 385025006351 substrate binding pocket [chemical binding]; other site 385025006352 active site 385025006353 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 385025006354 hypothetical protein; Provisional; Region: PRK05409 385025006355 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; cl01262 385025006356 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 385025006357 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 385025006358 inhibitor-cofactor binding pocket; inhibition site 385025006359 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025006360 catalytic residue [active] 385025006361 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 385025006362 apolar tunnel; other site 385025006363 heme binding site [chemical binding]; other site 385025006364 dimerization interface [polypeptide binding]; other site 385025006365 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 385025006366 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 385025006367 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025006368 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025006369 metal binding site [ion binding]; metal-binding site 385025006370 active site 385025006371 I-site; other site 385025006372 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 385025006373 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 385025006374 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 385025006375 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 385025006376 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 385025006377 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 385025006378 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 385025006379 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 385025006380 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 385025006381 active site 385025006382 metal binding site [ion binding]; metal-binding site 385025006383 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 385025006384 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 385025006385 folate binding site [chemical binding]; other site 385025006386 NADP+ binding site [chemical binding]; other site 385025006387 thymidylate synthase; Reviewed; Region: thyA; PRK01827 385025006388 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 385025006389 dimerization interface [polypeptide binding]; other site 385025006390 active site 385025006391 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 385025006392 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 385025006393 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 385025006394 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 385025006395 Protein of unknown function (DUF3465); Region: DUF3465; pfam11948 385025006396 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 385025006397 Inorganic H+ pyrophosphatase; Region: H_PPase; pfam03030 385025006398 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 385025006399 dimer interface [polypeptide binding]; other site 385025006400 substrate binding site [chemical binding]; other site 385025006401 metal binding sites [ion binding]; metal-binding site 385025006402 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 385025006403 MoaE homodimer interface [polypeptide binding]; other site 385025006404 MoaD interaction [polypeptide binding]; other site 385025006405 active site residues [active] 385025006406 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 385025006407 MoaE interaction surface [polypeptide binding]; other site 385025006408 MoeB interaction surface [polypeptide binding]; other site 385025006409 thiocarboxylated glycine; other site 385025006410 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 385025006411 trimer interface [polypeptide binding]; other site 385025006412 dimer interface [polypeptide binding]; other site 385025006413 putative active site [active] 385025006414 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 385025006415 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 385025006416 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 385025006417 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 385025006418 putative active site [active] 385025006419 putative substrate binding site [chemical binding]; other site 385025006420 putative cosubstrate binding site; other site 385025006421 catalytic site [active] 385025006422 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 385025006423 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 385025006424 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 385025006425 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 385025006426 substrate binding pocket [chemical binding]; other site 385025006427 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 385025006428 B12 binding site [chemical binding]; other site 385025006429 cobalt ligand [ion binding]; other site 385025006430 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 385025006431 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 385025006432 substrate binding site [chemical binding]; other site 385025006433 dimer interface [polypeptide binding]; other site 385025006434 ATP binding site [chemical binding]; other site 385025006435 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 385025006436 thiamine phosphate binding site [chemical binding]; other site 385025006437 active site 385025006438 pyrophosphate binding site [ion binding]; other site 385025006439 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 385025006440 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 385025006441 catalytic Zn binding site [ion binding]; other site 385025006442 NAD binding site [chemical binding]; other site 385025006443 structural Zn binding site [ion binding]; other site 385025006444 Amidohydrolase; Region: Amidohydro_2; pfam04909 385025006445 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 385025006446 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 385025006447 active site 385025006448 metal binding site [ion binding]; metal-binding site 385025006449 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 385025006450 active site 385025006451 metal binding site [ion binding]; metal-binding site 385025006452 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 385025006453 Fatty acid desaturase; Region: FA_desaturase; pfam00487 385025006454 putative di-iron ligands [ion binding]; other site 385025006455 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 385025006456 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 385025006457 catalytic Zn binding site [ion binding]; other site 385025006458 NAD binding site [chemical binding]; other site 385025006459 structural Zn binding site [ion binding]; other site 385025006460 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 385025006461 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 385025006462 argininosuccinate synthase; Provisional; Region: PRK13820 385025006463 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 385025006464 ANP binding site [chemical binding]; other site 385025006465 Substrate Binding Site II [chemical binding]; other site 385025006466 Substrate Binding Site I [chemical binding]; other site 385025006467 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 385025006468 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025006469 ligand binding site [chemical binding]; other site 385025006470 PGAP1-like protein; Region: PGAP1; pfam07819 385025006471 acyl-CoA esterase; Provisional; Region: PRK10673 385025006472 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 385025006473 E3 interaction surface; other site 385025006474 lipoyl attachment site [posttranslational modification]; other site 385025006475 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 385025006476 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 385025006477 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 385025006478 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 385025006479 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 385025006480 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 385025006481 E3 interaction surface; other site 385025006482 lipoyl attachment site [posttranslational modification]; other site 385025006483 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 385025006484 E3 interaction surface; other site 385025006485 lipoyl attachment site [posttranslational modification]; other site 385025006486 e3 binding domain; Region: E3_binding; pfam02817 385025006487 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 385025006488 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 385025006489 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 385025006490 dimer interface [polypeptide binding]; other site 385025006491 TPP-binding site [chemical binding]; other site 385025006492 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 385025006493 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 385025006494 feedback inhibition sensing region; other site 385025006495 homohexameric interface [polypeptide binding]; other site 385025006496 nucleotide binding site [chemical binding]; other site 385025006497 N-acetyl-L-glutamate binding site [chemical binding]; other site 385025006498 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 385025006499 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 385025006500 active site 385025006501 substrate binding site [chemical binding]; other site 385025006502 metal binding site [ion binding]; metal-binding site 385025006503 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 385025006504 trimer interface [polypeptide binding]; other site 385025006505 active site 385025006506 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 385025006507 Flavoprotein; Region: Flavoprotein; pfam02441 385025006508 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 385025006509 hypothetical protein; Reviewed; Region: PRK00024 385025006510 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 385025006511 MPN+ (JAMM) motif; other site 385025006512 Zinc-binding site [ion binding]; other site 385025006513 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 385025006514 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 385025006515 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 385025006516 iron-sulfur cluster [ion binding]; other site 385025006517 [2Fe-2S] cluster binding site [ion binding]; other site 385025006518 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 385025006519 ligand binding site [chemical binding]; other site 385025006520 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 385025006521 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 385025006522 ligand binding site [chemical binding]; other site 385025006523 flexible hinge region; other site 385025006524 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 385025006525 active site residue [active] 385025006526 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 385025006527 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 385025006528 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 385025006529 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 385025006530 protein binding site [polypeptide binding]; other site 385025006531 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 385025006532 protein binding site [polypeptide binding]; other site 385025006533 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 385025006534 MPT binding site; other site 385025006535 trimer interface [polypeptide binding]; other site 385025006536 Uncharacterized small membrane protein [Function unknown]; Region: COG2363 385025006537 aminopeptidase N; Provisional; Region: pepN; PRK14015 385025006538 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 385025006539 active site 385025006540 Zn binding site [ion binding]; other site 385025006541 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 385025006542 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 385025006543 DNA binding site [nucleotide binding] 385025006544 active site 385025006545 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4807 385025006546 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 385025006547 Protein of unknown function (DUF1456); Region: DUF1456; pfam07308 385025006548 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 385025006549 putative active site [active] 385025006550 putative CoA binding site [chemical binding]; other site 385025006551 nudix motif; other site 385025006552 metal binding site [ion binding]; metal-binding site 385025006553 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 385025006554 nudix motif; other site 385025006555 Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ; Region: Rsd_AlgQ; cl11478 385025006556 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 385025006557 Protein of unknown function, DUF482; Region: DUF482; pfam04339 385025006558 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 385025006559 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 385025006560 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025006561 multidrug efflux protein; Reviewed; Region: PRK09579 385025006562 Protein export membrane protein; Region: SecD_SecF; cl14618 385025006563 Protein of unknown function (DUF3379); Region: DUF3379; pfam11859 385025006564 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 385025006565 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 385025006566 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 385025006567 DNA binding residues [nucleotide binding] 385025006568 primosome assembly protein PriA; Validated; Region: PRK05580 385025006569 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 385025006570 ATP binding site [chemical binding]; other site 385025006571 putative Mg++ binding site [ion binding]; other site 385025006572 helicase superfamily c-terminal domain; Region: HELICc; smart00490 385025006573 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 385025006574 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 385025006575 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 385025006576 active site 385025006577 HIGH motif; other site 385025006578 nucleotide binding site [chemical binding]; other site 385025006579 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 385025006580 KMSK motif region; other site 385025006581 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 385025006582 tRNA binding surface [nucleotide binding]; other site 385025006583 anticodon binding site; other site 385025006584 Sporulation related domain; Region: SPOR; pfam05036 385025006585 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 385025006586 putative catalytic site [active] 385025006587 putative metal binding site [ion binding]; other site 385025006588 putative phosphate binding site [ion binding]; other site 385025006589 23S rRNA m(2)G2445 methyltransferase; Provisional; Region: rlmL; PRK11783 385025006590 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 385025006591 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 385025006592 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 385025006593 S-adenosylmethionine binding site [chemical binding]; other site 385025006594 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 385025006595 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 385025006596 S1 domain; Region: S1_2; pfam13509 385025006597 S1 domain; Region: S1_2; pfam13509 385025006598 Protein of unknown function (DUF3622); Region: DUF3622; pfam12286 385025006599 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 385025006600 hypothetical protein; Provisional; Region: PRK09256 385025006601 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 385025006602 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 385025006603 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 385025006604 PhnA protein; Region: PhnA; pfam03831 385025006605 Maltoporin periplasmic N-terminal extension; Region: Sugarporin_N; pfam11471 385025006606 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 385025006607 Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_c; cd01145 385025006608 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 385025006609 putative ligand binding site [chemical binding]; other site 385025006610 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 385025006611 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 385025006612 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 385025006613 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 385025006614 substrate binding site [chemical binding]; other site 385025006615 ATP binding site [chemical binding]; other site 385025006616 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 385025006617 tetramer interface [polypeptide binding]; other site 385025006618 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025006619 catalytic residue [active] 385025006620 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 385025006621 dimer interface [polypeptide binding]; other site 385025006622 catalytic triad [active] 385025006623 peroxidatic and resolving cysteines [active] 385025006624 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 385025006625 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 385025006626 tetramer interface [polypeptide binding]; other site 385025006627 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025006628 catalytic residue [active] 385025006629 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 385025006630 lipoyl attachment site [posttranslational modification]; other site 385025006631 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 385025006632 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 385025006633 TIGR02647 family protein; Region: DNA 385025006634 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 385025006635 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 385025006636 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 385025006637 2-polyprenyl-6-methoxyphenol 4-hydroxylase; Region: UbiH; TIGR01984 385025006638 proline aminopeptidase P II; Provisional; Region: PRK10879 385025006639 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 385025006640 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 385025006641 active site 385025006642 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 385025006643 TIGR02449 family protein; Region: TIGR02449 385025006644 Cell division protein ZapA; Region: ZapA; pfam05164 385025006645 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 385025006646 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 385025006647 tetramer (dimer of dimers) interface [polypeptide binding]; other site 385025006648 active site 385025006649 dimer interface [polypeptide binding]; other site 385025006650 high affinity sulphate transporter 1; Region: sulP; TIGR00815 385025006651 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 385025006652 Sulfate transporter family; Region: Sulfate_transp; pfam00916 385025006653 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 385025006654 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025006655 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025006656 metal binding site [ion binding]; metal-binding site 385025006657 active site 385025006658 I-site; other site 385025006659 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 385025006660 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 385025006661 23S rRNA interface [nucleotide binding]; other site 385025006662 L3 interface [polypeptide binding]; other site 385025006663 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 385025006664 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 385025006665 NAD(P) binding site [chemical binding]; other site 385025006666 homodimer interface [polypeptide binding]; other site 385025006667 substrate binding site [chemical binding]; other site 385025006668 active site 385025006669 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 385025006670 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 385025006671 active site 385025006672 dimer interface [polypeptide binding]; other site 385025006673 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 385025006674 dimer interface [polypeptide binding]; other site 385025006675 active site 385025006676 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 385025006677 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 385025006678 active site 385025006679 tetramer interface; other site 385025006680 Bacterial sugar transferase; Region: Bac_transf; pfam02397 385025006681 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 385025006682 UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs; Region: UDP_G4E_4_SDR_e; cd05232 385025006683 putative NAD(P) binding site [chemical binding]; other site 385025006684 active site 385025006685 putative substrate binding site [chemical binding]; other site 385025006686 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 385025006687 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 385025006688 active site 385025006689 Sulfotransferase family; Region: Sulfotransfer_2; pfam03567 385025006690 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 385025006691 Walker A motif; other site 385025006692 ATP binding site [chemical binding]; other site 385025006693 arginine finger; other site 385025006694 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 385025006695 active site 385025006696 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 385025006697 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 385025006698 active site 385025006699 The Sema domain, a protein interacting module, of semaphorins and plexins; Region: Sema; cl15693 385025006700 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 385025006701 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 385025006702 active site 385025006703 Sulfotransferase family; Region: Sulfotransfer_2; pfam03567 385025006704 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 385025006705 dimer interface [polypeptide binding]; other site 385025006706 [2Fe-2S] cluster binding site [ion binding]; other site 385025006707 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 385025006708 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 385025006709 active site 385025006710 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 385025006711 AAA domain; Region: AAA_18; pfam13238 385025006712 ligand-binding site [chemical binding]; other site 385025006713 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 385025006714 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 385025006715 ligand-binding site [chemical binding]; other site 385025006716 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 385025006717 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 385025006718 CysD dimerization site [polypeptide binding]; other site 385025006719 G1 box; other site 385025006720 putative GEF interaction site [polypeptide binding]; other site 385025006721 GTP/Mg2+ binding site [chemical binding]; other site 385025006722 Switch I region; other site 385025006723 G2 box; other site 385025006724 G3 box; other site 385025006725 Switch II region; other site 385025006726 G4 box; other site 385025006727 G5 box; other site 385025006728 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 385025006729 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 385025006730 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 385025006731 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 385025006732 Active Sites [active] 385025006733 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 385025006734 Cysteine-rich domain; Region: CCG; pfam02754 385025006735 Cysteine-rich domain; Region: CCG; pfam02754 385025006736 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 385025006737 diiron binding motif [ion binding]; other site 385025006738 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 385025006739 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 385025006740 inhibitor-cofactor binding pocket; inhibition site 385025006741 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025006742 catalytic residue [active] 385025006743 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 385025006744 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 385025006745 active site 385025006746 metal binding site [ion binding]; metal-binding site 385025006747 OsmC-like protein; Region: OsmC; cl00767 385025006748 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 385025006749 DNA-binding transcriptional dual regulator Crp; Provisional; Region: PRK11753 385025006750 ligand binding site [chemical binding]; other site 385025006751 flexible hinge region; other site 385025006752 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 385025006753 putative switch regulator; other site 385025006754 non-specific DNA interactions [nucleotide binding]; other site 385025006755 DNA binding site [nucleotide binding] 385025006756 sequence specific DNA binding site [nucleotide binding]; other site 385025006757 putative cAMP binding site [chemical binding]; other site 385025006758 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 385025006759 active site 385025006760 ribulose/triose binding site [chemical binding]; other site 385025006761 phosphate binding site [ion binding]; other site 385025006762 substrate (anthranilate) binding pocket [chemical binding]; other site 385025006763 product (indole) binding pocket [chemical binding]; other site 385025006764 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 385025006765 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 385025006766 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 385025006767 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 385025006768 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 385025006769 glutamine binding [chemical binding]; other site 385025006770 catalytic triad [active] 385025006771 anthranilate synthase component I; Provisional; Region: PRK13565 385025006772 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 385025006773 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 385025006774 phosphoglycolate phosphatase; Provisional; Region: PRK13222 385025006775 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 385025006776 motif II; other site 385025006777 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 385025006778 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 385025006779 substrate binding site [chemical binding]; other site 385025006780 hexamer interface [polypeptide binding]; other site 385025006781 metal binding site [ion binding]; metal-binding site 385025006782 Protein of unknown function (DUF2835); Region: DUF2835; pfam11197 385025006783 Protein of unknown function (DUF3530); Region: DUF3530; pfam12048 385025006784 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 385025006785 Predicted integral membrane protein [Function unknown]; Region: COG5615 385025006786 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 385025006787 Protein of unknown function (DUF445); Region: DUF445; pfam04286 385025006788 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 385025006789 ligand binding site [chemical binding]; other site 385025006790 flagellar motor protein MotA; Validated; Region: PRK08124 385025006791 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 385025006792 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 385025006793 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 385025006794 PAS domain; Region: PAS_8; pfam13188 385025006795 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 385025006796 PAS domain; Region: PAS_9; pfam13426 385025006797 putative active site [active] 385025006798 heme pocket [chemical binding]; other site 385025006799 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025006800 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025006801 metal binding site [ion binding]; metal-binding site 385025006802 active site 385025006803 I-site; other site 385025006804 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 385025006805 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 385025006806 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 385025006807 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 385025006808 putative metal binding site [ion binding]; other site 385025006809 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 385025006810 HSP70 interaction site [polypeptide binding]; other site 385025006811 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 385025006812 ATP binding site [chemical binding]; other site 385025006813 active site 385025006814 substrate binding site [chemical binding]; other site 385025006815 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 385025006816 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 385025006817 Nitrogen regulatory protein P-II; Region: P-II; smart00938 385025006818 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 385025006819 Membrane fusogenic activity; Region: BMFP; pfam04380 385025006820 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 385025006821 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 385025006822 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 385025006823 Walker A motif; other site 385025006824 ATP binding site [chemical binding]; other site 385025006825 Walker B motif; other site 385025006826 arginine finger; other site 385025006827 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 385025006828 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 385025006829 Part of AAA domain; Region: AAA_19; pfam13245 385025006830 Family description; Region: UvrD_C_2; pfam13538 385025006831 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 385025006832 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 385025006833 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 385025006834 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 385025006835 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 385025006836 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 385025006837 Walker A/P-loop; other site 385025006838 ATP binding site [chemical binding]; other site 385025006839 Q-loop/lid; other site 385025006840 ABC transporter signature motif; other site 385025006841 Walker B; other site 385025006842 D-loop; other site 385025006843 H-loop/switch region; other site 385025006844 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 385025006845 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 385025006846 HlyD family secretion protein; Region: HlyD_3; pfam13437 385025006847 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 385025006848 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 385025006849 DNA binding residues [nucleotide binding] 385025006850 dimerization interface [polypeptide binding]; other site 385025006851 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 385025006852 Predicted transglutaminase-like cysteine proteinase [General function prediction only]; Region: COG3672 385025006853 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025006854 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025006855 metal binding site [ion binding]; metal-binding site 385025006856 active site 385025006857 I-site; other site 385025006858 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 385025006859 6-phosphofructokinase; Provisional; Region: PRK14072 385025006860 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 385025006861 active site 385025006862 ADP/pyrophosphate binding site [chemical binding]; other site 385025006863 dimerization interface [polypeptide binding]; other site 385025006864 allosteric effector site; other site 385025006865 fructose-1,6-bisphosphate binding site; other site 385025006866 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 385025006867 Sodium Bile acid symporter family; Region: SBF; cl17470 385025006868 Predicted membrane protein [Function unknown]; Region: COG2259 385025006869 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 385025006870 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 385025006871 active site 385025006872 FMN binding site [chemical binding]; other site 385025006873 substrate binding site [chemical binding]; other site 385025006874 3Fe-4S cluster binding site [ion binding]; other site 385025006875 NAD-dependent deacetylase; Provisional; Region: PRK00481 385025006876 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 385025006877 NAD+ binding site [chemical binding]; other site 385025006878 substrate binding site [chemical binding]; other site 385025006879 Zn binding site [ion binding]; other site 385025006880 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 385025006881 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 385025006882 putative NAD(P) binding site [chemical binding]; other site 385025006883 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 385025006884 Glycosyl transferases group 1; Region: Glyco_trans_1_4; pfam13692 385025006885 elongation factor G; Reviewed; Region: PRK00007 385025006886 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 385025006887 G1 box; other site 385025006888 putative GEF interaction site [polypeptide binding]; other site 385025006889 GTP/Mg2+ binding site [chemical binding]; other site 385025006890 Switch I region; other site 385025006891 G2 box; other site 385025006892 G3 box; other site 385025006893 Switch II region; other site 385025006894 G4 box; other site 385025006895 G5 box; other site 385025006896 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 385025006897 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 385025006898 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 385025006899 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025006900 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 385025006901 putative C-terminal domain interface [polypeptide binding]; other site 385025006902 putative GSH binding site (G-site) [chemical binding]; other site 385025006903 putative dimer interface [polypeptide binding]; other site 385025006904 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 385025006905 dimer interface [polypeptide binding]; other site 385025006906 N-terminal domain interface [polypeptide binding]; other site 385025006907 putative substrate binding pocket (H-site) [chemical binding]; other site 385025006908 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 385025006909 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 385025006910 Nitrogen regulatory protein P-II; Region: P-II; smart00938 385025006911 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 385025006912 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 385025006913 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 385025006914 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 385025006915 Fatty acid desaturase; Region: FA_desaturase; pfam00487 385025006916 Di-iron ligands [ion binding]; other site 385025006917 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 385025006918 TIGR03503 family protein; Region: TIGR03503 385025006919 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 385025006920 Phosphoglycerate kinase; Region: PGK; pfam00162 385025006921 substrate binding site [chemical binding]; other site 385025006922 hinge regions; other site 385025006923 ADP binding site [chemical binding]; other site 385025006924 catalytic site [active] 385025006925 erythrose 4-phosphate dehydrogenase; Provisional; Region: PRK13535 385025006926 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 385025006927 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 385025006928 transketolase; Reviewed; Region: PRK12753 385025006929 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 385025006930 TPP-binding site [chemical binding]; other site 385025006931 dimer interface [polypeptide binding]; other site 385025006932 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 385025006933 PYR/PP interface [polypeptide binding]; other site 385025006934 dimer interface [polypeptide binding]; other site 385025006935 TPP binding site [chemical binding]; other site 385025006936 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 385025006937 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 385025006938 iron-sulfur cluster [ion binding]; other site 385025006939 [2Fe-2S] cluster binding site [ion binding]; other site 385025006940 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025006941 beta subunit interface [polypeptide binding]; other site 385025006942 alpha subunit interface [polypeptide binding]; other site 385025006943 active site 385025006944 substrate binding site [chemical binding]; other site 385025006945 Fe binding site [ion binding]; other site 385025006946 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025006947 inter-subunit interface; other site 385025006948 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 385025006949 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 385025006950 active site 385025006951 Predicted nuclease (RNAse H fold) [General function prediction only]; Region: COG4328 385025006952 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 385025006953 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 385025006954 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 385025006955 SCP-2 sterol transfer family; Region: SCP2; pfam02036 385025006956 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 385025006957 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 385025006958 S-adenosylmethionine binding site [chemical binding]; other site 385025006959 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 385025006960 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 385025006961 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 385025006962 Walker A motif; other site 385025006963 ATP binding site [chemical binding]; other site 385025006964 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 385025006965 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 385025006966 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 385025006967 active site 385025006968 HslU subunit interaction site [polypeptide binding]; other site 385025006969 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 385025006970 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 385025006971 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 385025006972 active site 385025006973 Int/Topo IB signature motif; other site 385025006974 Protein of unknown function, DUF484; Region: DUF484; cl17449 385025006975 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 385025006976 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 385025006977 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 385025006978 diaminopimelate decarboxylase; Region: lysA; TIGR01048 385025006979 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 385025006980 active site 385025006981 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 385025006982 substrate binding site [chemical binding]; other site 385025006983 catalytic residues [active] 385025006984 dimer interface [polypeptide binding]; other site 385025006985 Prokaryotic lipoprotein-attachment site; Region: LPAM_2; cl02361 385025006986 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 385025006987 putative hydrolase; Provisional; Region: PRK11460 385025006988 hypothetical protein; Provisional; Region: PRK10649 385025006989 Sulfatase; Region: Sulfatase; pfam00884 385025006990 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; pfam01219 385025006991 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 385025006992 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 385025006993 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 385025006994 dimerization interface [polypeptide binding]; other site 385025006995 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 385025006996 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 385025006997 catalytic triad [active] 385025006998 dimer interface [polypeptide binding]; other site 385025006999 adenylate cyclase; Provisional; Region: cyaA; PRK09450 385025007000 Adenylate cyclase NT domain; Region: Adenyl_cycl_N; pfam12633 385025007001 Adenylate cyclase, class-I; Region: Adenylate_cycl; pfam01295 385025007002 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025007003 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025007004 metal binding site [ion binding]; metal-binding site 385025007005 active site 385025007006 I-site; other site 385025007007 argininosuccinate lyase; Provisional; Region: PRK00855 385025007008 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 385025007009 active sites [active] 385025007010 tetramer interface [polypeptide binding]; other site 385025007011 Histidine kinase; Region: His_kinase; pfam06580 385025007012 putative two-component response-regulatory protein YehT; Provisional; Region: PRK11697 385025007013 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025007014 active site 385025007015 phosphorylation site [posttranslational modification] 385025007016 intermolecular recognition site; other site 385025007017 dimerization interface [polypeptide binding]; other site 385025007018 LytTr DNA-binding domain; Region: LytTR; smart00850 385025007019 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 385025007020 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 385025007021 domain interfaces; other site 385025007022 active site 385025007023 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 385025007024 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 385025007025 active site 385025007026 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 385025007027 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemX; COG2959 385025007028 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 385025007029 HemY protein N-terminus; Region: HemY_N; pfam07219 385025007030 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 385025007031 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 385025007032 binding surface 385025007033 TPR motif; other site 385025007034 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 385025007035 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 385025007036 CPxP motif; other site 385025007037 Bacterial SH3 domain; Region: SH3_3; pfam08239 385025007038 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 385025007039 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 385025007040 active site 385025007041 Zn binding site [ion binding]; other site 385025007042 E3 Ubiquitin ligase; Region: GIDE; pfam12483 385025007043 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 385025007044 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 385025007045 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 385025007046 trimer interface [polypeptide binding]; other site 385025007047 putative metal binding site [ion binding]; other site 385025007048 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 385025007049 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 385025007050 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 385025007051 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 385025007052 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 385025007053 shikimate binding site; other site 385025007054 NAD(P) binding site [chemical binding]; other site 385025007055 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 385025007056 dimer interface [polypeptide binding]; other site 385025007057 active site 385025007058 aspartate-rich active site metal binding site; other site 385025007059 allosteric magnesium binding site [ion binding]; other site 385025007060 Schiff base residues; other site 385025007061 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 385025007062 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 385025007063 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 385025007064 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 385025007065 AIR carboxylase; Region: AIRC; pfam00731 385025007066 DNA topoisomerase I; Validated; Region: PRK06599 385025007067 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 385025007068 active site 385025007069 interdomain interaction site; other site 385025007070 putative metal-binding site [ion binding]; other site 385025007071 nucleotide binding site [chemical binding]; other site 385025007072 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 385025007073 domain I; other site 385025007074 DNA binding groove [nucleotide binding] 385025007075 phosphate binding site [ion binding]; other site 385025007076 domain II; other site 385025007077 domain III; other site 385025007078 nucleotide binding site [chemical binding]; other site 385025007079 catalytic site [active] 385025007080 domain IV; other site 385025007081 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 385025007082 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 385025007083 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 385025007084 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 385025007085 Protein of unknown function (DUF494); Region: DUF494; pfam04361 385025007086 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 385025007087 DNA protecting protein DprA; Region: dprA; TIGR00732 385025007088 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 385025007089 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 385025007090 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 385025007091 active site 385025007092 catalytic residues [active] 385025007093 metal binding site [ion binding]; metal-binding site 385025007094 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 385025007095 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 385025007096 putative active site [active] 385025007097 substrate binding site [chemical binding]; other site 385025007098 putative cosubstrate binding site; other site 385025007099 catalytic site [active] 385025007100 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 385025007101 substrate binding site [chemical binding]; other site 385025007102 16S rRNA methyltransferase B; Provisional; Region: PRK10901 385025007103 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 385025007104 putative RNA binding site [nucleotide binding]; other site 385025007105 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 385025007106 S-adenosylmethionine binding site [chemical binding]; other site 385025007107 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 385025007108 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 385025007109 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 385025007110 dimerization interface [polypeptide binding]; other site 385025007111 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 385025007112 dimer interface [polypeptide binding]; other site 385025007113 phosphorylation site [posttranslational modification] 385025007114 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 385025007115 ATP binding site [chemical binding]; other site 385025007116 Mg2+ binding site [ion binding]; other site 385025007117 G-X-G motif; other site 385025007118 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 385025007119 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 385025007120 active site 385025007121 phosphorylation site [posttranslational modification] 385025007122 intermolecular recognition site; other site 385025007123 dimerization interface [polypeptide binding]; other site 385025007124 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 385025007125 Walker A motif; other site 385025007126 ATP binding site [chemical binding]; other site 385025007127 Walker B motif; other site 385025007128 arginine finger; other site 385025007129 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 385025007130 TrkA-N domain; Region: TrkA_N; pfam02254 385025007131 TrkA-C domain; Region: TrkA_C; pfam02080 385025007132 TrkA-N domain; Region: TrkA_N; pfam02254 385025007133 TrkA-C domain; Region: TrkA_C; pfam02080 385025007134 Cation transport protein; Region: TrkH; cl17365 385025007135 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 385025007136 Methyltransferase domain; Region: Methyltransf_23; pfam13489 385025007137 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 385025007138 S-adenosylmethionine binding site [chemical binding]; other site 385025007139 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 385025007140 active site residue [active] 385025007141 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 385025007142 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 385025007143 G1 box; other site 385025007144 putative GEF interaction site [polypeptide binding]; other site 385025007145 GTP/Mg2+ binding site [chemical binding]; other site 385025007146 Switch I region; other site 385025007147 G2 box; other site 385025007148 G3 box; other site 385025007149 Switch II region; other site 385025007150 G4 box; other site 385025007151 G5 box; other site 385025007152 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 385025007153 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 385025007154 Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]; Region: COG2414 385025007155 Aldehyde ferredoxin oxidoreductase, N-terminal domain; Region: AFOR_N; pfam02730 385025007156 Aldehyde ferredoxin oxidoreductase, domains 2 & 3; Region: AFOR_C; pfam01314 385025007157 Ubiquitin-like proteins; Region: UBQ; cl00155 385025007158 charged pocket; other site 385025007159 hydrophobic patch; other site 385025007160 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 385025007161 putative active site pocket [active] 385025007162 4-fold oligomerization interface [polypeptide binding]; other site 385025007163 metal binding residues [ion binding]; metal-binding site 385025007164 3-fold/trimer interface [polypeptide binding]; other site 385025007165 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 385025007166 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 385025007167 putative active site [active] 385025007168 oxyanion strand; other site 385025007169 catalytic triad [active] 385025007170 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 385025007171 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 385025007172 catalytic residues [active] 385025007173 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 385025007174 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 385025007175 substrate binding site [chemical binding]; other site 385025007176 glutamase interaction surface [polypeptide binding]; other site 385025007177 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 385025007178 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 385025007179 metal binding site [ion binding]; metal-binding site 385025007180 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 385025007181 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 385025007182 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 385025007183 hypothetical protein; Provisional; Region: PRK01254 385025007184 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 385025007185 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 385025007186 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 385025007187 PBP superfamily domain; Region: PBP_like_2; cl17296 385025007188 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 385025007189 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 385025007190 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 385025007191 metal binding site [ion binding]; metal-binding site 385025007192 active site 385025007193 I-site; other site 385025007194 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 385025007195 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 385025007196 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 385025007197 transmembrane helices; other site 385025007198 Domain of unknown function (DUF4212); Region: DUF4212; pfam13937 385025007199 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 385025007200 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 385025007201 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 385025007202 Na binding site [ion binding]; other site 385025007203 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; pfam02639 385025007204 DNA ligase; Provisional; Region: PRK09125 385025007205 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 385025007206 DNA binding site [nucleotide binding] 385025007207 active site 385025007208 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 385025007209 DNA binding site [nucleotide binding] 385025007210 elongation factor P; Provisional; Region: PRK04542 385025007211 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 385025007212 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 385025007213 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 385025007214 RNA binding site [nucleotide binding]; other site 385025007215 HopJ type III effector protein; Region: HopJ; pfam08888 385025007216 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 385025007217 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 385025007218 ATP binding site [chemical binding]; other site 385025007219 Mg++ binding site [ion binding]; other site 385025007220 motif III; other site 385025007221 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 385025007222 nucleotide binding region [chemical binding]; other site 385025007223 ATP-binding site [chemical binding]; other site 385025007224 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 385025007225 putative RNA binding site [nucleotide binding]; other site 385025007226 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 385025007227 putative acyl-acceptor binding pocket; other site 385025007228 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 385025007229 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 385025007230 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 385025007231 Sulfate transporter family; Region: Sulfate_transp; pfam00916 385025007232 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 385025007233 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 385025007234 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 385025007235 ATP binding site [chemical binding]; other site 385025007236 putative Mg++ binding site [ion binding]; other site 385025007237 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 385025007238 nucleotide binding region [chemical binding]; other site 385025007239 ATP-binding site [chemical binding]; other site 385025007240 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 385025007241 HRDC domain; Region: HRDC; pfam00570 385025007242 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 385025007243 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 385025007244 Walker A/P-loop; other site 385025007245 ATP binding site [chemical binding]; other site 385025007246 Q-loop/lid; other site 385025007247 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025007248 ABC transporter signature motif; other site 385025007249 Walker B; other site 385025007250 D-loop; other site 385025007251 ABC transporter; Region: ABC_tran_2; pfam12848 385025007252 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 385025007253 Uncharacterized conserved protein (DUF2132); Region: DUF2132; pfam09905 385025007254 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 385025007255 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 385025007256 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 385025007257 Putative rRNA methylase; Region: rRNA_methylase; pfam06962 385025007258 VanZ like family; Region: VanZ; pfam04892 385025007259 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiB; COG0543 385025007260 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 385025007261 FAD binding pocket [chemical binding]; other site 385025007262 FAD binding motif [chemical binding]; other site 385025007263 phosphate binding motif [ion binding]; other site 385025007264 beta-alpha-beta structure motif; other site 385025007265 NAD binding pocket [chemical binding]; other site 385025007266 Iron coordination center [ion binding]; other site 385025007267 dihydroorotase; Provisional; Region: PRK07627 385025007268 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 385025007269 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 385025007270 active site 385025007271 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 385025007272 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 385025007273 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 385025007274 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 385025007275 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 385025007276 active site 385025007277 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 385025007278 hypothetical protein; Validated; Region: PRK00228 385025007279 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 385025007280 glutathione synthetase; Provisional; Region: PRK05246 385025007281 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 385025007282 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 385025007283 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 385025007284 RNA methyltransferase, RsmE family; Region: TIGR00046 385025007285 YcgL domain; Region: YcgL; pfam05166 385025007286 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 385025007287 FAD binding site [chemical binding]; other site 385025007288 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 385025007289 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 385025007290 homotetramer interface [polypeptide binding]; other site 385025007291 ligand binding site [chemical binding]; other site 385025007292 catalytic site [active] 385025007293 NAD binding site [chemical binding]; other site 385025007294 S-adenosylmethionine synthetase; Validated; Region: PRK05250 385025007295 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 385025007296 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 385025007297 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 385025007298 Phospholipid methyltransferase; Region: PEMT; cl17370 385025007299 Domain of unknown function (DUF4202); Region: DUF4202; pfam13875 385025007300 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 385025007301 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 385025007302 dimerization interface [polypeptide binding]; other site 385025007303 substrate binding site [chemical binding]; other site 385025007304 active site 385025007305 calcium binding site [ion binding]; other site 385025007306 methionine sulfoxide reductase B; Provisional; Region: PRK00222 385025007307 SelR domain; Region: SelR; pfam01641 385025007308 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 385025007309 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 385025007310 active site 385025007311 metal binding site [ion binding]; metal-binding site 385025007312 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 385025007313 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 385025007314 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 385025007315 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 385025007316 putative active site [active] 385025007317 metal binding site [ion binding]; metal-binding site 385025007318 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 385025007319 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025007320 NAD(P) binding site [chemical binding]; other site 385025007321 active site 385025007322 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 385025007323 classical (c) SDRs; Region: SDR_c; cd05233 385025007324 NAD(P) binding site [chemical binding]; other site 385025007325 active site 385025007326 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025007327 inter-subunit interface; other site 385025007328 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 385025007329 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 385025007330 iron-sulfur cluster [ion binding]; other site 385025007331 [2Fe-2S] cluster binding site [ion binding]; other site 385025007332 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025007333 beta subunit interface [polypeptide binding]; other site 385025007334 alpha subunit interface [polypeptide binding]; other site 385025007335 active site 385025007336 substrate binding site [chemical binding]; other site 385025007337 Fe binding site [ion binding]; other site 385025007338 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 385025007339 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025007340 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 385025007341 N-terminal domain interface [polypeptide binding]; other site 385025007342 dimer interface [polypeptide binding]; other site 385025007343 substrate binding pocket (H-site) [chemical binding]; other site 385025007344 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 385025007345 classical (c) SDRs; Region: SDR_c; cd05233 385025007346 NAD(P) binding site [chemical binding]; other site 385025007347 active site 385025007348 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 385025007349 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 385025007350 [2Fe-2S] cluster binding site [ion binding]; other site 385025007351 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 385025007352 alpha subunit interface [polypeptide binding]; other site 385025007353 active site 385025007354 substrate binding site [chemical binding]; other site 385025007355 Fe binding site [ion binding]; other site 385025007356 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 385025007357 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 385025007358 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 385025007359 classical (c) SDRs; Region: SDR_c; cd05233 385025007360 NAD(P) binding site [chemical binding]; other site 385025007361 active site 385025007362 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 385025007363 UbiA prenyltransferase family; Region: UbiA; pfam01040 385025007364 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 385025007365 PhoH-like protein; Region: PhoH; pfam02562 385025007366 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 385025007367 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 385025007368 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 385025007369 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 385025007370 Protein of unknown function (DUF962); Region: DUF962; cl01879 385025007371 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; pfam02666 385025007372 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 385025007373 active site 385025007374 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 385025007375 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 385025007376 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 385025007377 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 385025007378 catalytic residue [active] 385025007379 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 385025007380 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 385025007381 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 385025007382 acyl-activating enzyme (AAE) consensus motif; other site 385025007383 acyl-activating enzyme (AAE) consensus motif; other site 385025007384 putative AMP binding site [chemical binding]; other site 385025007385 putative active site [active] 385025007386 putative CoA binding site [chemical binding]; other site 385025007387 Rubredoxin-like zinc ribbon domain (DUF35_N); Region: DUF35_N; pfam12172 385025007388 DUF35 OB-fold domain; Region: DUF35; pfam01796 385025007389 lipid-transfer protein; Provisional; Region: PRK07855 385025007390 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 385025007391 active site 385025007392 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 385025007393 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 385025007394 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 385025007395 [2Fe-2S] cluster binding site [ion binding]; other site 385025007396 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 385025007397 putative alpha subunit interface [polypeptide binding]; other site 385025007398 putative active site [active] 385025007399 putative substrate binding site [chemical binding]; other site 385025007400 Fe binding site [ion binding]; other site 385025007401 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 385025007402 Fatty acid desaturase; Region: FA_desaturase; pfam00487 385025007403 Di-iron ligands [ion binding]; other site 385025007404 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 385025007405 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 385025007406 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 385025007407 iron-sulfur cluster [ion binding]; other site 385025007408 [2Fe-2S] cluster binding site [ion binding]; other site 385025007409 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 385025007410 putative alpha subunit interface [polypeptide binding]; other site 385025007411 putative active site [active] 385025007412 putative substrate binding site [chemical binding]; other site 385025007413 Fe binding site [ion binding]; other site 385025007414 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 385025007415 Sterol-sensing domain of SREBP cleavage-activation; Region: Sterol-sensing; pfam12349 385025007416 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 385025007417 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 385025007418 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 385025007419 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 385025007420 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 385025007421 glutaminase active site [active] 385025007422 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 385025007423 dimer interface [polypeptide binding]; other site 385025007424 active site 385025007425 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 385025007426 dimer interface [polypeptide binding]; other site 385025007427 active site 385025007428 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 385025007429 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 385025007430 Substrate binding site; other site 385025007431 Mg++ binding site; other site 385025007432 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 385025007433 active site 385025007434 substrate binding site [chemical binding]; other site 385025007435 CoA binding site [chemical binding]; other site 385025007436 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 385025007437 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 385025007438 gamma subunit interface [polypeptide binding]; other site 385025007439 epsilon subunit interface [polypeptide binding]; other site 385025007440 LBP interface [polypeptide binding]; other site 385025007441 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 385025007442 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 385025007443 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 385025007444 alpha subunit interaction interface [polypeptide binding]; other site 385025007445 Walker A motif; other site 385025007446 ATP binding site [chemical binding]; other site 385025007447 Walker B motif; other site 385025007448 inhibitor binding site; inhibition site 385025007449 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 385025007450 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 385025007451 core domain interface [polypeptide binding]; other site 385025007452 delta subunit interface [polypeptide binding]; other site 385025007453 epsilon subunit interface [polypeptide binding]; other site 385025007454 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 385025007455 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 385025007456 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 385025007457 beta subunit interaction interface [polypeptide binding]; other site 385025007458 Walker A motif; other site 385025007459 ATP binding site [chemical binding]; other site 385025007460 Walker B motif; other site 385025007461 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 385025007462 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 385025007463 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 385025007464 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 385025007465 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 385025007466 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 385025007467 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 385025007468 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 385025007469 ParB-like nuclease domain; Region: ParBc; pfam02195 385025007470 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 385025007471 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 385025007472 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 385025007473 P-loop; other site 385025007474 Magnesium ion binding site [ion binding]; other site 385025007475 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 385025007476 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 385025007477 S-adenosylmethionine binding site [chemical binding]; other site 385025007478 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 385025007479 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 385025007480 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 385025007481 MoxR-like ATPases [General function prediction only]; Region: COG0714 385025007482 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 385025007483 Walker A motif; other site 385025007484 ATP binding site [chemical binding]; other site 385025007485 Walker B motif; other site 385025007486 arginine finger; other site 385025007487 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 385025007488 Coenzyme A binding pocket [chemical binding]; other site 385025007489 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 385025007490 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 385025007491 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 385025007492 putative catalytic residue [active] 385025007493 Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a...; Region: Rieske_RO_ferredoxin; cd03528 385025007494 [2Fe-2S] cluster binding site [ion binding]; other site 385025007495 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 385025007496 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 385025007497 catalytic loop [active] 385025007498 iron binding site [ion binding]; other site 385025007499 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 385025007500 FAD binding pocket [chemical binding]; other site 385025007501 FAD binding motif [chemical binding]; other site 385025007502 phosphate binding motif [ion binding]; other site 385025007503 beta-alpha-beta structure motif; other site 385025007504 NAD binding pocket [chemical binding]; other site 385025007505 Conserved hypothetical protein (DUF2461); Region: DUF2461; pfam09365 385025007506 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 385025007507 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 385025007508 pyridoxal 5'-phosphate binding site [chemical binding]; other site 385025007509 catalytic residue [active] 385025007510 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 385025007511 apolar tunnel; other site 385025007512 heme binding site [chemical binding]; other site 385025007513 dimerization interface [polypeptide binding]; other site 385025007514 2,3-dihydroxybiphenyl 1,2-dioxygenase; Region: 23dbph12diox; TIGR03213 385025007515 N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_N_like; cd07252 385025007516 C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins; Region: BphC1-RGP6_C_like; cd07237 385025007517 active site 385025007518 Fe binding site [ion binding]; other site 385025007519 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025007520 inter-subunit interface; other site 385025007521 anthranilate 1,2-dioxygenase, large subunit; Region: anthran_1_2_A; TIGR03228 385025007522 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 385025007523 [2Fe-2S] cluster binding site [ion binding]; other site 385025007524 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025007525 beta subunit interface [polypeptide binding]; other site 385025007526 alpha subunit interface [polypeptide binding]; other site 385025007527 active site 385025007528 substrate binding site [chemical binding]; other site 385025007529 Fe binding site [ion binding]; other site 385025007530 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 385025007531 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 385025007532 iron-sulfur cluster [ion binding]; other site 385025007533 [2Fe-2S] cluster binding site [ion binding]; other site 385025007534 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 385025007535 putative alpha subunit interface [polypeptide binding]; other site 385025007536 putative active site [active] 385025007537 putative substrate binding site [chemical binding]; other site 385025007538 Fe binding site [ion binding]; other site 385025007539 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 385025007540 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 385025007541 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025007542 inter-subunit interface; other site 385025007543 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 385025007544 iron-sulfur cluster [ion binding]; other site 385025007545 [2Fe-2S] cluster binding site [ion binding]; other site 385025007546 C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins; Region: RHO_alpha_C_ahdA1c-like; cd08880 385025007547 putative alpha subunit interface [polypeptide binding]; other site 385025007548 putative active site [active] 385025007549 putative substrate binding site [chemical binding]; other site 385025007550 Fe binding site [ion binding]; other site 385025007551 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 385025007552 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 385025007553 ligand binding site [chemical binding]; other site 385025007554 flexible hinge region; other site 385025007555 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 385025007556 putative switch regulator; other site 385025007557 non-specific DNA interactions [nucleotide binding]; other site 385025007558 DNA binding site [nucleotide binding] 385025007559 sequence specific DNA binding site [nucleotide binding]; other site 385025007560 putative cAMP binding site [chemical binding]; other site 385025007561 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 385025007562 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 385025007563 [2Fe-2S] cluster binding site [ion binding]; other site 385025007564 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 385025007565 hydrophobic ligand binding site; other site 385025007566 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 385025007567 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional; Region: PRK06200 385025007568 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025007569 NAD(P) binding site [chemical binding]; other site 385025007570 active site 385025007571 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 385025007572 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 385025007573 Trp docking motif [polypeptide binding]; other site 385025007574 active site 385025007575 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 385025007576 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 385025007577 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 385025007578 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 385025007579 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 385025007580 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 385025007581 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 385025007582 NADP binding site [chemical binding]; other site 385025007583 dimer interface [polypeptide binding]; other site 385025007584 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 385025007585 EamA-like transporter family; Region: EamA; pfam00892 385025007586 EamA-like transporter family; Region: EamA; pfam00892 385025007587 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 385025007588 inter-subunit interface; other site 385025007589 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 385025007590 iron-sulfur cluster [ion binding]; other site 385025007591 [2Fe-2S] cluster binding site [ion binding]; other site 385025007592 C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_NDO-like; cd08881 385025007593 beta subunit interface [polypeptide binding]; other site 385025007594 alpha subunit interface [polypeptide binding]; other site 385025007595 active site 385025007596 substrate binding site [chemical binding]; other site 385025007597 Fe binding site [ion binding]; other site 385025007598 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional; Region: benD; PRK12823 385025007599 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 385025007600 NAD(P) binding site [chemical binding]; other site 385025007601 active site 385025007602 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 385025007603 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 385025007604 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 385025007605 N-terminal domain interface [polypeptide binding]; other site 385025007606 dimer interface [polypeptide binding]; other site 385025007607 substrate binding pocket (H-site) [chemical binding]; other site 385025007608 Protein of unknown function DUF58; Region: DUF58; pfam01882 385025007609 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 385025007610 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 385025007611 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 385025007612 Domain of unknown function (DUF4129); Region: DUF4129; pfam13559 385025007613 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 385025007614 dimer interface [polypeptide binding]; other site 385025007615 FMN binding site [chemical binding]; other site 385025007616 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 385025007617 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 385025007618 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 385025007619 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 385025007620 trmE is a tRNA modification GTPase; Region: trmE; cd04164 385025007621 G1 box; other site 385025007622 GTP/Mg2+ binding site [chemical binding]; other site 385025007623 Switch I region; other site 385025007624 G2 box; other site 385025007625 Switch II region; other site 385025007626 G3 box; other site 385025007627 G4 box; other site 385025007628 G5 box; other site 385025007629 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 385025007630 membrane protein insertase; Provisional; Region: PRK01318 385025007631 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 385025007632 Haemolytic domain; Region: Haemolytic; pfam01809 385025007633 Ribonuclease P; Region: Ribonuclease_P; cl00457 385025007634 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399