-- dump date 20111121_010807 -- class Genbank::misc_feature -- table misc_feature_note -- id note 224914000001 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 224914000002 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This...; Region: URO-D; cd00717 224914000003 substrate binding site; other site 224914000004 active site 224914000005 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 224914000006 transcription termination factor Rho; Provisional; Region: rho; PRK09376 224914000007 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 224914000008 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent...; Region: Rho_CSD; cd04459 224914000009 RNA binding site; other site 224914000010 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of...; Region: rho_factor; cd01128 224914000011 multimer interface; other site 224914000012 Walker A motif; other site 224914000013 ATP binding site; other site 224914000014 Walker B motif; other site 224914000015 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 224914000016 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 224914000017 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein...; Region: SSP411; cd02955 224914000018 catalytic residues; other site 224914000019 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 224914000020 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 224914000021 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 224914000022 G1 box; other site 224914000023 GTP/Mg2+ binding site; other site 224914000024 Switch I region; other site 224914000025 G2 box; other site 224914000026 Switch II region; other site 224914000027 G3 box; other site 224914000028 G4 box; other site 224914000029 G5 box; other site 224914000030 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 224914000031 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 224914000032 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914000033 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 224914000034 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 224914000035 P-loop; other site 224914000036 Magnesium ion binding site; other site 224914000037 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 224914000038 Magnesium ion binding site; other site 224914000039 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 224914000040 ParB-like nuclease domain; Region: ParBc; cl02129 224914000041 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 224914000042 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 224914000043 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 224914000044 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 224914000045 Walker A/P-loop; other site 224914000046 ATP binding site; other site 224914000047 Q-loop/lid; other site 224914000048 ABC transporter signature motif; other site 224914000049 Walker B; other site 224914000050 D-loop; other site 224914000051 H-loop/switch region; other site 224914000052 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 224914000053 TM-ABC transporter signature motif; other site 224914000054 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 224914000055 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 224914000056 zinc binding site; other site 224914000057 putative ligand binding site; other site 224914000058 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 224914000059 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 224914000060 Protein of unknown function (DUF993); Region: DUF993; pfam06187 224914000061 Transcriptional regulators [Transcription]; Region: PurR; COG1609 224914000062 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 224914000063 DNA binding site 224914000064 domain linker motif; other site 224914000065 Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; Region: PBP1_MalI_like; cd06289 224914000066 putative dimerization interface; other site 224914000067 putative ligand binding site; other site 224914000068 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914000069 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000070 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914000071 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 224914000072 Coenzyme A transferase; Region: CoA_trans; cl00773 224914000073 Coenzyme A transferase; Region: CoA_trans; cl00773 224914000074 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 224914000075 substrate binding site; other site 224914000076 oxyanion hole (OAH) forming residues; other site 224914000077 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 224914000078 oxyanion hole (OAH) forming residues; other site 224914000079 trimer interface; other site 224914000080 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; cl11392 224914000081 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 224914000082 Gluconobacter oxydans L-sorbosone dehydrogenase-like; Region: ALDH_SNDH; cd07118 224914000083 NAD(P) binding site; other site 224914000084 catalytic residues; other site 224914000085 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 224914000086 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914000087 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914000088 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000089 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 224914000090 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000091 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914000092 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914000093 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914000094 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914000095 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 224914000096 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; cl01553 224914000097 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000098 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 224914000099 Peptidase dimerization domain; Region: M20_dimer; cl09126 224914000100 Peptidase dimerization domain; Region: M20_dimer; cl09126 224914000101 Beta-lactamase; Region: Beta-lactamase; cl01009 224914000102 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 224914000103 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914000104 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 224914000105 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cd00291 224914000106 CPxP motif; other site 224914000107 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 224914000108 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914000109 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 224914000110 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 224914000111 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 224914000112 DNA binding site 224914000113 Int/Topo IB signature motif; other site 224914000114 active site 224914000115 shikimate kinase; Reviewed; Region: aroK; PRK00131 224914000116 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the...; Region: SK; cd00464 224914000117 ADP binding site; other site 224914000118 magnesium binding site; other site 224914000119 putative shikimate binding site; other site 224914000120 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 224914000121 active site 224914000122 dimer interface; other site 224914000123 metal-binding site 224914000124 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 224914000125 Domain of unknown function DUF21; Region: DUF21; pfam01595 224914000126 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 224914000127 Transporter associated domain; Region: CorC_HlyC; pfam03471 224914000128 BolA-like protein; Region: BolA; cl00386 224914000129 DnaJ-class molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: CbpA; COG2214 224914000130 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 224914000131 HSP70 interaction site; other site 224914000132 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 224914000133 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 224914000134 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 224914000135 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 224914000136 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 224914000137 metal ion-dependent adhesion site (MIDAS); other site 224914000138 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 224914000139 metal-binding site 224914000140 zinc/cadmium/mercury/lead-transporting ATPase; Provisional; Region: zntA; PRK11033 224914000141 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 224914000142 metal-binding site 224914000143 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 224914000144 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914000145 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 224914000146 DNA binding residues 224914000147 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 224914000148 dimer interface; other site 224914000149 putative metal binding site; other site 224914000150 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 224914000151 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 224914000152 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 224914000153 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 224914000154 Type V secretory pathway, adhesin AidA [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: AidA; COG3468 224914000155 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43...; Region: PL2_Passenger_AT; cd01344 224914000156 Autotransporter beta-domain; Region: Autotransporter; cl02365 224914000157 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 224914000158 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 224914000159 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 224914000160 active site 224914000161 phosphorylation site 224914000162 intermolecular recognition site; other site 224914000163 dimerization interface; other site 224914000164 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914000165 DNA binding site 224914000166 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 224914000167 ligand binding site; other site 224914000168 flexible hinge region; other site 224914000169 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 224914000170 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 224914000171 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-...; Region: MIP; cl00200 224914000172 amphipathic channel; other site 224914000173 Asn-Pro-Ala signature motifs; other site 224914000174 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 224914000175 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914000176 Walker A/P-loop; other site 224914000177 ATP binding site; other site 224914000178 Q-loop/lid; other site 224914000179 ABC transporter signature motif; other site 224914000180 Walker B; other site 224914000181 D-loop; other site 224914000182 H-loop/switch region; other site 224914000183 Predicted permease; Region: FtsX; cl11418 224914000184 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 224914000185 putative active site; other site 224914000186 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 224914000187 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 224914000188 putative acyl-acceptor binding pocket; other site 224914000189 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 224914000190 dimer interface; other site 224914000191 substrate binding site; other site 224914000192 metal binding sites; metal-binding site 224914000193 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 224914000194 putative active site pocket; other site 224914000195 dimerization interface; other site 224914000196 putative catalytic residue; other site 224914000197 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; cl11537 224914000198 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 224914000199 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000200 histidinol-phosphate aminotransferase; Validated; Region: PRK00950 224914000201 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 224914000202 pyridoxal 5'-phosphate binding site; other site 224914000203 homodimer interface; other site 224914000204 catalytic residue; other site 224914000205 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914000206 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914000207 conserved hypothetical protein TIGR02302; Region: aProt_lowcomp 224914000208 diaminopimelate decarboxylase; Region: lysA; TIGR01048 224914000209 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 224914000210 active site 224914000211 pyridoxal 5'-phosphate (PLP) binding site; other site 224914000212 substrate binding site; other site 224914000213 catalytic residues; other site 224914000214 dimer interface; other site 224914000215 Predicted small periplasmic lipoprotein [Cell motility and secretion]; Region: COG5567 224914000216 argininosuccinate lyase; Provisional; Region: PRK00855 224914000217 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 224914000218 active sites 224914000219 tetramer interface; other site 224914000220 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing...; Region: TlpA_like_family; cd02966 224914000221 catalytic residues; other site 224914000222 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 224914000223 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 224914000224 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000225 short chain dehydrogenase; Provisional; Region: PRK06914 224914000226 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 224914000227 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 224914000228 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl14056 224914000229 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 224914000230 active site 224914000231 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 224914000232 Ligand Binding Site; other site 224914000233 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 224914000234 Ligand binding site; other site 224914000235 etfA (electron transfer flavoprotein alpha subunit); Provisional; Region: PLN00022 224914000236 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 224914000237 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 224914000238 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 224914000239 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000240 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 224914000241 cysteine synthases; Region: cysKM; TIGR01136 224914000242 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 224914000243 dimer interface; other site 224914000244 pyridoxal 5'-phosphate binding site; other site 224914000245 catalytic residue; other site 224914000246 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 224914000247 Ligand Binding Site; other site 224914000248 methionine gamma-lyase; Validated; Region: PRK07049 224914000249 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 224914000250 homodimer interface; other site 224914000251 substrate-cofactor binding pocket; other site 224914000252 pyridoxal 5'-phosphate binding site; other site 224914000253 catalytic residue; other site 224914000254 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 224914000255 d-galactonate transporter; Region: 2A0114; TIGR00893 224914000256 putative substrate translocation pore; other site 224914000257 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cd00411 224914000258 active site/substrate binding site 224914000259 tetramer interface; other site 224914000260 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914000261 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914000262 DNA binding site 224914000263 FCD domain; Region: FCD; cl11656 224914000264 Asparaginase (amidohydrolase): Asparaginases are tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localised to the...; Region: Asparaginase; cl00216 224914000265 active site/substrate binding site 224914000266 tetramer interface; other site 224914000267 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 224914000268 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 224914000269 Walker A/P-loop; other site 224914000270 ATP binding site; other site 224914000271 Q-loop/lid; other site 224914000272 ABC transporter signature motif; other site 224914000273 Walker B; other site 224914000274 D-loop; other site 224914000275 H-loop/switch region; other site 224914000276 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 224914000277 Aspartase; Region: Aspartase; cd01357 224914000278 active sites 224914000279 tetramer interface; other site 224914000280 Arginase family; Region: Arginase; cl00306 224914000281 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 224914000282 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 224914000283 Walker A/P-loop; other site 224914000284 ATP binding site; other site 224914000285 Q-loop/lid; other site 224914000286 ABC transporter signature motif; other site 224914000287 Walker B; other site 224914000288 D-loop; other site 224914000289 H-loop/switch region; other site 224914000290 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 224914000291 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914000292 dimer interface; other site 224914000293 conserved gate region; other site 224914000294 putative PBP binding loops; other site 224914000295 ABC-ATPase subunit interface; other site 224914000296 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914000297 dimer interface; other site 224914000298 conserved gate region; other site 224914000299 putative PBP binding loops; other site 224914000300 ABC-ATPase subunit interface; other site 224914000301 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914000302 membrane-bound complex binding site; other site 224914000303 hinge residues; other site 224914000304 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914000305 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914000306 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914000307 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 224914000308 dimerization interface; other site 224914000309 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 224914000310 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 224914000311 Sulfatase; Region: Sulfatase; cl10460 224914000312 FemAB family; Region: FemAB; cl11444 224914000313 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 224914000314 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; cl12029 224914000315 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 224914000316 SecA Wing and Scaffold domain; Region: SecA_SW; pfam07516 224914000317 hypothetical protein; Provisional; Region: PRK00183 224914000318 SEC-C motif; Region: SEC-C; cl12132 224914000319 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 224914000320 PPIC-type PPIASE domain; Region: Rotamase; cl08278 224914000321 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group...; Region: OAT; cd02152 224914000322 heterotetramer interface; other site 224914000323 active site pocket 224914000324 cleavage site 224914000325 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914000326 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 224914000327 active site 224914000328 8-oxo-dGMP binding site; other site 224914000329 nudix motif; other site 224914000330 metal-binding site 224914000331 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 224914000332 Intracellular septation protein A; Region: IspA; cl01098 224914000333 Signal recognition particle GTPase [Intracellular trafficking and secretion]; Region: FtsY; COG0552 224914000334 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 224914000335 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914000336 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 224914000337 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 224914000338 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 224914000339 FeS/SAM binding site; other site 224914000340 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 224914000341 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 224914000342 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 224914000343 Protease inhibitor Inh; Region: Inh; pfam02974 224914000344 Predicted ATPase [General function prediction only]; Region: COG1485 224914000345 malate dehydrogenase; Reviewed; Region: PRK06223 224914000346 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 224914000347 NAD(P) binding site; other site 224914000348 dimer interface; other site 224914000349 tetramer (dimer of dimers) interface; other site 224914000350 substrate binding site; other site 224914000351 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 224914000352 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914000353 CoA-ligase; Region: Ligase_CoA; pfam00549 224914000354 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 224914000355 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000356 CoA-ligase; Region: Ligase_CoA; pfam00549 224914000357 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 224914000358 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 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of...; Region: TPP_E1_OGDC_like; cd02016 224914000359 TPP-binding site; other site 224914000360 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 224914000361 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 224914000362 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 224914000363 E3 interaction surface; other site 224914000364 lipoyl attachment site; other site 224914000365 e3 binding domain; Region: E3_binding; pfam02817 224914000366 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 224914000367 MAPEG family; Region: MAPEG; cl09190 224914000368 LysE type translocator; Region: LysE; cl00565 224914000369 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 224914000370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000371 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000372 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl10040 224914000373 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 224914000374 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3735 224914000375 GumN protein; Region: GumN; cl12050 224914000376 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 224914000377 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 224914000378 DNA binding site 224914000379 Int/Topo IB signature motif; other site 224914000380 active site 224914000381 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 224914000382 RimM N-terminal domain; Region: RimM; pfam01782 224914000383 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 224914000384 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 224914000385 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 224914000386 dimerization interface; other site 224914000387 putative DNA binding site; other site 224914000388 putative Zn2+ binding site; other site 224914000389 NIPSNAP; Region: NIPSNAP; pfam07978 224914000390 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 224914000391 Sodium:solute symporter family; Region: SSF; cl00456 224914000392 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 224914000393 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 224914000394 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 224914000395 substrate binding site; other site 224914000396 ligand binding site; other site 224914000397 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914000398 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 224914000399 Coenzyme A binding pocket; other site 224914000400 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 224914000401 Iron-sulfur protein interface; other site 224914000402 proximal quinone binding site; other site 224914000403 SdhD (CybS) interface; other site 224914000404 proximal heme binding site; other site 224914000405 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...; Region: SQR_TypeC_SdhD_like; cd03495 224914000406 putative SdhC subunit interface; other site 224914000407 putative proximal heme binding site; other site 224914000408 putative Iron-sulfur protein interface; other site 224914000409 putative proximal quinone binding site; other site 224914000410 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 224914000411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000412 domain; Region: Succ_DH_flav_C; pfam02910 224914000413 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 224914000414 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914000415 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07333 224914000416 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000417 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 224914000418 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 224914000419 active site 224914000420 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 224914000421 catalytic triad; other site 224914000422 dimer interface; other site 224914000423 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 224914000424 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 224914000425 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914000426 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 224914000427 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 224914000428 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914000429 DNA binding site 224914000430 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 224914000431 pyridoxal 5'-phosphate binding site; other site 224914000432 homodimer interface; other site 224914000433 catalytic residue; other site 224914000434 hypothetical protein; Provisional; Region: PRK11272 224914000435 EamA-like transporter family; Region: EamA; cl01037 224914000436 Predicted methyltransferase [General function prediction only]; Region: COG3897 224914000437 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914000438 Protein of unknown function DUF55; Region: DUF55; cl00728 224914000439 YCII-related domain; Region: YCII; cl00999 224914000440 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 224914000441 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000442 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 224914000443 putative DNA-binding/iron metalloprotein/AP endonuclease; Reviewed; Region: PRK09604 224914000444 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 224914000445 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 224914000446 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 224914000447 domain interfaces; other site 224914000448 active site 224914000449 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 224914000450 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations...; Region: HemD; cd06578 224914000451 active site 224914000452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 224914000453 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 224914000454 HemY protein N-terminus; Region: HemY_N; pfam07219 224914000455 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 224914000456 putative metal binding site; other site 224914000457 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 224914000458 putative substrate translocation pore; other site 224914000459 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 224914000460 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914000461 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 224914000462 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914000463 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 224914000464 GSH binding site; other site 224914000465 catalytic residues; other site 224914000466 Predicted amidohydrolase [General function prediction only]; Region: COG0388 224914000467 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 224914000468 putative active site; other site 224914000469 catalytic triad; other site 224914000470 dimer interface; other site 224914000471 Protein of unknown function (DUF1178); Region: DUF1178; cl02196 224914000472 EamA-like transporter family; Region: EamA; cl01037 224914000473 3-demethylubiquinone-9 3-methyltransferase; Provisional; Region: PRK05134 224914000474 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 224914000475 S-adenosylmethionine binding site; other site 224914000476 aspartate kinase; Reviewed; Region: PRK06635 224914000477 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 224914000478 putative nucleotide binding site; other site 224914000479 putative catalytic residues; other site 224914000480 putative Mg ion binding site; other site 224914000481 putative aspartate binding site; other site 224914000482 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 224914000483 putative allosteric regulatory site; other site 224914000484 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 224914000485 putative allosteric regulatory residue; other site 224914000486 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 224914000487 GAF domain; Region: GAF; cl00853 224914000488 PEP-utilising enzyme, N-terminal; Region: PEP-utilizers_N; pfam05524 224914000489 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 224914000490 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 224914000491 peptide chain release factor 1; Validated; Region: prfA; PRK00591 224914000492 RF-1 domain; Region: RF-1; cl02875 224914000493 RF-1 domain; Region: RF-1; cl02875 224914000494 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 224914000495 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 224914000496 S-adenosylmethionine binding site; other site 224914000497 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 224914000498 Clp amino terminal domain; Region: Clp_N; pfam02861 224914000499 Clp amino terminal domain; Region: Clp_N; pfam02861 224914000500 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914000501 Walker A motif; other site 224914000502 ATP binding site; other site 224914000503 Walker B motif; other site 224914000504 arginine finger; other site 224914000505 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914000506 Walker A motif; other site 224914000507 ATP binding site; other site 224914000508 Walker B motif; other site 224914000509 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 224914000510 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 224914000511 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914000512 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 224914000513 Peptidase family M23; Region: Peptidase_M23; pfam01551 224914000514 Integrase core domain; Region: rve; cl01316 224914000515 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 224914000516 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 224914000517 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 224914000518 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 224914000519 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914000520 YadA-like C-terminal region; Region: YadA; pfam03895 224914000521 GTPase ObgE; Reviewed; Region: obgE; PRK12299 224914000522 GTP1/OBG; Region: GTP1_OBG; pfam01018 224914000523 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 224914000524 G1 box; other site 224914000525 GTP/Mg2+ binding site; other site 224914000526 Switch I region; other site 224914000527 G2 box; other site 224914000528 G3 box; other site 224914000529 Switch II region; other site 224914000530 G4 box; other site 224914000531 G5 box; other site 224914000532 gamma-glutamyl kinase; Provisional; Region: PRK05429 224914000533 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 224914000534 nucleotide binding site; other site 224914000535 homotetrameric interface; other site 224914000536 putative phosphate binding site; other site 224914000537 putative allosteric binding site; other site 224914000538 PUA domain; Region: PUA; cl00607 224914000539 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 224914000540 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 224914000541 putative catalytic cysteine; other site 224914000542 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 224914000543 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 224914000544 active site 224914000545 substrate binding site; other site 224914000546 Domain of unknown function DUF143; Region: DUF143; cl00519 224914000547 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 224914000548 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 224914000549 Peptidase family M23; Region: Peptidase_M23; pfam01551 224914000550 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 224914000551 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 224914000552 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 224914000553 protein binding site; other site 224914000554 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 224914000555 Catalytic dyad; other site 224914000556 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where...; Region: Ap4A_hydrolase_plant_like; cd03671 224914000557 putative active site; other site 224914000558 Ap4A binding site; other site 224914000559 nudix motif; other site 224914000560 putative metal binding site; other site 224914000561 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 224914000562 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914000563 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914000564 dimerization interface; other site 224914000565 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 224914000566 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 224914000567 tetrameric interface; other site 224914000568 NAD binding site; other site 224914000569 catalytic residues; other site 224914000570 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 224914000571 dimer interface; other site 224914000572 pyridoxal binding site; other site 224914000573 ATP binding site; other site 224914000574 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 224914000575 active site clefts 224914000576 zinc binding site; other site 224914000577 dimer interface; other site 224914000578 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 224914000579 lytic murein transglycosylase; Region: MltB_2; TIGR02283 224914000580 signal recognition particle protein; Region: ffh; TIGR00959 224914000581 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 224914000582 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 224914000583 P loop; other site 224914000584 GTP binding site; other site 224914000585 Signal peptide binding domain; Region: SRP_SPB; pfam02978 224914000586 Chorismate mutase type II; Region: CM_2; cl00693 224914000587 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 224914000588 LemA family; Region: LemA; cl00742 224914000589 Domain of unknown function (DUF477); Region: DUF477; cl01535 224914000590 Domain of unknown function (DUF477); Region: DUF477; cl01535 224914000591 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 224914000592 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 224914000593 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 224914000594 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 224914000595 purine monophosphate binding site; other site 224914000596 dimer interface; other site 224914000597 putative catalytic residues; other site 224914000598 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 224914000599 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 224914000600 Heparinase II/III-like protein; Region: Hepar_II_III; cl02215 224914000601 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-...; Region: NusB_Sun; cl00223 224914000602 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 224914000603 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 224914000604 S-adenosylmethionine binding site; other site 224914000605 Peptidase family M48; Region: Peptidase_M48; cl12018 224914000606 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 224914000607 acetyl-CoA synthetase; Provisional; Region: PRK00174 224914000608 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 224914000609 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914000610 Usg-like family; Region: Usg; cl11567 224914000611 Predicted membrane protein [Function unknown]; Region: COG1289 224914000612 hypothetical membrane protein, TIGR01666; Region: YCCS 224914000613 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 224914000614 pyridoxal 5'-phosphate (PLP) binding site; other site 224914000615 catalytic residue; other site 224914000616 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 224914000617 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 224914000618 HIGH motif; other site 224914000619 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914000620 KMSKS motif; other site 224914000621 active site 224914000622 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 224914000623 tRNA binding surface; other site 224914000624 Predicted secreted (periplasmic) protein (DUF2159); Region: DUF2159; cl11572 224914000625 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1...; Region: Transaldolase_FSA; cd00956 224914000626 active site 224914000627 intersubunit interactions; other site 224914000628 catalytic residue; other site 224914000629 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 224914000630 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; cl12029 224914000631 primosome assembly protein PriA; Validated; Region: PRK05580 224914000632 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; cl12029 224914000633 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl00491 224914000634 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 224914000635 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 224914000636 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 224914000637 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 224914000638 beta subunit interaction interface; other site 224914000639 Walker A motif; other site 224914000640 ATP binding site; other site 224914000641 Walker B motif; other site 224914000642 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 224914000643 ATP synthase; Region: ATP-synt; cl00365 224914000644 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 224914000645 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 224914000646 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 224914000647 alpha subunit interaction interface; other site 224914000648 Walker A motif; other site 224914000649 ATP binding site; other site 224914000650 Walker B motif; other site 224914000651 inhibitor binding site; inhibition site 224914000652 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 224914000653 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 224914000654 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 224914000655 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914000656 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914000657 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914000658 DNA binding site 224914000659 FCD domain; Region: FCD; cl11656 224914000660 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 224914000661 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000662 hydroxyproline-2-epimerase; Provisional; Region: PRK13971; cl11700 224914000663 Proline racemase; Region: Pro_racemase; pfam05544 224914000664 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 224914000665 TM-ABC transporter signature motif; other site 224914000666 leucine/isoleucine/valine transporter permease subunit; Provisional; Region: livM; PRK11301 224914000667 Domain of unknown function (DUF3382); Region: DUF3382; pfam11862 224914000668 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 224914000669 TM-ABC transporter signature motif; other site 224914000670 leucine/isoleucine/valine transporter ATP-binding subunit; Provisional; Region: livG; PRK11300 224914000671 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 224914000672 Walker A/P-loop; other site 224914000673 ATP binding site; other site 224914000674 Q-loop/lid; other site 224914000675 ABC transporter signature motif; other site 224914000676 Walker B; other site 224914000677 D-loop; other site 224914000678 H-loop/switch region; other site 224914000679 Uncharacterized conserved protein [Function unknown]; Region: COG3743 224914000680 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914000681 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914000682 Walker A/P-loop; other site 224914000683 ATP binding site; other site 224914000684 Q-loop/lid; other site 224914000685 ABC transporter signature motif; other site 224914000686 Walker B; other site 224914000687 D-loop; other site 224914000688 H-loop/switch region; other site 224914000689 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914000690 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 224914000691 dimerization interface; other site 224914000692 ligand binding site; other site 224914000693 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914000694 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914000695 pyruvate carboxylase; Reviewed; Region: PRK12999 224914000696 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 224914000697 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914000698 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 224914000699 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 224914000700 active site 224914000701 catalytic residues; other site 224914000702 metal-binding site 224914000703 homodimer binding site; other site 224914000704 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 224914000705 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 224914000706 carboxyltransferase (CT) interaction site; other site 224914000707 biotinylation site; other site 224914000708 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 224914000709 putative substrate translocation pore; other site 224914000710 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000711 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK13394 224914000712 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; cl11686 224914000713 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]; Region: gcpE; COG0821 224914000714 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 224914000715 substrate binding pocket; other site 224914000716 chain length determination region; other site 224914000717 substrate-Mg2+ binding site; other site 224914000718 catalytic residues; other site 224914000719 aspartate-rich region 1; other site 224914000720 active site lid residues 224914000721 aspartate-rich region 2; other site 224914000722 Transglycosylase; Region: Transgly; cl07896 224914000723 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 224914000724 Domain of unknown function (DUF336); Region: DUF336; cl01249 224914000725 acetyl-CoA acetyltransferase; Provisional; Region: PRK05790 224914000726 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 224914000727 dimer interface; other site 224914000728 active site 224914000729 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; cl12029 224914000730 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 224914000731 nucleotide binding region; other site 224914000732 Superfamily II helicase [General function prediction only]; Region: COG1204 224914000733 ATP-binding site; other site 224914000734 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 224914000735 RNA binding surface; other site 224914000736 Ferredoxin [Energy production and conversion]; Region: COG1146 224914000737 4Fe-4S binding domain; Region: Fer4; pfam00037 224914000738 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 224914000739 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 224914000740 RNA polymerase factor sigma-32; Reviewed; Region: rpoH2; PRK07500 224914000741 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 224914000742 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cl01055 224914000743 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 224914000744 MOSC domain; Region: MOSC; pfam03473 224914000745 3-alpha domain; Region: 3-alpha; pfam03475 224914000746 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 224914000747 Peptidase family M48; Region: Peptidase_M48; cl12018 224914000748 ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]; Region: ThiQ; COG3840 224914000749 ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP. Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins...; Region: ABC_ThiQ_thiamine_transporter; cd03298 224914000750 Walker A/P-loop; other site 224914000751 ATP binding site; other site 224914000752 Q-loop/lid; other site 224914000753 ABC transporter signature motif; other site 224914000754 Walker B; other site 224914000755 D-loop; other site 224914000756 H-loop/switch region; other site 224914000757 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 224914000758 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914000759 dimer interface; other site 224914000760 conserved gate region; other site 224914000761 putative PBP binding loops; other site 224914000762 ABC-ATPase subunit interface; other site 224914000763 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914000764 dimer interface; other site 224914000765 conserved gate region; other site 224914000766 putative PBP binding loops; other site 224914000767 ABC-ATPase subunit interface; other site 224914000768 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 224914000769 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914000770 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 224914000771 Thiamine pyrophosphokinase; Region: TPK; cd07995 224914000772 active site 224914000773 dimerization interface; other site 224914000774 thiamine binding site; other site 224914000775 ABC transporter ATPase component; Reviewed; Region: PRK11147 224914000776 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 224914000777 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 224914000778 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 224914000779 N-formylglutamate amidohydrolase; Region: FGase; cl01522 224914000780 Protein of unknown function (DUF1036); Region: DUF1036; cl02296 224914000781 pyruvate kinase; Provisional; Region: PRK06247 224914000782 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; cl10032 224914000783 domain interfaces; other site 224914000784 active site 224914000785 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 224914000786 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 224914000787 TPR motif; other site 224914000788 binding surface 224914000789 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 224914000790 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 224914000791 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000792 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914000793 AIR carboxylase; Region: AIRC; cl00310 224914000794 Protein of unknown function (DUF465); Region: DUF465; cl01070 224914000795 Uncharacterized small protein [Function unknown]; Region: COG5570 224914000796 putative MFS family transporter protein; Provisional; Region: PRK03633 224914000797 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 224914000798 putative substrate translocation pore; other site 224914000799 Protein of unknown function (DUF1192); Region: DUF1192; cl11573 224914000800 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 224914000801 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 224914000802 NAD(P) binding site; other site 224914000803 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 224914000804 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 224914000805 CoenzymeA binding site; other site 224914000806 subunit interaction site; other site 224914000807 PHB binding site; other site 224914000808 Predicted transcriptional regulator [Transcription]; Region: COG2378 224914000809 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914000810 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 224914000811 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 224914000812 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914000813 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 224914000814 substrate binding site; other site 224914000815 hinge regions; other site 224914000816 ADP binding site; other site 224914000817 catalytic site; other site 224914000818 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl12058 224914000819 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 224914000820 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 224914000821 transketolase; Reviewed; Region: PRK05899 224914000822 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 224914000823 TPP-binding site; other site 224914000824 dimer interface; other site 224914000825 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 224914000826 PYR/PP interface; other site 224914000827 dimer interface; other site 224914000828 TPP binding site; other site 224914000829 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 224914000830 Cell division protein ZapA; Region: ZapA; cl01146 224914000831 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 224914000832 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 224914000833 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 224914000834 putative active site; other site 224914000835 metal-binding site 224914000836 homodimer binding site; other site 224914000837 Integral membrane protein TerC family; Region: TerC; cl10468 224914000838 Protein of unknown function (DUF1284); Region: DUF1284; cl01419 224914000839 BioY family; Region: BioY; cl00560 224914000840 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914000841 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914000842 DNA binding site 224914000843 FCD domain; Region: FCD; cl11656 224914000844 Domain of unknown function DUF28; Region: DUF28; cl00361 224914000845 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 224914000846 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 224914000847 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914000848 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914000849 Walker A/P-loop; other site 224914000850 ATP binding site; other site 224914000851 Q-loop/lid; other site 224914000852 ABC transporter signature motif; other site 224914000853 Walker B; other site 224914000854 D-loop; other site 224914000855 H-loop/switch region; other site 224914000856 hypothetical protein; Validated; Region: PRK09039 224914000857 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 224914000858 ligand binding site; other site 224914000859 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 224914000860 active site 224914000861 dimerization interface; other site 224914000862 elongation factor P; Validated; Region: PRK00529 224914000863 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 224914000864 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 224914000865 RNA binding site; other site 224914000866 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 224914000867 RNA binding site; other site 224914000868 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 224914000869 Sel1 repeat; Region: Sel1; cl02723 224914000870 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-...; Region: TMP_TenI; cd00564 224914000871 active site 224914000872 thiamine phosphate binding site; other site 224914000873 pyrophosphate binding site; other site 224914000874 OpgC protein; Region: OpgC_C; cl10497 224914000875 Acyltransferase family; Region: Acyl_transf_3; pfam01757 224914000876 Protein of unknown function (DUF1465); Region: DUF1465; cl11562 224914000877 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 224914000878 active site 224914000879 putative DNA-binding cleft; other site 224914000880 dimer interface; other site 224914000881 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 224914000882 RuvA N terminal domain; Region: RuvA_N; pfam01330 224914000883 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 224914000884 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 224914000885 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914000886 Walker A motif; other site 224914000887 ATP binding site; other site 224914000888 Walker B motif; other site 224914000889 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 224914000890 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active...; Region: 4HBT; cd00586 224914000891 active site 224914000892 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 224914000893 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 224914000894 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 224914000895 translocation protein TolB; Provisional; Region: tolB; PRK05137 224914000896 TolB amino-terminal domain; Region: TolB_N; pfam04052 224914000897 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 224914000898 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 224914000899 ligand binding site; other site 224914000900 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 224914000901 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 224914000902 NNMT/PNMT/TEMT family; Region: NNMT_PNMT_TEMT; pfam01234 224914000903 FtsH Extracellular; Region: FtsH_ext; pfam06480 224914000904 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 224914000905 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914000906 Walker A motif; other site 224914000907 ATP binding site; other site 224914000908 Walker B motif; other site 224914000909 arginine finger; other site 224914000910 Peptidase family M41; Region: Peptidase_M41; pfam01434 224914000911 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 224914000912 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-...; Region: GlmM; cd05802 224914000913 active site 224914000914 substrate binding site; other site 224914000915 metal-binding site 224914000916 Surface antigen; Region: Surface_Ag_2; cl01155 224914000917 Membrane transport protein; Region: Mem_trans; cl09117 224914000918 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; cd01494 224914000919 pyridoxal 5'-phosphate binding pocket; other site 224914000920 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 224914000921 catalytic residue; other site 224914000922 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 224914000923 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914000924 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 224914000925 putative L-serine binding site; other site 224914000926 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 224914000927 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914000928 adenylosuccinate synthetase; Provisional; Region: PRK01117 224914000929 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-...; Region: AdSS; cd03108 224914000930 GDP-binding site; other site 224914000931 ACT binding site; other site 224914000932 IMP binding site; other site 224914000933 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 224914000934 metabolite-proton symporter; Region: 2A0106; TIGR00883 224914000935 putative substrate translocation pore; other site 224914000936 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 224914000937 diiron binding motif; other site 224914000938 Uncharacterized conserved protein [Function unknown]; Region: COG1633 224914000939 CCC1-related protein family; Region: CCC1_like_1; cd02437 224914000940 conserved hypothetical protein TIGR03442; Region: TIGR03442 224914000941 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 224914000942 putative dimer interface; other site 224914000943 putative active site; other site 224914000944 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914000945 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914000946 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 224914000947 trimer interface; other site 224914000948 active site 224914000949 macrolide transporter subunit MacA; Provisional; Region: PRK11578 224914000950 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 224914000951 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 224914000952 Walker A/P-loop; other site 224914000953 ATP binding site; other site 224914000954 Q-loop/lid; other site 224914000955 ABC transporter signature motif; other site 224914000956 Walker B; other site 224914000957 D-loop; other site 224914000958 H-loop/switch region; other site 224914000959 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 224914000960 Predicted permease; Region: FtsX; cl11418 224914000961 Predicted periplasmic protein (DUF2233); Region: DUF2233; cl10481 224914000962 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 224914000963 Gram-negative bacterial tonB protein; Region: TonB; cl10048 224914000964 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 224914000965 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 224914000966 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 224914000967 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 224914000968 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to...; Region: PRCH; cl09959 224914000969 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 224914000970 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 224914000971 Histidine kinase; Region: HisKA_2; cl06527 224914000972 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 224914000973 ATP binding site; other site 224914000974 Mg2+ binding site; other site 224914000975 G-X-G motif; other site 224914000976 RNA polymerase sigma factor; Provisional; Region: PRK12516 224914000977 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 224914000978 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 224914000979 DNA binding residues 224914000980 two-component response regulator; Provisional; Region: PRK09191 224914000981 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 224914000982 active site 224914000983 phosphorylation site 224914000984 intermolecular recognition site; other site 224914000985 dimerization interface; other site 224914000986 PAS fold; Region: PAS_4; pfam08448 224914000987 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 224914000988 Histidine kinase; Region: HisKA_2; cl06527 224914000989 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 224914000990 metal binding site 2; metal-binding site 224914000991 putative DNA binding helix; other site 224914000992 metal binding site 1; metal-binding site 224914000993 dimer interface; other site 224914000994 structural Zn2+ binding site; other site 224914000995 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 224914000996 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 224914000997 RNA binding surface; other site 224914000998 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 224914000999 active site 224914001000 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 224914001001 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 224914001002 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 224914001003 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 224914001004 DNA binding residues 224914001005 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914001006 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 224914001007 Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate...; Region: malate_synt_G; cd00728 224914001008 active site 224914001009 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914001010 HIGH motif; other site 224914001011 active site 224914001012 nucleotide binding site; other site 224914001013 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914001014 KMSKS motif; other site 224914001015 active site 224914001016 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 224914001017 minor groove reading motif; other site 224914001018 helix-hairpin-helix signature motif; other site 224914001019 substrate binding pocket; other site 224914001020 active site 224914001021 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...; Region: HNHc; cd00085 224914001022 active site 224914001023 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 224914001024 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 224914001025 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative; Region: D1pyr5carbox2; TIGR01237 224914001026 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 224914001027 tetramerization interface; other site 224914001028 NAD(P) binding site; other site 224914001029 catalytic residues; other site 224914001030 Transcriptional regulator [Transcription]; Region: IclR; COG1414 224914001031 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914001032 Bacterial transcriptional regulator; Region: IclR; pfam01614 224914001033 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 224914001034 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914001035 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914001036 Uncharacterized conserved protein [Function unknown]; Region: COG5591 224914001037 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 224914001038 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001039 Walker A/P-loop; other site 224914001040 ATP binding site; other site 224914001041 Q-loop/lid; other site 224914001042 ABC transporter signature motif; other site 224914001043 Walker B; other site 224914001044 D-loop; other site 224914001045 H-loop/switch region; other site 224914001046 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 224914001047 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914001048 TM-ABC transporter signature motif; other site 224914001049 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 224914001050 Periplasmic binding proteins specific to rhizopines; Region: PBP1_rhizopine_binding_like; cd06301 224914001051 putative ligand binding site; other site 224914001052 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001053 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001054 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 224914001055 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 224914001056 DAK2 domain; Region: Dak2; cl03685 224914001057 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 224914001058 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 224914001059 DNA binding residues 224914001060 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 224914001061 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 224914001062 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]; Region: DAK1; COG2376 224914001063 DAK2 domain; Region: Dak2; cl03685 224914001064 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 224914001065 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 224914001066 active site 224914001067 nucleophile elbow; other site 224914001068 Surface antigen; Region: Surface_Ag_2; cl01155 224914001069 MarC family integral membrane protein; Region: MarC; cl00919 224914001070 7-alpha-hydroxysteroid dehydrogenase; Validated; Region: PRK06113 224914001071 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001072 7-alpha-hydroxysteroid dehydrogenase; Validated; Region: PRK06113 224914001073 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001074 PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]; Region: PrpB; COG2513 224914001075 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 224914001076 tetramer interface; other site 224914001077 active site 224914001078 Mg2+/Mn2+ binding site; other site 224914001079 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 224914001080 Domain of unknown function (DUF955); Region: DUF955; cl01076 224914001081 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 224914001082 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914001083 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 224914001084 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 224914001085 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues...; Region: ABC_PotA_N; cd03300 224914001086 Walker A/P-loop; other site 224914001087 ATP binding site; other site 224914001088 Q-loop/lid; other site 224914001089 ABC transporter signature motif; other site 224914001090 Walker B; other site 224914001091 D-loop; other site 224914001092 H-loop/switch region; other site 224914001093 TOBE domain; Region: TOBE_2; cl01440 224914001094 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001095 dimer interface; other site 224914001096 conserved gate region; other site 224914001097 putative PBP binding loops; other site 224914001098 ABC-ATPase subunit interface; other site 224914001099 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001100 dimer interface; other site 224914001101 conserved gate region; other site 224914001102 putative PBP binding loops; other site 224914001103 ABC-ATPase subunit interface; other site 224914001104 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 224914001105 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 224914001106 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 224914001107 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 224914001108 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans...; Region: HisKA; cd00082 224914001109 dimer interface; other site 224914001110 phosphorylation site 224914001111 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 224914001112 ATP binding site; other site 224914001113 Mg2+ binding site; other site 224914001114 G-X-G motif; other site 224914001115 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 224914001116 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914001117 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001118 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914001119 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 224914001120 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 224914001121 inhibitor-cofactor binding pocket; inhibition site 224914001122 pyridoxal 5'-phosphate binding site; other site 224914001123 catalytic residue; other site 224914001124 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 224914001125 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 224914001126 active site 224914001127 phosphorylation site 224914001128 intermolecular recognition site; other site 224914001129 dimerization interface; other site 224914001130 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914001131 DNA binding site 224914001132 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5385 224914001133 Protein of unknown function (DUF1134); Region: DUF1134; cl02235 224914001134 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914001135 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 224914001136 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 224914001137 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 224914001138 Ligand Binding Site; other site 224914001139 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 224914001140 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 224914001141 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 224914001142 dimerization interface; other site 224914001143 putative DNA binding site; other site 224914001144 putative Zn2+ binding site; other site 224914001145 Putative heme iron utilization protein [Inorganic ion transport and metabolism]; Region: HugZ; COG0748 224914001146 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 224914001147 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 224914001148 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001149 dimer interface; other site 224914001150 conserved gate region; other site 224914001151 putative PBP binding loops; other site 224914001152 ABC-ATPase subunit interface; other site 224914001153 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001154 dimer interface; other site 224914001155 conserved gate region; other site 224914001156 putative PBP binding loops; other site 224914001157 ABC-ATPase subunit interface; other site 224914001158 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914001159 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 224914001160 Walker A/P-loop; other site 224914001161 ATP binding site; other site 224914001162 Q-loop/lid; other site 224914001163 ABC transporter signature motif; other site 224914001164 Walker B; other site 224914001165 D-loop; other site 224914001166 H-loop/switch region; other site 224914001167 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914001168 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914001169 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 224914001170 Walker A/P-loop; other site 224914001171 ATP binding site; other site 224914001172 Q-loop/lid; other site 224914001173 ABC transporter signature motif; other site 224914001174 Walker B; other site 224914001175 D-loop; other site 224914001176 H-loop/switch region; other site 224914001177 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914001178 choline ABC transporter, ATP-binding protein; Region: ABC_choXWV_ATP; TIGR03415 224914001179 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001180 Walker A/P-loop; other site 224914001181 ATP binding site; other site 224914001182 Q-loop/lid; other site 224914001183 ABC transporter signature motif; other site 224914001184 Walker B; other site 224914001185 D-loop; other site 224914001186 H-loop/switch region; other site 224914001187 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001188 dimer interface; other site 224914001189 conserved gate region; other site 224914001190 putative PBP binding loops; other site 224914001191 ABC-ATPase subunit interface; other site 224914001192 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914001193 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 224914001194 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 224914001195 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914001196 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 224914001197 putative substrate translocation pore; other site 224914001198 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 224914001199 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914001200 anthranilate synthase; Provisional; Region: PRK13566 224914001201 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 224914001202 chorismate binding enzyme; Region: Chorismate_bind; cl10555 224914001203 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 224914001204 glutamine binding; other site 224914001205 catalytic triad; other site 224914001206 Cation efflux family; Region: Cation_efflux; cl00316 224914001207 2-isopropylmalate synthase; Validated; Region: PRK03739 224914001208 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 224914001209 active site 224914001210 catalytic residues; other site 224914001211 metal-binding site 224914001212 LeuA allosteric (dimerization) domain; Region: LeuA_dimer; pfam08502 224914001213 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 224914001214 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 224914001215 active site 224914001216 metal-binding site 224914001217 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_21; cd04680 224914001218 nudix motif; other site 224914001219 Surface antigen; Region: Surface_Ag_2; cl01155 224914001220 Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: ECM4; COG0435 224914001221 GST_C family, ECM4-like subfamily; composed of predominantly uncharacterized and taxonomically diverse proteins with similarity to the translation product of the Saccharomyces cerevisiae gene ECM4. ECM4, a gene of unknown function, is involved in cell...; Region: GST_C_ECM4_like; cd03190 224914001222 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 224914001223 Coenzyme A binding pocket; other site 224914001224 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 224914001225 Aerotolerance regulator N-terminal; Region: BatA; cl06567 224914001226 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 224914001227 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 224914001228 Protein of unknown function DUF58; Region: DUF58; pfam01882 224914001229 MoxR-like ATPases [General function prediction only]; Region: COG0714 224914001230 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001231 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001232 Protein of unknown function (DUF1285); Region: DUF1285; cl01571 224914001233 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 224914001234 putative active site; other site 224914001235 putative CoA binding site; other site 224914001236 nudix motif; other site 224914001237 metal-binding site 224914001238 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 224914001239 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 224914001240 active site 224914001241 NTP binding site; other site 224914001242 metal binding triad; metal-binding site 224914001243 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl01426 224914001244 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl01426 224914001245 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914001246 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 224914001247 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 224914001248 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 224914001249 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 224914001250 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914001251 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 224914001252 Walker A/P-loop; other site 224914001253 ATP binding site; other site 224914001254 Q-loop/lid; other site 224914001255 ABC transporter signature motif; other site 224914001256 Walker B; other site 224914001257 D-loop; other site 224914001258 H-loop/switch region; other site 224914001259 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 224914001260 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914001261 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001262 Walker A/P-loop; other site 224914001263 ATP binding site; other site 224914001264 Q-loop/lid; other site 224914001265 ABC transporter signature motif; other site 224914001266 Walker B; other site 224914001267 D-loop; other site 224914001268 H-loop/switch region; other site 224914001269 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 224914001270 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 224914001271 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 224914001272 [2Fe-2S] cluster binding site; other site 224914001273 cytochrome b; Provisional; Region: CYTB; MTH00191 224914001274 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 224914001275 Qi binding site; other site 224914001276 intrachain domain interface; other site 224914001277 interchain domain interface; other site 224914001278 heme bH binding site; other site 224914001279 heme bL binding site; other site 224914001280 Qo binding site; other site 224914001281 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 224914001282 interchain domain interface; other site 224914001283 intrachain domain interface; other site 224914001284 Qi binding site; other site 224914001285 Qo binding site; other site 224914001286 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 224914001287 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914001288 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 224914001289 putative active site; other site 224914001290 putative catalytic site; other site 224914001291 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 224914001292 putative active site; other site 224914001293 putative catalytic site; other site 224914001294 GTP-dependent nucleic acid-binding protein EngD; Reviewed; Region: PRK09601 224914001295 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 224914001296 G1 box; other site 224914001297 GTP/Mg2+ binding site; other site 224914001298 Switch I region; other site 224914001299 G2 box; other site 224914001300 Switch II region; other site 224914001301 G3 box; other site 224914001302 G4 box; other site 224914001303 G5 box; other site 224914001304 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 224914001305 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 224914001306 putative active site; other site 224914001307 catalytic residue; other site 224914001308 Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this...; Region: Ribosomal_L25_TL5_CTC; cd00495 224914001309 5S rRNA interface; other site 224914001310 CTC domain interface; other site 224914001311 L16 interface; other site 224914001312 HerA helicase [Replication, recombination, and repair]; Region: COG0433 224914001313 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 224914001314 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914001315 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 224914001316 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 224914001317 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate...; Region: APP_MetAP; cd01066 224914001318 active site 224914001319 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 224914001320 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 224914001321 Uncharacterized conserved protein [Function unknown]; Region: COG1565 224914001322 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 224914001323 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 224914001324 Protein of unknown function (DUF526); Region: DUF526; cl01115 224914001325 Family of unknown function (DUF1790); Region: DUF1790; cl02283 224914001326 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 224914001327 dimer interface; other site 224914001328 putative tRNA-binding site; other site 224914001329 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 224914001330 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 224914001331 ATP binding site; other site 224914001332 Mg2+ binding site; other site 224914001333 G-X-G motif; other site 224914001334 osmolarity response regulator; Provisional; Region: ompR; PRK09468 224914001335 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 224914001336 active site 224914001337 phosphorylation site 224914001338 intermolecular recognition site; other site 224914001339 dimerization interface; other site 224914001340 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914001341 DNA binding site 224914001342 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914001343 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 224914001344 BA14K-like protein; Region: BA14K; pfam07886 224914001345 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 224914001346 DNA binding site 224914001347 RNA-binding motif; other site 224914001348 Sporulation related domain; Region: SPOR; cl10051 224914001349 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914001350 N-acetyl-D-glucosamine binding site; other site 224914001351 catalytic residue; other site 224914001352 excinuclease ABC subunit B; Provisional; Region: PRK05298 224914001353 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 224914001354 ATP binding site; other site 224914001355 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 224914001356 nucleotide binding region; other site 224914001357 ATP-binding site; other site 224914001358 Ultra-violet resistance protein B; Region: UvrB; pfam12344 224914001359 UvrB/uvrC motif; Region: UVR; pfam02151 224914001360 Uncharacterized protein with a bacterial SH3 domain homologue [Function unknown]; Region: COG4991 224914001361 Bacterial SH3 domain; Region: SH3_3; cl02551 224914001362 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain...; Region: BFIT_BACH; cd03442 224914001363 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 224914001364 Protein of unknown function, DUF486; Region: DUF486; cl01236 224914001365 EamA-like transporter family; Region: EamA; cl01037 224914001366 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 224914001367 EamA-like transporter family; Region: EamA; cl01037 224914001368 Protein of unknown function (DUF1176); Region: DUF1176; pfam06674 224914001369 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 224914001370 domain; Region: GreA_GreB_N; pfam03449 224914001371 C-term; Region: GreA_GreB; pfam01272 224914001372 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 224914001373 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914001374 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 224914001375 dimerization interface; other site 224914001376 putative DNA binding site; other site 224914001377 putative Zn2+ binding site; other site 224914001378 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914001379 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 224914001380 Cation transport protein; Region: TrkH; cl10514 224914001381 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 224914001382 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001383 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914001384 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914001385 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 224914001386 putative effector binding pocket; other site 224914001387 dimerization interface; other site 224914001388 aspartate aminotransferase; Provisional; Region: PRK06108 224914001389 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 224914001390 pyridoxal 5'-phosphate binding site; other site 224914001391 homodimer interface; other site 224914001392 catalytic residue; other site 224914001393 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 224914001394 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 224914001395 putative C-terminal domain interface; other site 224914001396 putative GSH binding site (G-site); other site 224914001397 putative dimer interface; other site 224914001398 GST_C family, unknown subfamily 1; composed of uncharacterized bacterial proteins, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_C_1; cd03179 224914001399 putative N-terminal domain interface; other site 224914001400 putative dimer interface; other site 224914001401 putative substrate binding pocket (H-site); other site 224914001402 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 224914001403 DNA binding site 224914001404 RNA-binding motif; other site 224914001405 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...; Region: Nudix_Hydrolase; cl00447 224914001406 nudix motif; other site 224914001407 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 224914001408 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914001409 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 224914001410 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 224914001411 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 224914001412 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914001413 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 224914001414 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 224914001415 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914001416 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 224914001417 IMP binding site; other site 224914001418 dimer interface; other site 224914001419 partial ornithine binding site; other site 224914001420 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 224914001421 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 224914001422 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; cl00988 224914001423 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 224914001424 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 224914001425 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 224914001426 catalytic site; other site 224914001427 subunit interface; other site 224914001428 GatB domain; Region: GatB_Yqey; cl11497 224914001429 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 224914001430 PhoU domain; Region: PhoU; pfam01895 224914001431 PhoU domain; Region: PhoU; pfam01895 224914001432 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 224914001433 DNA primase; Validated; Region: dnaG; PRK05667 224914001434 CHC2 zinc finger; Region: zf-CHC2; cl02597 224914001435 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 224914001436 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 224914001437 active site 224914001438 metal-binding site 224914001439 interdomain interaction site; other site 224914001440 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 224914001441 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 224914001442 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 224914001443 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 224914001444 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 224914001445 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 224914001446 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial...; Region: Sigma70_r4; cd06171 224914001447 DNA binding residues 224914001448 Transcriptional activator HlyU; Region: HlyU; cl02273 224914001449 Uncharacterized protein family (UPF0153); Region: UPF0153; cl00497 224914001450 Protein of unknown function (DUF541); Region: SIMPL; cl01077 224914001451 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 224914001452 DNA binding site 224914001453 Int/Topo IB signature motif; other site 224914001454 active site 224914001455 Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N...; Region: Ntn_PVA; cd00542 224914001456 active site 224914001457 Integral membrane protein TerC family; Region: TerC; cl10468 224914001458 Isochorismatase family; Region: Isochorismatase; pfam00857 224914001459 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 224914001460 catalytic triad; other site 224914001461 metal-binding site 224914001462 conserved cis-peptide bond; other site 224914001463 PhnA protein; Region: PhnA; pfam03831 224914001464 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 224914001465 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron...; Region: FNR_iron_sulfur_binding_1; cd06215 224914001466 FAD binding pocket; other site 224914001467 FAD binding motif; other site 224914001468 phosphate binding motif; other site 224914001469 beta-alpha-beta structure motif; other site 224914001470 NAD binding pocket; other site 224914001471 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 224914001472 catalytic loop; other site 224914001473 iron binding site; other site 224914001474 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 224914001475 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 224914001476 [2Fe-2S] cluster binding site; other site 224914001477 Ring hydroxylating alpha subunit (catalytic domain). This CD includes the catalytic domain (alpha) of aromatic-ring-hydroxylating dioxygenase systems of eubacteria. Eubacterial ring hydroxylating dioxygenases are multicomponent 1,2-dioxygenase...; Region: Ring_hydroxylating_alpha; cl00265 224914001478 substrate binding pocket; other site 224914001479 active site 224914001480 Protein of unknown function (DUF1498); Region: DUF1498; cl01576 224914001481 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 224914001482 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914001483 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914001484 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 224914001485 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001486 Walker A/P-loop; other site 224914001487 ATP binding site; other site 224914001488 Q-loop/lid; other site 224914001489 ABC transporter signature motif; other site 224914001490 Walker B; other site 224914001491 D-loop; other site 224914001492 H-loop/switch region; other site 224914001493 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 224914001494 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 224914001495 S-adenosylmethionine binding site; other site 224914001496 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 224914001497 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 224914001498 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 224914001499 putative substrate translocation pore; other site 224914001500 Uncharacterized conserved protein (DUF2293); Region: DUF2293; cl02373 224914001501 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 224914001502 dimerization interface; other site 224914001503 putative DNA binding site; other site 224914001504 putative Zn2+ binding site; other site 224914001505 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 224914001506 S-adenosylmethionine binding site; other site 224914001507 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine...; Region: MTHFR; cd00537 224914001508 FAD binding site; other site 224914001509 Membrane transport protein; Region: Mem_trans; cl09117 224914001510 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 224914001511 lytic murein transglycosylase; Region: MltB_2; TIGR02283 224914001512 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914001513 Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell envelope biogenesis, outer membrane]; Region: Acm; COG3757 224914001514 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the...; Region: GH25_muramidase_1; cd06413 224914001515 active site 224914001516 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 224914001517 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 224914001518 putative metal binding site; other site 224914001519 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 224914001520 HSP70 interaction site; other site 224914001521 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 224914001522 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 224914001523 amidase catalytic site; other site 224914001524 Zn binding residues; other site 224914001525 substrate binding site; other site 224914001526 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914001527 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914001528 N-acetyl-D-glucosamine binding site; other site 224914001529 catalytic residue; other site 224914001530 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 224914001531 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914001532 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 224914001533 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 224914001534 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 224914001535 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 224914001536 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 224914001537 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 224914001538 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 224914001539 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 224914001540 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 224914001541 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 224914001542 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 224914001543 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 224914001544 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 224914001545 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of undecaprenyl-pyrophosphoryl-N-...; Region: GT_MraY; cd06852 224914001546 Mg++ binding site; other site 224914001547 putative catalytic motif; other site 224914001548 putative substrate binding site; other site 224914001549 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 224914001550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001551 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 224914001552 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 224914001553 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl...; Region: GT1_MurG; cd03785 224914001554 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 224914001555 active site 224914001556 homodimer interface; other site 224914001557 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 224914001558 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 224914001559 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 224914001560 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 224914001561 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 224914001562 FAD binding domain; Region: FAD_binding_4; cl10516 224914001563 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 224914001564 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 224914001565 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 224914001566 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914001567 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 224914001568 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 224914001569 Cell division protein FtsQ; Region: FtsQ; pfam03799 224914001570 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 224914001571 Cell division protein FtsA; Region: FtsA; cl11496 224914001572 Cell division protein FtsA; Region: FtsA; cl11496 224914001573 cell division protein FtsZ; Validated; Region: PRK09330 224914001574 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum...; Region: FtsZ_type1; cd02201 224914001575 nucleotide binding site; other site 224914001576 SulA interaction site; other site 224914001577 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 224914001578 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 224914001579 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 224914001580 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 224914001581 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 224914001582 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 224914001583 Walker A/P-loop; other site 224914001584 ATP binding site; other site 224914001585 Q-loop/lid; other site 224914001586 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides...; Region: ABC_RecN; cd03241 224914001587 ABC transporter signature motif; other site 224914001588 Walker B; other site 224914001589 D-loop; other site 224914001590 H-loop/switch region; other site 224914001591 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 224914001592 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 224914001593 nucleotide binding pocket; other site 224914001594 K-X-D-G motif; other site 224914001595 catalytic site; other site 224914001596 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 224914001597 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 224914001598 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 224914001599 Dimer interface; other site 224914001600 BRCT sequence motif; other site 224914001601 Conserved hypothetical protein (DUF2461); Region: DUF2461; cl02374 224914001602 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 224914001603 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 224914001604 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline...; Region: APP; cd01085 224914001605 active site 224914001606 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 224914001607 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 224914001608 S-adenosylmethionine binding site; other site 224914001609 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 224914001610 Cu(I) binding site; other site 224914001611 phosphonate metabolim protein, transferase hexapeptide repeat family; Region: phn_thr-fam; TIGR03308 224914001612 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 224914001613 trimer interface; other site 224914001614 active site 224914001615 substrate binding site; other site 224914001616 CoA binding site; other site 224914001617 CreA protein; Region: CreA; cl01154 224914001618 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 224914001619 UvrD/REP helicase; Region: UvrD-helicase; cl14126 224914001620 serine/threonine protein kinase; Provisional; Region: PRK09188 224914001621 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 224914001622 Domain of unknown function (DUF336); Region: DUF336; cl01249 224914001623 FAD binding domain; Region: FAD_binding_4; cl10516 224914001624 D-lactate dehydrogenase; Region: PLN02805 224914001625 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 224914001626 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 224914001627 Uncharacterized ACR, YdiU/UPF0061 family; Region: UPF0061; cl00428 224914001628 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 224914001629 Stringent starvation protein B; Region: SspB; cl01120 224914001630 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 224914001631 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914001632 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 224914001633 putative substrate translocation pore; other site 224914001634 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 224914001635 Protein of unknown function (DUF2853); Region: DUF2853; pfam11015 224914001636 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 224914001637 dimerization interface; other site 224914001638 active site 224914001639 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cd00209 224914001640 folate binding site; other site 224914001641 NADP+ binding site; other site 224914001642 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 224914001643 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 224914001644 HflK protein; Region: hflK; TIGR01933 224914001645 FtsH protease regulator HflC; Provisional; Region: PRK11029 224914001646 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 224914001647 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; cl01275 224914001648 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 224914001649 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 224914001650 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 224914001651 protein binding site; other site 224914001652 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 224914001653 protein binding site; other site 224914001654 Predicted flavoproteins [General function prediction only]; Region: COG2081 224914001655 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001656 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914001657 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 224914001658 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 224914001659 motif II; other site 224914001660 IPP transferase; Region: IPPT; cl00403 224914001661 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 224914001662 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 224914001663 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 224914001664 PYR/PP interface; other site 224914001665 dimer interface; other site 224914001666 TPP binding site; other site 224914001667 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 224914001668 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 224914001669 TPP-binding site; other site 224914001670 dimer interface; other site 224914001671 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 224914001672 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 224914001673 putative valine binding site; other site 224914001674 dimer interface; other site 224914001675 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 224914001676 ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair]; Region: RecD; COG0507 224914001677 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001678 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001679 Walker A motif; other site 224914001680 ATP binding site; other site 224914001681 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 224914001682 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 224914001683 active site 224914001684 hydrophilic channel; other site 224914001685 dimerization interface; other site 224914001686 catalytic residues; other site 224914001687 active site lid 224914001688 K+ potassium transporter; Region: K_trans; cl01227 224914001689 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 224914001690 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914001691 ketol-acid reductoisomerase; Provisional; Region: PRK05479 224914001692 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001693 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 224914001694 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 224914001695 aspartate aminotransferase; Provisional; Region: PRK06108 224914001696 pyridoxal 5'-phosphate binding site; other site 224914001697 homodimer interface; other site 224914001698 catalytic residue; other site 224914001699 BA14K-like protein; Region: BA14K; pfam07886 224914001700 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 224914001701 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...; Region: Nudix_Hydrolase; cl00447 224914001702 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 224914001703 hypothetical protein; Provisional; Region: PRK10281 224914001704 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 224914001705 CrcB-like protein; Region: CRCB; cl09114 224914001706 CrcB-like protein; Region: CRCB; cl09114 224914001707 Domain of unknown function DUF302; Region: DUF302; cl01364 224914001708 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001709 ABC transporter signature motif; other site 224914001710 Walker B; other site 224914001711 D-loop; other site 224914001712 H-loop/switch region; other site 224914001713 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001714 Walker A/P-loop; other site 224914001715 ATP binding site; other site 224914001716 Q-loop/lid; other site 224914001717 Cobalt transport protein; Region: CbiQ; cl00463 224914001718 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 224914001719 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 224914001720 ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CbiK; COG5266 224914001721 Nickel uptake substrate-specific transmembrane region; Region: NikM; pfam10670 224914001722 Urea transporter; Region: UT; cl01829 224914001723 UreD urease accessory protein; Region: UreD; cl00530 224914001724 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914001725 UreF; Region: UreF; cl00531 224914001726 urease accessory protein UreE; Provisional; Region: ureE; PRK14711 224914001727 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-...; Region: UreE; cd00571 224914001728 dimer interface; other site 224914001729 catalytic residues; other site 224914001730 urease subunit alpha; Reviewed; Region: ureC; PRK13309 224914001731 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 224914001732 subunit interactions; other site 224914001733 active site 224914001734 flap region; other site 224914001735 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_beta; cd00407 224914001736 alpha-beta subunit interface; other site 224914001737 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 224914001738 alpha-gamma subunit interface; other site 224914001739 beta-gamma subunit interface; other site 224914001740 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1649 224914001741 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 224914001742 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914001743 hypothetical protein; Provisional; Region: PRK03598 224914001744 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001745 ABC transporter signature motif; other site 224914001746 Walker B; other site 224914001747 D-loop; other site 224914001748 H-loop/switch region; other site 224914001749 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 224914001750 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914001751 Walker A/P-loop; other site 224914001752 ATP binding site; other site 224914001753 Q-loop/lid; other site 224914001754 ABC transporter signature motif; other site 224914001755 Walker B; other site 224914001756 D-loop; other site 224914001757 H-loop/switch region; other site 224914001758 ABC-2 type transporter; Region: ABC2_membrane; cl11417 224914001759 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 224914001760 ABC-2 type transporter; Region: ABC2_membrane; cl11417 224914001761 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 224914001762 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 224914001763 N-terminal plug; other site 224914001764 ligand-binding site; other site 224914001765 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...; Region: TroA-like; cl00262 224914001766 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 224914001767 intersubunit interface; other site 224914001768 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 224914001769 ABC-ATPase subunit interface; other site 224914001770 dimer interface; other site 224914001771 putative PBP binding regions; other site 224914001772 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 224914001773 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 224914001774 Walker A/P-loop; other site 224914001775 ATP binding site; other site 224914001776 Q-loop/lid; other site 224914001777 ABC transporter signature motif; other site 224914001778 Walker B; other site 224914001779 D-loop; other site 224914001780 H-loop/switch region; other site 224914001781 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914001782 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001783 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914001784 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914001785 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914001786 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914001787 TM-ABC transporter signature motif; other site 224914001788 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 224914001789 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914001790 Walker A/P-loop; other site 224914001791 ATP binding site; other site 224914001792 Q-loop/lid; other site 224914001793 ABC transporter signature motif; other site 224914001794 Walker B; other site 224914001795 D-loop; other site 224914001796 H-loop/switch region; other site 224914001797 short chain dehydrogenase; Provisional; Region: PRK06198 224914001798 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001799 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 224914001800 Secreted protein acidic and rich in cysteine Ca binding region; Region: SPARC_Ca_bdg; pfam10591 224914001801 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 224914001802 Integral membrane protein TerC family; Region: TerC; cl10468 224914001803 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 224914001804 Transporter associated domain; Region: CorC_HlyC; pfam03471 224914001805 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914001806 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001807 dimer interface; other site 224914001808 conserved gate region; other site 224914001809 putative PBP binding loops; other site 224914001810 ABC-ATPase subunit interface; other site 224914001811 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914001812 dimer interface; other site 224914001813 conserved gate region; other site 224914001814 putative PBP binding loops; other site 224914001815 ABC-ATPase subunit interface; other site 224914001816 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914001817 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914001818 Predicted integral membrane protein [Function unknown]; Region: COG0392 224914001819 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 224914001820 putative cation:proton antiport protein; Provisional; Region: PRK10669 224914001821 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 224914001822 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001823 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13023 224914001824 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 224914001825 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 224914001826 Protein export membrane protein; Region: SecD_SecF; cl14618 224914001827 Protein export membrane protein; Region: SecD_SecF; cl14618 224914001828 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 224914001829 Mechanosensitive ion channel; Region: MS_channel; pfam00924 224914001830 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 224914001831 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001832 Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]; Region: GcvT; COG0404 224914001833 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 224914001834 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 224914001835 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 224914001836 conserved cys residue; other site 224914001837 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914001838 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914001839 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914001840 dimerization interface; other site 224914001841 Entericidin EcnA/B family; Region: Entericidin; cl02322 224914001842 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001843 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 224914001844 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914001845 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 224914001846 substrate binding pocket; other site 224914001847 FAD binding site; other site 224914001848 catalytic base; other site 224914001849 cobyric acid synthase; Provisional; Region: PRK00784 224914001850 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914001851 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 224914001852 catalytic triad; other site 224914001853 Probable cobalt transporter subunit (CbtB); Region: CbtB; cl09723 224914001854 Probable cobalt transporter subunit (CbtA); Region: CbtA; cl02266 224914001855 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is...; Region: CobU; cd00544 224914001856 homotrimer interface; other site 224914001857 Walker A motif; other site 224914001858 GTP binding site; other site 224914001859 Walker B motif; other site 224914001860 cobalamin biosynthesis protein CobW; Region: CobW; TIGR02475 224914001861 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914001862 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 224914001863 cobaltochelatase subunit CobN; Reviewed; Region: cobN; PRK05989 224914001864 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 224914001865 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a...; Region: CobA_CobO_BtuR; cd00561 224914001866 homodimer interface; other site 224914001867 Walker A motif; other site 224914001868 ATP binding site; other site 224914001869 hydroxycobalamin binding site; other site 224914001870 Walker B motif; other site 224914001871 EamA-like transporter family; Region: EamA; cl01037 224914001872 Sulfite exporter TauE/SafE; Region: TauE; cl00498 224914001873 tellurium resistance terB-like protein; Region: terB_like; cd07177 224914001874 metal-binding site 224914001875 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 224914001876 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914001877 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 224914001878 CbiD; Region: CbiD; cl00828 224914001879 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914001880 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 224914001881 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 224914001882 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 224914001883 pyridoxal 5'-phosphate binding site; other site 224914001884 homodimer interface; other site 224914001885 catalytic residue; other site 224914001886 CobD/Cbib protein; Region: CobD_Cbib; cl00561 224914001887 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914001888 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 224914001889 ligand binding site; other site 224914001890 Flavin Reductases; Region: FlaRed; cl00801 224914001891 Cobalamin biosynthesis protein CbiG [Coenzyme metabolism]; Region: CbiG; COG2073 224914001892 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 224914001893 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 224914001894 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914001895 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914001896 Precorrin-8X methylmutase; Region: CbiC; cl00913 224914001897 precorrin-3B synthase; Region: CobG; TIGR02435 224914001898 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 224914001899 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 224914001900 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914001901 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914001902 Surface antigen; Region: Surface_Ag_2; cl01155 224914001903 DNA repair protein RadC; Reviewed; Region: radC; PRK00024 224914001904 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 224914001905 MPN+ (JAMM) motif; other site 224914001906 Zinc-binding site; other site 224914001907 methionine aminopeptidase; Reviewed; Region: PRK07281 224914001908 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 224914001909 active site 224914001910 Sugar fermentation stimulation protein; Region: SfsA; cl00647 224914001911 Uncharacterized protein conserved in bacteria (DUF2218); Region: DUF2218; cl01424 224914001912 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 224914001913 Peptidase M15; Region: Peptidase_M15_3; cl01194 224914001914 aspartate aminotransferase; Provisional; Region: PRK07681 224914001915 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 224914001916 pyridoxal 5'-phosphate binding site; other site 224914001917 homodimer interface; other site 224914001918 catalytic residue; other site 224914001919 homoserine dehydrogenase; Provisional; Region: PRK06349 224914001920 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914001921 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 224914001922 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 224914001923 Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase and related proteins [Carbohydrate transport and metabolism]; Region: GlpX; COG1494 224914001924 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 224914001925 putative active site; other site 224914001926 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 224914001927 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 224914001928 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914001929 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 224914001930 DHH family; Region: DHH; pfam01368 224914001931 Tim44-like domain; Region: Tim44; cl09208 224914001932 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914001933 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 224914001934 DNA binding site 224914001935 RNA-binding motif; other site 224914001936 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 224914001937 DNA binding site 224914001938 RNA-binding motif; other site 224914001939 Uncharacterized ACR, COG1430; Region: DUF192; cl00627 224914001940 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914001941 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 224914001942 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914001943 serine acetyltransferase; Provisional; Region: cysE; PRK11132 224914001944 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 224914001945 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-...; Region: LbH_SAT; cd03354 224914001946 trimer interface; other site 224914001947 active site 224914001948 substrate binding site; other site 224914001949 CoA binding site; other site 224914001950 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 224914001951 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 224914001952 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 224914001953 trimer interface; other site 224914001954 putative metal binding site; other site 224914001955 Bacterial protein of unknown function (DUF920); Region: DUF920; cl01479 224914001956 PAS domain; Region: PAS_5; cl11565 224914001957 Rhomboid family; Region: Rhomboid; cl11446 224914001958 FOG: CBS domain [General function prediction only]; Region: COG0517 224914001959 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair_10; cd04623 224914001960 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 224914001961 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 224914001962 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 224914001963 elongation factor Tu; Reviewed; Region: PRK12735 224914001964 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 224914001965 G1 box; other site 224914001966 GEF interaction site; other site 224914001967 GTP/Mg2+ binding site; other site 224914001968 Switch I region; other site 224914001969 G2 box; other site 224914001970 G3 box; other site 224914001971 Switch II region; other site 224914001972 G4 box; other site 224914001973 G5 box; other site 224914001974 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 224914001975 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 224914001976 Antibiotic Binding Site; other site 224914001977 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 224914001978 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 224914001979 Transcription termination factor nusG; Region: NusG; cl02766 224914001980 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 224914001981 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 224914001982 23S rRNA interface; other site 224914001983 L7/L12 interface; other site 224914001984 putative thiostrepton binding site; other site 224914001985 L25 interface; other site 224914001986 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that...; Region: Ribosomal_L1; cd00403 224914001987 mRNA/rRNA interface; other site 224914001988 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11...; Region: Ribosomal_L10; cd05797 224914001989 23S rRNA interface; other site 224914001990 Interface with L7/L12 ribosomal proteins; other site 224914001991 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 224914001992 L11 interface; other site 224914001993 putative EF-Tu interaction site; other site 224914001994 putative EF-G interaction site; other site 224914001995 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 224914001996 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 224914001997 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 224914001998 RPB11 interaction site; other site 224914001999 RPB12 interaction site; other site 224914002000 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 224914002001 RPB1 interaction site; other site 224914002002 RPB11 interaction site; other site 224914002003 RPB10 interaction site; other site 224914002004 RPB3 interaction site; other site 224914002005 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 224914002006 DNA-directed RNA polymerase, gamma subunit; Region: rpoC1_cyan; TIGR02387 224914002007 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 224914002008 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 224914002009 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK02597 224914002010 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 224914002011 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 224914002012 Rpb1 - Rpb6 interaction site; other site 224914002013 DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 224914002014 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 224914002015 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 224914002016 DNA binding site 224914002017 Rpb1 (beta') - Rpb2 (beta) interaction site; other site 224914002018 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 224914002019 S17 interaction site; other site 224914002020 S8 interaction site; other site 224914002021 16S rRNA interaction site; other site 224914002022 streptomycin interaction site; other site 224914002023 23S rRNA interaction site; other site 224914002024 aminoacyl-tRNA interaction site (A-site); other site 224914002025 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 224914002026 elongation factor G; Reviewed; Region: PRK00007 224914002027 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 224914002028 G1 box; other site 224914002029 putative GEF interaction site; other site 224914002030 GTP/Mg2+ binding site; other site 224914002031 Switch I region; other site 224914002032 G2 box; other site 224914002033 G3 box; other site 224914002034 Switch II region; other site 224914002035 G4 box; other site 224914002036 G5 box; other site 224914002037 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide...; Region: EFG_mtEFG_II; cd04088 224914002038 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor...; Region: EFG_mtEFG1_IV; cd01434 224914002039 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor...; Region: EFG_mtEFG_C; cd03713 224914002040 elongation factor Tu; Reviewed; Region: PRK12735 224914002041 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 224914002042 G1 box; other site 224914002043 GEF interaction site; other site 224914002044 GTP/Mg2+ binding site; other site 224914002045 Switch I region; other site 224914002046 G2 box; other site 224914002047 G3 box; other site 224914002048 Switch II region; other site 224914002049 G4 box; other site 224914002050 G5 box; other site 224914002051 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 224914002052 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 224914002053 Antibiotic Binding Site; other site 224914002054 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 224914002055 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 224914002056 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 224914002057 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 224914002058 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 224914002059 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 224914002060 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 224914002061 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 224914002062 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 224914002063 putative translocon binding site; other site 224914002064 protein-rRNA interface; other site 224914002065 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 224914002066 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The...; Region: 30S_S3_KH; cd02412 224914002067 G-X-X-G motif; other site 224914002068 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 224914002069 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 224914002070 23S rRNA interface; other site 224914002071 5S rRNA interface; other site 224914002072 putative antibiotic binding site; other site 224914002073 L25 interface; other site 224914002074 L27 interface; other site 224914002075 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where...; Region: Ribosomal_L29_HIP; cd00427 224914002076 23S rRNA interface; other site 224914002077 putative translocon interaction site; other site 224914002078 signal recognition particle (SRP54) interaction site; other site 224914002079 L23 interface; other site 224914002080 trigger factor interaction site; other site 224914002081 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 224914002082 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 224914002083 KOW motif; Region: KOW; cl00354 224914002084 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 224914002085 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 224914002086 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 224914002087 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 224914002088 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 224914002089 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 224914002090 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 224914002091 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 224914002092 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 224914002093 5S rRNA interface; other site 224914002094 23S rRNA interface; other site 224914002095 L5 interface; other site 224914002096 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 224914002097 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 224914002098 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 224914002099 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins...; Region: Ribosomal_L30; cd01658 224914002100 23S rRNA binding site; other site 224914002101 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 224914002102 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 224914002103 eubacterial secY protein; Region: SecY; pfam00344 224914002104 adenylate kinase; Reviewed; Region: adk; PRK00279 224914002105 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 224914002106 AMP-binding site; other site 224914002107 ATP-AMP (Ap5A)-binding site; other site 224914002108 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 224914002109 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 224914002110 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 224914002111 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 224914002112 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 224914002113 alphaNTD homodimer interface; other site 224914002114 alphaNTD - beta interaction site; other site 224914002115 alphaNTD - beta' interaction site; other site 224914002116 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 224914002117 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 224914002118 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 224914002119 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 224914002120 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 224914002121 protein binding site; other site 224914002122 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 224914002123 protein binding site; other site 224914002124 recombination factor protein RarA; Reviewed; Region: PRK13342 224914002125 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002126 Walker A motif; other site 224914002127 ATP binding site; other site 224914002128 Walker B motif; other site 224914002129 arginine finger; other site 224914002130 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 224914002131 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914002132 N-acetyl-D-glucosamine binding site; other site 224914002133 catalytic residue; other site 224914002134 putative outer membrane lipoprotein; Provisional; Region: PRK10510 224914002135 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 224914002136 ligand binding site; other site 224914002137 recombinase A; Provisional; Region: recA; PRK09354 224914002138 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 224914002139 hexamer interface; other site 224914002140 Walker A motif; other site 224914002141 ATP binding site; other site 224914002142 Walker B motif; other site 224914002143 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 224914002144 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: AlaRS_core; cd00673 224914002145 motif 1; other site 224914002146 active site 224914002147 motif 2; other site 224914002148 motif 3; other site 224914002149 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 224914002150 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH...; Region: alkPPc; cd00016 224914002151 dimer interface; other site 224914002152 Alkaline phosphatase homologues; Region: alkPPc; smart00098 224914002153 active site 224914002154 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 224914002155 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 224914002156 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 224914002157 conserved cys residue; other site 224914002158 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 224914002159 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 224914002160 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 224914002161 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 224914002162 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914002163 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914002164 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 224914002165 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily...; Region: MM_CoA_mutase_alpha_like; cd03679 224914002166 active site 224914002167 substrate binding site; other site 224914002168 coenzyme B12 binding site; other site 224914002169 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...; Region: MM_CoA_mut_B12_BD; cd02071 224914002170 B12 binding site; other site 224914002171 cobalt ligand; other site 224914002172 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 224914002173 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 224914002174 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914002175 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 224914002176 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 224914002177 carboxyltransferase (CT) interaction site; other site 224914002178 biotinylation site; other site 224914002179 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 224914002180 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 224914002181 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 224914002182 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 224914002183 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 224914002184 non-specific DNA binding site; other site 224914002185 salt bridge; other site 224914002186 sequence-specific DNA binding site; other site 224914002187 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 224914002188 Domain of unknown function (DUF955); Region: DUF955; cl01076 224914002189 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 224914002190 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 224914002191 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 224914002192 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 224914002193 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 224914002194 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 224914002195 DNA binding residues 224914002196 putative dimer interface; other site 224914002197 Protein of unknown function (DUF1624); Region: DUF1624; cl01394 224914002198 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 224914002199 putative active site; other site 224914002200 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 224914002201 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 224914002202 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 224914002203 Protein of unknown function (DUF1489); Region: DUF1489; cl11570 224914002204 Beta-lactamase; Region: Beta-lactamase; cl01009 224914002205 Sporulation related domain; Region: SPOR; cl10051 224914002206 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 224914002207 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 224914002208 Clp amino terminal domain; Region: Clp_N; pfam02861 224914002209 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002210 Walker A motif; other site 224914002211 ATP binding site; other site 224914002212 Walker B motif; other site 224914002213 arginine finger; other site 224914002214 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002215 Walker A motif; other site 224914002216 ATP binding site; other site 224914002217 Walker B motif; other site 224914002218 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 224914002219 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life...; Region: HINT_subgroup; cd01277 224914002220 HIT family signature motif; other site 224914002221 catalytic residue; other site 224914002222 FemAB family; Region: FemAB; cl11444 224914002223 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_like_3; cd08585 224914002224 Glycerophosphoryl diester phosphodiesterase family; Region: GDPD; pfam03009 224914002225 putative active site; other site 224914002226 catalytic site; other site 224914002227 putative metal binding site; other site 224914002228 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 224914002229 homotrimer interaction site; other site 224914002230 putative active site; other site 224914002231 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 224914002232 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 224914002233 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 224914002234 rRNA interaction site; other site 224914002235 S8 interaction site; other site 224914002236 putative laminin-1 binding site; other site 224914002237 elongation factor Ts; Provisional; Region: tsf; PRK09377 224914002238 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 224914002239 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 224914002240 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control...; Region: AAK_UMPK-PyrH-Ec; cd04254 224914002241 putative nucleotide binding site; other site 224914002242 uridine monophosphate binding site; other site 224914002243 homohexameric interface; other site 224914002244 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 224914002245 hinge region; other site 224914002246 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 224914002247 catalytic residue; other site 224914002248 putative FPP diphosphate binding site; other site 224914002249 putative FPP binding hydrophobic cleft; other site 224914002250 dimer interface; other site 224914002251 putative IPP diphosphate binding site; other site 224914002252 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 224914002253 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 224914002254 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 224914002255 active site 224914002256 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most...; Region: PDZ_metalloprotease; cd00989 224914002257 protein binding site; other site 224914002258 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 224914002259 putative substrate binding region; other site 224914002260 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 224914002261 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 224914002262 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 224914002263 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 224914002264 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 224914002265 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 224914002266 Surface antigen; Region: Bac_surface_Ag; cl03097 224914002267 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 224914002268 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 224914002269 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2,3-...; Region: LbH_LpxD; cd03352 224914002270 trimer interface; other site 224914002271 active site 224914002272 UDP-GlcNAc binding site; other site 224914002273 lipid-binding site 224914002274 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 224914002275 acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; Region: lipid_A_lpxA; TIGR01852 224914002276 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A...; Region: LbH_UDP-GlcNAc_AT; cd03351 224914002277 active site 224914002278 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 224914002279 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 224914002280 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 224914002281 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 224914002282 dimer interface; other site 224914002283 Citrate synthase; Region: Citrate_synt; pfam00285 224914002284 active site 224914002285 citrylCoA binding site; other site 224914002286 NADH binding; other site 224914002287 cationic pore residues; other site 224914002288 oxalacetate/citrate binding site; other site 224914002289 coenzyme A binding site; other site 224914002290 catalytic triad; other site 224914002291 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 224914002292 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914002293 HIGH motif; other site 224914002294 active site 224914002295 nucleotide binding site; other site 224914002296 catalytic core domain of descriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 224914002297 KMSKS motif; other site 224914002298 Competence protein; Region: Competence; cl00471 224914002299 LexA repressor; Validated; Region: PRK00215 224914002300 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914002301 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (...; Region: S24_LexA-like; cd06529 224914002302 Catalytic site; other site 224914002303 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 224914002304 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 224914002305 dimer interface; other site 224914002306 putative functional site; other site 224914002307 putative MPT binding site; other site 224914002308 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a...; Region: MoaC_PE; cd01420 224914002309 trimer interface; other site 224914002310 dimer interface; other site 224914002311 putative active site; other site 224914002312 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 224914002313 active site 224914002314 ribulose/triose binding site; other site 224914002315 phosphate binding site; other site 224914002316 substrate (anthranilate) binding pocket; other site 224914002317 product (indole) binding pocket; other site 224914002318 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 224914002319 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 224914002320 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 224914002321 peptidyl-prolyl cis-trans isomerase (rotamase D); Provisional; Region: PRK10788 224914002322 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 224914002323 substrate binding site; other site 224914002324 dimer interface; other site 224914002325 catalytic triad; other site 224914002326 Preprotein translocase SecG subunit; Region: SecG; cl09123 224914002327 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914002328 CTP synthetase; Validated; Region: pyrG; PRK05380 224914002329 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer...; Region: CTGs; cd03113 224914002330 Catalytic site; other site 224914002331 active site 224914002332 UTP binding site; other site 224914002333 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 224914002334 active site 224914002335 putative oxyanion hole; other site 224914002336 catalytic triad; other site 224914002337 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 224914002338 NeuB family; Region: NeuB; cl00496 224914002339 phosphopyruvate hydratase; Provisional; Region: eno; PRK00077 224914002340 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 224914002341 dimer interface; other site 224914002342 metal-binding site 224914002343 substrate binding pocket; other site 224914002344 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 224914002345 S-adenosylmethionine binding site; other site 224914002346 Septum formation initiator; Region: DivIC; cl11433 224914002347 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 224914002348 TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 224914002349 tetramer interface; other site 224914002350 TPP-binding site; other site 224914002351 heterodimer interface; other site 224914002352 phosphorylation loop region 224914002353 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 224914002354 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 224914002355 E3 interaction surface; other site 224914002356 lipoyl attachment site; other site 224914002357 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 224914002358 alpha subunit interface; other site 224914002359 TPP binding site; other site 224914002360 heterodimer interface; other site 224914002361 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 224914002362 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 224914002363 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 224914002364 E3 interaction surface; other site 224914002365 lipoyl attachment site; other site 224914002366 e3 binding domain; Region: E3_binding; pfam02817 224914002367 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 224914002368 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 224914002369 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002371 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 224914002372 lipoyl synthase; Provisional; Region: PRK05481 224914002373 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 224914002374 FeS/SAM binding site; other site 224914002375 Polyketide cyclase / dehydrase and lipid transport; Region: Polyketide_cyc2; cl10449 224914002376 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002377 Competence-damaged protein; Region: CinA; cl00666 224914002378 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 224914002379 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 224914002380 substrate binding site; other site 224914002381 dimer interface; other site 224914002382 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid...; Region: MECDP_synthase; cd00554 224914002383 homotrimer interaction site; other site 224914002384 zinc binding site; other site 224914002385 CDP-binding sites; other site 224914002386 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 224914002387 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and...; Region: DUS_like_FMN; cd02801 224914002388 FMN binding site; other site 224914002389 active site 224914002390 catalytic residues; other site 224914002391 substrate binding site; other site 224914002392 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 224914002393 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans...; Region: HisKA; cd00082 224914002394 dimer interface; other site 224914002395 phosphorylation site 224914002396 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 224914002397 ATP binding site; other site 224914002398 Mg2+ binding site; other site 224914002399 G-X-G motif; other site 224914002400 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 224914002401 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 224914002402 active site 224914002403 phosphorylation site 224914002404 intermolecular recognition site; other site 224914002405 dimerization interface; other site 224914002406 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002407 Walker A motif; other site 224914002408 ATP binding site; other site 224914002409 Walker B motif; other site 224914002410 arginine finger; other site 224914002411 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 224914002412 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 224914002413 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 224914002414 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 224914002415 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 224914002416 ATP binding site; other site 224914002417 Mg2+ binding site; other site 224914002418 G-X-G motif; other site 224914002419 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 224914002420 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 224914002421 active site 224914002422 phosphorylation site 224914002423 intermolecular recognition site; other site 224914002424 dimerization interface; other site 224914002425 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002426 Walker A motif; other site 224914002427 ATP binding site; other site 224914002428 Walker B motif; other site 224914002429 arginine finger; other site 224914002430 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 224914002431 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 224914002432 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002433 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914002434 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002435 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914002436 Capsular polysaccharide synthesis protein; Region: Caps_synth; pfam05704 224914002437 Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotrophic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that...; Region: Hfq; cd01716 224914002438 Sm1 motif; other site 224914002439 intra - hexamer interaction site; other site 224914002440 inter - hexamer interaction site; other site 224914002441 nucleotide binding pocket; other site 224914002442 Sm2 motif; other site 224914002443 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 224914002444 HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual...; Region: HflX; cd01878 224914002445 G1 box; other site 224914002446 GTP/Mg2+ binding site; other site 224914002447 Switch I region; other site 224914002448 G2 box; other site 224914002449 G3 box; other site 224914002450 Switch II region; other site 224914002451 G4 box; other site 224914002452 G5 box; other site 224914002453 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 224914002454 oligomer interface; other site 224914002455 active site residues 224914002456 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 224914002457 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 224914002458 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002459 Walker A motif; other site 224914002460 ATP binding site; other site 224914002461 Walker B motif; other site 224914002462 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 224914002463 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 224914002464 Found in ATP-dependent protease La (LON); Region: LON; cl01056 224914002465 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002466 Walker A motif; other site 224914002467 ATP binding site; other site 224914002468 Walker B motif; other site 224914002469 arginine finger; other site 224914002470 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 224914002471 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 224914002472 IHF dimer interface; other site 224914002473 IHF - DNA interface; other site 224914002474 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 224914002475 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 224914002476 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 224914002477 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 224914002478 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 224914002479 dimer interface; other site 224914002480 ssDNA binding site; other site 224914002481 tetramer (dimer of dimers) interface; other site 224914002482 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 224914002483 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914002484 DNA binding site 224914002485 UTRA domain; Region: UTRA; cl06649 224914002486 Guanylate kinase; Region: Guanylate_kin; cl12021 224914002487 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 224914002488 MarC family integral membrane protein; Region: MarC; cl00919 224914002489 DNA Topoisomerase IV; Region: TOP4c; smart00434 224914002490 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 224914002491 CAP-like domain; other site 224914002492 active site 224914002493 primary dimer interface; other site 224914002494 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 224914002495 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 224914002496 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 224914002497 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 224914002498 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 224914002499 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 224914002500 Phosphopantetheine adenylyltransferase; Region: PPAT_a; cd02163 224914002501 active site 224914002502 substrate binding site; other site 224914002503 active site motif 224914002504 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 224914002505 active site 224914002506 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 224914002507 active site 224914002508 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 224914002509 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 224914002510 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 224914002511 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914002512 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914002513 multidrug efflux protein; Reviewed; Region: PRK09579 224914002514 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 224914002515 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 224914002516 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914002517 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914002518 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914002519 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914002520 dimerization interface; other site 224914002521 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 224914002522 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914002523 FAD binding site; other site 224914002524 substrate binding pocket; other site 224914002525 catalytic base; other site 224914002526 CoA-transferase family III; Region: CoA_transf_3; cl00778 224914002527 BRO family, N-terminal domain; Region: Bro-N; pfam02498 224914002528 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 224914002529 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 224914002530 catalytic residues; other site 224914002531 catalytic nucleophile; other site 224914002532 Presynaptic Site I dimer interface; other site 224914002533 Synaptic Antiparallel dimer interface; other site 224914002534 Synaptic Flat tetramer interface; other site 224914002535 Synaptic Site I dimer interface; other site 224914002536 DNA binding site 224914002537 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 224914002538 DNA-binding interface; DNA binding site 224914002539 hypothetical protein; Provisional; Region: PRK10279 224914002540 Bacterial patatin-like phospholipase domain containing protein 6; Region: Pat_NTE_like_bacteria; cd07228 224914002541 nucleophile elbow; other site 224914002542 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 224914002543 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 224914002544 homodecamer interface; other site 224914002545 GTP cyclohydrolase I; Provisional; Region: PLN03044 224914002546 active site 224914002547 putative catalytic site residues; other site 224914002548 zinc binding site; other site 224914002549 GTP-CH-I/GFRP interaction surface; other site 224914002550 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 224914002551 trimerization site; other site 224914002552 active site 224914002553 Domain of unknown function DUF37; Region: DUF37; cl00506 224914002554 Beta-lactamase; Region: Beta-lactamase; cl01009 224914002555 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional; Region: PRK10793 224914002556 Beta-lactamase; Region: Beta-lactamase; cl01009 224914002557 Sporulation related domain; Region: SPOR; cl10051 224914002558 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 224914002559 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase...; Region: TGS_ThrRS_N; cd01667 224914002560 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 224914002561 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 224914002562 active site 224914002563 dimer interface; other site 224914002564 motif 1; other site 224914002565 motif 2; other site 224914002566 motif 3; other site 224914002567 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 224914002568 anticodon binding site; other site 224914002569 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 224914002570 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 224914002571 dimer interface; other site 224914002572 Flavin Reductases; Region: FlaRed; cl00801 224914002573 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 224914002574 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00737 224914002575 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00737 224914002576 UDP-glucose 4-epimerase; Region: PLN02240 224914002577 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002578 Membrane transport protein; Region: Mem_trans; cl09117 224914002579 Predicted methyltransferase (contains TPR repeat) [General function prediction only]; Region: COG4976 224914002580 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 224914002581 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 224914002582 S-adenosylmethionine binding site; other site 224914002583 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 224914002584 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate...; Region: APP_MetAP; cl00279 224914002585 active site 224914002586 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 224914002587 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD2; cd08298 224914002588 putative NAD(P) binding site; other site 224914002589 putative substrate binding site; other site 224914002590 catalytic Zn binding site; other site 224914002591 structural Zn binding site; other site 224914002592 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 224914002593 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 224914002594 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 224914002595 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 224914002596 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 224914002597 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914002598 metal-binding site 224914002599 active site 224914002600 I-site; other site 224914002601 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914002602 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 224914002603 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but...; Region: TST_Repeat_1; cd01448 224914002604 active site residue 224914002605 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 224914002606 active site residue 224914002607 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 224914002608 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 224914002609 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 224914002610 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 224914002611 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 224914002612 dimer interface; other site 224914002613 pyridoxal 5'-phosphate binding site; other site 224914002614 catalytic residue; other site 224914002615 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 224914002616 DEAD-like helicases superfamily; Region: DEXDc; smart00487 224914002617 ATP binding site; other site 224914002618 Mg++ binding site; other site 224914002619 motif III; other site 224914002620 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 224914002621 nucleotide binding region; other site 224914002622 ATP-binding site; other site 224914002623 threonine dehydratase; Validated; Region: PRK08639 224914002624 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 224914002625 tetramer interface; other site 224914002626 pyridoxal 5'-phosphate binding site; other site 224914002627 catalytic residue; other site 224914002628 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 224914002629 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 224914002630 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 224914002631 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 224914002632 putative MPT binding site; other site 224914002633 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 224914002634 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 224914002635 Ligand Binding Site; other site 224914002636 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914002637 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_9; cd04666 224914002638 nudix motif; other site 224914002639 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07562 224914002640 Class II vitamin B12-dependent ribonucleotide reductase; Region: Ribonuc_red_2_N; pfam08471 224914002641 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 224914002642 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 224914002643 active site 224914002644 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 224914002645 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 224914002646 Mechanosensitive ion channel; Region: MS_channel; pfam00924 224914002647 Beta-lactamase; Region: Beta-lactamase; cl01009 224914002648 Predicted flavoproteins [General function prediction only]; Region: COG2081 224914002649 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002650 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002651 PAS fold; Region: PAS_4; pfam08448 224914002652 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans...; Region: HisKA; cd00082 224914002653 dimer interface; other site 224914002654 phosphorylation site 224914002655 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 224914002656 ATP binding site; other site 224914002657 Mg2+ binding site; other site 224914002658 G-X-G motif; other site 224914002659 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 224914002660 active site 224914002661 phosphorylation site 224914002662 intermolecular recognition site; other site 224914002663 dimerization interface; other site 224914002664 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 224914002665 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 224914002666 catalytic core; other site 224914002667 YcjX-like family, DUF463; Region: DUF463; cl01193 224914002668 Predicted membrane protein [Function unknown]; Region: COG3768 224914002669 Domain of unknown function (DUF697); Region: DUF697; cl12064 224914002670 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 224914002671 catalytic center binding site; other site 224914002672 ATP binding site; other site 224914002673 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines...; Region: DHNA_DHNTPE; cd00534 224914002674 homooctamer interface; other site 224914002675 active site 224914002676 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 224914002677 substrate binding pocket; other site 224914002678 dimer interface; other site 224914002679 inhibitor binding site; inhibition site 224914002680 Bacterial protein of unknown function (DUF922); Region: DUF922; cl02415 224914002681 putative oxidoreductase; Provisional; Region: PRK11749 224914002682 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 224914002683 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 224914002684 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 224914002685 Protein of unknown function (DUF330); Region: DUF330; cl01135 224914002686 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 224914002687 mce related protein; Region: MCE; pfam02470 224914002688 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 224914002689 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 224914002690 Walker A/P-loop; other site 224914002691 ATP binding site; other site 224914002692 Q-loop/lid; other site 224914002693 ABC transporter signature motif; other site 224914002694 Walker B; other site 224914002695 D-loop; other site 224914002696 H-loop/switch region; other site 224914002697 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 224914002698 Domain of unknown function DUF140; Region: DUF140; cl00510 224914002699 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 224914002700 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism...; Region: L-Ala-DL-Glu_epimerase; cd03319 224914002701 active site 224914002702 malic enzyme; Reviewed; Region: PRK12862 224914002703 Malic enzyme, N-terminal domain; Region: malic; pfam00390 224914002704 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 224914002705 putative NAD(P) binding site; other site 224914002706 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 224914002707 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 224914002708 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914002709 HIGH motif; other site 224914002710 active site 224914002711 nucleotide binding site; other site 224914002712 catalytic core domain of descriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 224914002713 KMSKS motif; other site 224914002714 NAD synthetase; Provisional; Region: PRK13981 224914002715 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 224914002716 multimer interface; other site 224914002717 active site 224914002718 catalytic triad; other site 224914002719 protein interface 1; other site 224914002720 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to...; Region: NAD_synthase; cd00553 224914002721 homodimer interface; other site 224914002722 NAD binding pocket; other site 224914002723 ATP binding pocket; other site 224914002724 Mg binding site; other site 224914002725 active-site loop 224914002726 Prokaryotic diacylglycerol kinase; Region: DAGK_prokar; cl00526 224914002727 Class-II DAHP synthetase family; Region: DAHP_synth_2; cl03230 224914002728 glutathione reductase; Validated; Region: PRK06116 224914002729 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002730 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 224914002731 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; cl01243 224914002732 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 224914002733 tetramer (dimer of dimers) interface; other site 224914002734 active site 224914002735 dimer interface; other site 224914002736 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 224914002737 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 224914002738 motif II; other site 224914002739 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 224914002740 hypothetical protein; Provisional; Region: PRK10565 224914002741 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 224914002742 putative substrate binding site; other site 224914002743 putative ATP binding site; other site 224914002744 Nitrogen regulatory protein P-II; Region: P-II; cl00412 224914002745 glutamine synthetase; Provisional; Region: glnA; PRK09469 224914002746 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 224914002747 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 224914002748 ATP12 chaperone protein; Region: ATP12; cl02228 224914002749 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 224914002750 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 224914002751 motif II; other site 224914002752 EamA-like transporter family; Region: EamA; cl01037 224914002753 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 224914002754 EamA-like transporter family; Region: EamA; cl01037 224914002755 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 224914002756 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF...; Region: PseudoU_synth_RluCD_like; cd02869 224914002757 active site 224914002758 cyclic beta-1,2-glucan ABC transporter; Provisional; Region: PRK13657 224914002759 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914002760 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914002761 Walker A/P-loop; other site 224914002762 ATP binding site; other site 224914002763 Q-loop/lid; other site 224914002764 ABC transporter signature motif; other site 224914002765 Walker B; other site 224914002766 D-loop; other site 224914002767 H-loop/switch region; other site 224914002768 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 224914002769 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 224914002770 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 224914002771 active site 224914002772 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 224914002773 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 224914002774 active site 224914002775 HIGH motif; other site 224914002776 KMSKS motif; other site 224914002777 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 224914002778 tRNA binding surface; other site 224914002779 anticodon binding site; other site 224914002780 DNA polymerase III subunit delta'; Validated; Region: PRK09112 224914002781 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914002782 thymidylate kinase; Validated; Region: tmk; PRK00698 224914002783 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting...; Region: TMPK; cd01672 224914002784 TMP-binding site; other site 224914002785 ATP-binding site; other site 224914002786 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 224914002787 Beta-lactamase; Region: Beta-lactamase; cl01009 224914002788 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 224914002789 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 224914002790 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 224914002791 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 224914002792 catalytic residues; other site 224914002793 Lysozyme family protein [General function prediction only]; Region: zliS; COG3926 224914002794 Predicted lysozyme (DUF847); Region: DUF847; pfam05838 224914002795 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 224914002796 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 224914002797 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 224914002798 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 224914002799 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914002800 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914002801 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 224914002802 Protein of unknown function (DUF497); Region: DUF497; cl01108 224914002803 Domain of unknown function (DUF1508); Region: DUF1508; cl01356 224914002804 Surface antigen; Region: Surface_Ag_2; cl01155 224914002805 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 224914002806 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 include the bacteriophage lambda integrase, the...; Region: INT_REC_C; cd01182 224914002807 Int/Topo IB signature motif; other site 224914002808 active site 224914002809 catalytic residues; other site 224914002810 DNA binding site 224914002811 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 224914002812 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 224914002813 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914002814 fumarate hydratase; Provisional; Region: PTZ00226 224914002815 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 224914002816 Fumarase C-terminus; Region: Fumerase_C; cl00795 224914002817 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 224914002818 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002819 Protein of unknown function (DUF971); Region: DUF971; cl01414 224914002820 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 224914002821 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 224914002822 FeS/SAM binding site; other site 224914002823 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 224914002824 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 224914002825 GTP binding site; other site 224914002826 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914002827 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914002828 substrate binding pocket; other site 224914002829 GST_C family, unknown subfamily 2; composed of uncharacterized bacterial proteins, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_C_2; cd03180 224914002830 putative substrate binding pocket (H-site); other site 224914002831 putative N-terminal domain interface; other site 224914002832 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914002833 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 224914002834 NAD(P) binding pocket; other site 224914002835 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl09488 224914002836 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 224914002837 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914002838 HIGH motif; other site 224914002839 active site 224914002840 nucleotide binding site; other site 224914002841 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 224914002842 active site 224914002843 KMSKS motif; other site 224914002844 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 224914002845 tRNA binding surface; other site 224914002846 anticodon binding site; other site 224914002847 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 224914002848 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 224914002849 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 224914002850 Outer membrane efflux protein; Region: OEP; pfam02321 224914002851 Outer membrane efflux protein; Region: OEP; pfam02321 224914002852 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 224914002853 S-adenosylmethionine binding site; other site 224914002854 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 224914002855 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 224914002856 helicase 45; Provisional; Region: PTZ00424 224914002857 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 224914002858 ATP binding site; other site 224914002859 Mg++ binding site; other site 224914002860 motif III; other site 224914002861 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 224914002862 nucleotide binding region; other site 224914002863 ATP-binding site; other site 224914002864 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 224914002865 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 224914002866 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 224914002867 active site 224914002868 Domain of unknown function DUF59; Region: DUF59; cl00941 224914002869 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 224914002870 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 224914002871 pyridoxal 5'-phosphate binding pocket; other site 224914002872 catalytic residue; other site 224914002873 FeS assembly protein SufD, group 1; Region: sufD; TIGR01981 224914002874 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 224914002875 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 224914002876 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 224914002877 Walker A/P-loop; other site 224914002878 ATP binding site; other site 224914002879 Q-loop/lid; other site 224914002880 ABC transporter signature motif; other site 224914002881 Walker B; other site 224914002882 D-loop; other site 224914002883 H-loop/switch region; other site 224914002884 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 224914002885 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 224914002886 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 224914002887 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 224914002888 pyridoxal 5'-phosphate binding pocket; other site 224914002889 catalytic residue; other site 224914002890 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 224914002891 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914002892 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 224914002893 Uncharacterized protein family (UPF0075); Region: UPF0075; cl04217 224914002894 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 224914002895 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 224914002896 active site 224914002897 HIGH motif; other site 224914002898 dimer interface; other site 224914002899 KMSKS motif; other site 224914002900 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 224914002901 RNA binding surface; other site 224914002902 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by...; Region: PRX_BCP; cd03017 224914002903 catalytic triad; other site 224914002904 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 224914002905 dinuclear metal binding motif; other site 224914002906 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914002907 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914002908 peptide chain release factor 2; Provisional; Region: PRK07342 224914002909 RF-1 domain; Region: RF-1; cl02875 224914002910 RF-1 domain; Region: RF-1; cl02875 224914002911 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 224914002912 Transglycosylase; Region: Transgly; cl07896 224914002913 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 224914002914 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 224914002915 active site 224914002916 metal-binding site 224914002917 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 224914002918 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 224914002919 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 224914002920 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 224914002921 pyridoxal 5'-phosphate binding site; other site 224914002922 homodimer interface; other site 224914002923 catalytic residue; other site 224914002924 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 224914002925 Peptidase family M48; Region: Peptidase_M48; cl12018 224914002926 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 224914002927 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a...; Region: DsbA_Com1_like; cd03023 224914002928 catalytic residues; other site 224914002929 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 224914002930 trimer interface; other site 224914002931 active site 224914002932 dimer interface; other site 224914002933 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 224914002934 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 224914002935 carboxyltransferase (CT) interaction site; other site 224914002936 biotinylation site; other site 224914002937 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 224914002938 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 224914002939 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914002940 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 224914002941 Leucyl/phenylalanyl-tRNA protein transferase; Region: Leu_Phe_trans; cl01006 224914002942 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 224914002943 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 224914002944 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 224914002945 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914002946 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 224914002947 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 224914002948 GatB domain; Region: GatB_Yqey; cl11497 224914002949 trigger factor; Provisional; Region: tig; PRK01490 224914002950 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 224914002951 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 224914002952 Uncharacterized membrane-anchored protein [Function unknown]; Region: COG4929 224914002953 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 224914002954 Domain of unknown function (DUF1127); Region: DUF1127; cl02276 224914002955 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 224914002956 Glucose inhibited division protein A; Region: GIDA; pfam01134 224914002957 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 224914002958 substrate binding pocket; other site 224914002959 substrate-Mg2+ binding site; other site 224914002960 aspartate-rich region 1; other site 224914002961 aspartate-rich region 2; other site 224914002962 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as...; Region: Mth938-like; cd00248 224914002963 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13023 224914002964 Protein export membrane protein; Region: SecD_SecF; cl14618 224914002965 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 224914002966 Protein export membrane protein; Region: SecD_SecF; cl14618 224914002967 Preprotein translocase subunit; Region: YajC; cl00806 224914002968 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 224914002969 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914002970 Walker A motif; other site 224914002971 ATP binding site; other site 224914002972 Walker B motif; other site 224914002973 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 224914002974 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 224914002975 putative peptidoglycan binding site; other site 224914002976 Peptidase family M23; Region: Peptidase_M23; pfam01551 224914002977 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 224914002978 S-adenosylmethionine binding site; other site 224914002979 Survival protein SurE; Region: SurE; cl00448 224914002980 seryl-tRNA synthetase; Provisional; Region: PRK05431 224914002981 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 224914002982 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 224914002983 dimer interface; other site 224914002984 active site 224914002985 motif 1; other site 224914002986 motif 2; other site 224914002987 motif 3; other site 224914002988 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 224914002989 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 224914002990 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 224914002991 ScpA/B protein; Region: ScpA_ScpB; cl00598 224914002992 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 224914002993 Sporulation related domain; Region: SPOR; cl10051 224914002994 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 224914002995 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 224914002996 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 224914002997 active site 224914002998 HIGH motif; other site 224914002999 KMSK motif region; other site 224914003000 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 224914003001 tRNA binding surface; other site 224914003002 anticodon binding site; other site 224914003003 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 224914003004 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 224914003005 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 224914003006 putative metal binding site; other site 224914003007 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 224914003008 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 224914003009 Sel1 repeat; Region: Sel1; cl02723 224914003010 Staphylococcal nuclease homologues; Region: SNc; smart00318 224914003011 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 224914003012 Catalytic site; other site 224914003013 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 224914003014 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914003015 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914003016 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 224914003017 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 224914003018 putative dimer interface; other site 224914003019 active site pocket 224914003020 putative cataytic base; other site 224914003021 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 224914003022 Protein of unknown function (DUF1289); Region: DUF1289; cl01304 224914003023 Predicted aspartyl protease [General function prediction only]; Region: COG3577 224914003024 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 224914003025 catalytic motif; other site 224914003026 Catalytic residue; other site 224914003027 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 224914003028 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and...; Region: DUS_like_FMN; cd02801 224914003029 FMN binding site; other site 224914003030 active site 224914003031 catalytic residues; other site 224914003032 substrate binding site; other site 224914003033 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 224914003034 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914003035 substrate binding pocket; other site 224914003036 membrane-bound complex binding site; other site 224914003037 hinge residues; other site 224914003038 beta-phosphoglucomutase family hydrolase; Region: PGMB-YQAB-SF; TIGR02009 224914003039 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914003040 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 224914003041 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 224914003042 active site 224914003043 Protein of unknown function (DUF1045); Region: DUF1045; cl05676 224914003044 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 224914003045 substrate binding site; other site 224914003046 ATP binding site; other site 224914003047 Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; Region: GalM; COG2017 224914003048 Aldose 1-epimerase; Region: Aldose_epim; cl00476 224914003049 Lysozyme family protein [General function prediction only]; Region: zliS; COG3926 224914003050 Predicted lysozyme (DUF847); Region: DUF847; pfam05838 224914003051 Predicted Peptidoglycan domain; Region: PG_binding_3; pfam09374 224914003052 Phosphopantetheine attachment site; Region: PP-binding; cl09936 224914003053 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06519 224914003054 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 224914003055 active site 224914003056 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK06501 224914003057 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 224914003058 dimer interface; other site 224914003059 active site 224914003060 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 224914003061 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH_like1; cd08266 224914003062 putative NAD(P) binding site; other site 224914003063 structural Zn binding site; other site 224914003064 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 224914003065 putative acyl-acceptor binding pocket; other site 224914003066 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative...; Region: RPE; cd00429 224914003067 substrate binding site; other site 224914003068 hexamer interface; other site 224914003069 metal-binding site 224914003070 adenylosuccinate lyase; Provisional; Region: PRK07492 224914003071 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 224914003072 tetramer interface; other site 224914003073 active site 224914003074 Predicted ring-cleavage extradiol dioxygenase [General function prediction only]; Region: COG2514 224914003075 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914003076 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914003077 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 224914003078 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 224914003079 Domain of unknown function (DUF1476); Region: DUF1476; cl11571 224914003080 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 224914003081 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 224914003082 ATP binding site; other site 224914003083 active site 224914003084 substrate binding site; other site 224914003085 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 224914003086 Glutamine amidotransferase [Amino acid transport and metabolism]; Region: HisH; COG0118 224914003087 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 224914003088 putative active site; other site 224914003089 catalytic triad; other site 224914003090 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 224914003091 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 224914003092 C-terminal domain interface; other site 224914003093 GSH binding site (G-site); other site 224914003094 dimer interface; other site 224914003095 Glutathione S-transferase (GST) family, C-terminal alpha helical 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...; Region: GST_C_family; cd00299 224914003096 N-terminal domain interface; other site 224914003097 dimer interface; other site 224914003098 substrate binding pocket (H-site); other site 224914003099 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 224914003100 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 224914003101 dimerization interface; other site 224914003102 ATP binding site; other site 224914003103 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 224914003104 dimerization interface; other site 224914003105 ATP binding site; other site 224914003106 BolA-like protein; Region: BolA; cl00386 224914003107 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 224914003108 putative GSH binding site; other site 224914003109 catalytic residues; other site 224914003110 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 224914003111 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 224914003112 putative substrate translocation pore; other site 224914003113 PAP-phosphatase_like domains. PAP-phosphatase is a member of the inositol monophosphatase family, and catalyses the hydrolysis of 3'-phosphoadenosine-5'-phosphate (PAP) to AMP. In Saccharomyces cerevisiae, HAL2 (MET22) is involved in methionine...; Region: PAP_phosphatase; cd01517 224914003114 active site 224914003115 putative lithium-binding site; other site 224914003116 substrate binding site; other site 224914003117 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This...; Region: Alpha_ANH_like_II; cd01993 224914003118 Ligand Binding Site; other site 224914003119 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 224914003120 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 224914003121 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 224914003122 RNA binding surface; other site 224914003123 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 224914003124 Protein of unknwon function (DUF3008); Region: DUF3008; pfam11450 224914003125 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 224914003126 DNA polymerase alpha chain like domain; Region: POLIIIAc; cl02625 224914003127 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 224914003128 Protein of unknown function, DUF655; Region: DUF655; cl00648 224914003129 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli...; Region: DnaE_OBF; cd04485 224914003130 generic binding surface II; other site 224914003131 generic binding surface I; other site 224914003132 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 224914003133 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 224914003134 Walker A/P-loop; other site 224914003135 ATP binding site; other site 224914003136 Q-loop/lid; other site 224914003137 ABC transporter signature motif; other site 224914003138 Walker B; other site 224914003139 D-loop; other site 224914003140 H-loop/switch region; other site 224914003141 LolC/E family; Region: lolCE; TIGR02212 224914003142 Predicted permease; Region: FtsX; cl11418 224914003143 prolyl-tRNA synthetase; Provisional; Region: PRK12325 224914003144 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation...; Region: ProRS_core_prok; cd00779 224914003145 dimer interface; other site 224914003146 motif 1; other site 224914003147 active site 224914003148 motif 2; other site 224914003149 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 224914003150 active site 224914003151 motif 3; other site 224914003152 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-...; Region: ProRS_anticodon_short; cd00861 224914003153 anticodon binding site; other site 224914003154 Protein of unknown function (DUF1467); Region: DUF1467; cl11569 224914003155 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914003156 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 224914003157 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 224914003158 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 224914003159 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 224914003160 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 224914003161 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 224914003162 NADH dehydrogenase subunit N; Provisional; Region: PRK05777 224914003163 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 224914003164 NADH dehydrogenase subunit M; Reviewed; Region: PRK05846 224914003165 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 224914003166 NADH dehydrogenase subunit L; Reviewed; Region: PRK06590 224914003167 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 224914003168 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 224914003169 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 224914003170 NADH-ubiquinone/plastoquinone oxidoreductase chain 6; Region: Oxidored_q3; cl00676 224914003171 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 224914003172 4Fe-4S binding domain; Region: Fer4; pfam00037 224914003173 NADH dehydrogenase; Region: NADHdh; cl00469 224914003174 NADH dehydrogenase subunit G; Validated; Region: PRK09130 224914003175 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 224914003176 catalytic loop; other site 224914003177 iron binding site; other site 224914003178 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 224914003179 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 224914003180 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 224914003181 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 224914003182 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 224914003183 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 224914003184 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 224914003185 NADH dehydrogenase subunit E; Provisional; Region: PRK12373 224914003186 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of...; Region: TRX_Fd_NuoE; cd03064 224914003187 putative dimer interface; other site 224914003188 [2Fe-2S] cluster binding site; other site 224914003189 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 224914003190 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 224914003191 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 224914003192 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 224914003193 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003194 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003195 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK05994 224914003196 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 224914003197 homodimer interface; other site 224914003198 substrate-cofactor binding pocket; other site 224914003199 pyridoxal 5'-phosphate binding site; other site 224914003200 catalytic residue; other site 224914003201 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 224914003202 CoenzymeA binding site; other site 224914003203 subunit interaction site; other site 224914003204 PHB binding site; other site 224914003205 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 224914003206 23S rRNA interface; other site 224914003207 L3 interface; other site 224914003208 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 224914003209 Arginase family; Region: Arginase; cl00306 224914003210 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 224914003211 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003212 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl00696 224914003213 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 224914003214 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 224914003215 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 224914003216 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 224914003217 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 224914003218 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 224914003219 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 224914003220 Bacterial sugar transferase; Region: Bac_transf; cl00939 224914003221 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 224914003222 DNA binding residues 224914003223 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher...; Region: HU_IHF; cd00591 224914003224 IHF dimer interface; other site 224914003225 IHF - DNA interface; other site 224914003226 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 224914003227 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 224914003228 dimer interface; other site 224914003229 active site 224914003230 CoA binding pocket; other site 224914003231 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 224914003232 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 224914003233 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; cl12045 224914003234 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 224914003235 Inorganic pyrophosphatase [Energy production and conversion]; Region: OVP1; cl11452 224914003236 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 224914003237 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-...; Region: NusB_Sun; cl00223 224914003238 putative RNA binding site; other site 224914003239 6,7-dimethyl-8-ribityllumazine synthase; Region: DMRL_synthase; cl00317 224914003240 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 224914003241 Lumazine binding domain; Region: Lum_binding; pfam00677 224914003242 Lumazine binding domain; Region: Lum_binding; pfam00677 224914003243 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 224914003244 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 224914003245 catalytic motif; other site 224914003246 Zn binding site; other site 224914003247 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cl00161 224914003248 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 224914003249 ATP cone domain; Region: ATP-cone; pfam03477 224914003250 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of...; Region: SHMT; cd00378 224914003251 active site 224914003252 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 224914003253 pyridoxal 5'-phosphate binding pocket; other site 224914003254 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914003255 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914003256 Transcriptional regulators [Transcription]; Region: MarR; COG1846 224914003257 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914003258 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 224914003259 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 224914003260 substrate binding site; other site 224914003261 oxyanion hole (OAH) forming residues; other site 224914003262 trimer interface; other site 224914003263 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 224914003264 dimer interface; other site 224914003265 allosteric magnesium binding site; other site 224914003266 active site 224914003267 aspartate-rich active site metal binding site; other site 224914003268 Schiff base residues; other site 224914003269 RDD family; Region: RDD; cl00746 224914003270 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 224914003271 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 224914003272 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 224914003273 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 224914003274 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in...; Region: TOP4c; cd00187 224914003275 CAP-like domain; other site 224914003276 active site 224914003277 primary dimer interface; other site 224914003278 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 224914003279 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 224914003280 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 224914003281 dimer interface; other site 224914003282 anticodon binding site; other site 224914003283 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 224914003284 homodimer interface; other site 224914003285 motif 1; other site 224914003286 active site 224914003287 motif 2; other site 224914003288 GAD domain; Region: GAD; pfam02938 224914003289 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 224914003290 active site 224914003291 motif 3; other site 224914003292 ribonuclease D; Region: rnd; TIGR01388 224914003293 Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and...; Region: RNaseD_exo; cd06142 224914003294 putative active site; other site 224914003295 catalytic site; other site 224914003296 putative substrate binding site; other site 224914003297 HRDC domain; Region: HRDC; cl02578 224914003298 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 224914003299 exopolyphosphatase; Region: exo_poly_only; TIGR03706 224914003300 polyphosphate kinase; Provisional; Region: PRK05443 224914003301 Zinc-finger domain; Region: zf-CHCC; cl01821 224914003302 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003303 salicylate hydroxylase; Provisional; Region: PRK08163 224914003304 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 224914003305 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 224914003306 Walker A/P-loop; other site 224914003307 ATP binding site; other site 224914003308 Q-loop/lid; other site 224914003309 ABC transporter signature motif; other site 224914003310 Walker B; other site 224914003311 D-loop; other site 224914003312 H-loop/switch region; other site 224914003313 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 224914003314 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914003315 dimer interface; other site 224914003316 conserved gate region; other site 224914003317 putative PBP binding loops; other site 224914003318 ABC-ATPase subunit interface; other site 224914003319 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 224914003320 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914003321 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914003322 putative PBP binding loops; other site 224914003323 dimer interface; other site 224914003324 ABC-ATPase subunit interface; other site 224914003325 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 224914003326 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914003327 substrate binding pocket; other site 224914003328 membrane-bound complex binding site; other site 224914003329 hinge residues; other site 224914003330 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 224914003331 active site 224914003332 cystathionine beta-lyase; Provisional; Region: PRK05967 224914003333 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 224914003334 homodimer interface; other site 224914003335 substrate-cofactor binding pocket; other site 224914003336 pyridoxal 5'-phosphate binding site; other site 224914003337 catalytic residue; other site 224914003338 Bacterial SH3 domain; Region: SH3_3; cl02551 224914003339 TIR domain; Region: TIR; cl02060 224914003340 Domain of unknown function (DUF955); Region: DUF955; cl01076 224914003341 Integrase core domain; Region: rve; cl01316 224914003342 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 224914003343 TnsA endonuclease N terminal; Region: TnsA_N; cl07370 224914003344 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 224914003345 non-specific DNA binding site; other site 224914003346 salt bridge; other site 224914003347 sequence-specific DNA binding site; other site 224914003348 Uncharacterized conserved protein [Function unknown]; Region: COG4933 224914003349 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside...; Region: NK; cl11962 224914003350 This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three...; Region: ERI-1_3'hExo_like; cd06133 224914003351 active site 224914003352 substrate binding site; other site 224914003353 catalytic site; other site 224914003354 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 224914003355 L-lactate permease; Region: Lactate_perm; cl00701 224914003356 L-lactate permease; Region: Lactate_perm; cl00701 224914003357 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 224914003358 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003359 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003360 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 224914003361 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914003362 Domain of unknown function DUF20; Region: UPF0118; cl00465 224914003363 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 224914003364 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine...; Region: PurM; cd02196 224914003365 dimerization interface; other site 224914003366 putative ATP binding site; other site 224914003367 phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent; Region: PurN; TIGR00639 224914003368 Formyl transferase; Region: Formyl_trans_N; cl00395 224914003369 Protein of unknown function (DUF992); Region: DUF992; pfam06186 224914003370 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 224914003371 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These...; Region: MopB_3; cd02766 224914003372 putative [4Fe-4S] binding site; other site 224914003373 putative molybdopterin cofactor binding site; other site 224914003374 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 224914003375 putative molybdopterin cofactor binding site; other site 224914003376 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 224914003377 Protein of unknown function (DUF519); Region: DUF519; cl04492 224914003378 Bacteriophage capsid protein [General function prediction only]; Region: COG5511 224914003379 Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf...; Region: RNase_T2_prok; cd01062 224914003380 B1 nucleotide binding pocket; other site 224914003381 B2 nucleotide binding pocket; other site 224914003382 CAS motifs; other site 224914003383 active site 224914003384 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 224914003385 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 224914003386 putative C-terminal domain interface; other site 224914003387 putative GSH binding site (G-site); other site 224914003388 putative dimer interface; other site 224914003389 GST_C family, unknown subfamily 6; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_C_6; cd03205 224914003390 putative N-terminal domain interface; other site 224914003391 putative dimer interface; other site 224914003392 putative substrate binding pocket (H-site); other site 224914003393 Surface antigen; Region: Surface_Ag_2; cl01155 224914003394 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003395 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 224914003396 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 224914003397 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 224914003398 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 224914003399 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 224914003400 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 224914003401 MoaE interaction surface; other site 224914003402 MoeB interaction surface; other site 224914003403 thiocarboxylated glycine; other site 224914003404 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 224914003405 MoaE homodimer interface; other site 224914003406 MoaD interaction; other site 224914003407 active site residues 224914003408 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3126 224914003409 META domain; Region: META; cl01245 224914003410 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 224914003411 active site 224914003412 multimer interface; other site 224914003413 DinB family; Region: DinB; cl00986 224914003414 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 224914003415 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 224914003416 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914003417 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 224914003418 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 224914003419 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 224914003420 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 224914003421 leucyl aminopeptidase; Provisional; Region: PRK00913 224914003422 interface (dimer of trimers); other site 224914003423 Substrate-binding/catalytic site; other site 224914003424 Zn-binding sites; other site 224914003425 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; cl12074 224914003426 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; cl12074 224914003427 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 224914003428 OstA-like protein; Region: OstA; cl00844 224914003429 Organic solvent tolerance protein; Region: OstA_C; pfam04453 224914003430 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 224914003431 SurA N-terminal domain; Region: SurA_N; pfam09312 224914003432 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 224914003433 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 224914003434 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 224914003435 S-adenosylmethionine binding site; other site 224914003436 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 224914003437 Peptidase family M23; Region: Peptidase_M23; pfam01551 224914003438 Predicted permeases [General function prediction only]; Region: RarD; COG2962 224914003439 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 224914003440 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 224914003441 active site 224914003442 catalytic residues; other site 224914003443 metal-binding site 224914003444 LeuA allosteric (dimerization) domain; Region: LeuA_dimer; pfam08502 224914003445 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 224914003446 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 224914003447 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914003448 HIGH motif; other site 224914003449 active site 224914003450 nucleotide binding site; other site 224914003451 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 224914003452 KMSKS motif; other site 224914003453 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 224914003454 LysE type translocator; Region: LysE; cl00565 224914003455 Uncharacterized ACR, COG2135; Region: DUF159; cl03646 224914003456 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...; Region: Nudix_Hydrolase; cl00447 224914003457 nudix motif; other site 224914003458 Protein of unknown function (DUF2385); Region: DUF2385; cl11490 224914003459 dihydroorotase; Validated; Region: PRK09060 224914003460 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 224914003461 active site 224914003462 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 224914003463 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 224914003464 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 224914003465 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 224914003466 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 224914003467 Recombination protein O N terminal; Region: RecO_N; pfam11967 224914003468 DNA repair protein RecO; Region: reco; TIGR00613 224914003469 Recombination protein O C terminal; Region: RecO_C; pfam02565 224914003470 GTP-binding protein Era; Reviewed; Region: era; PRK00089 224914003471 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 224914003472 G1 box; other site 224914003473 GTP/Mg2+ binding site; other site 224914003474 Switch I region; other site 224914003475 G2 box; other site 224914003476 Switch II region; other site 224914003477 G3 box; other site 224914003478 G4 box; other site 224914003479 G5 box; other site 224914003480 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 224914003481 ribonuclease III; Reviewed; Region: PRK12371 224914003482 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-...; Region: RIBOc; cd00593 224914003483 dimerization interface; other site 224914003484 active site 224914003485 metal-binding site 224914003486 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase...; Region: DSRM; cd00048 224914003487 dsRNA binding site; other site 224914003488 signal peptidase I; Provisional; Region: PRK10861 224914003489 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 224914003490 Catalytic site; other site 224914003491 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 224914003492 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 224914003493 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 224914003494 Cupin domain; Region: Cupin_2; cl09118 224914003495 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 224914003496 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 224914003497 Major Facilitator Superfamily; Region: MFS_1; pfam07690 224914003498 putative substrate translocation pore; other site 224914003499 coproporphyrinogen III oxidase; Provisional; Region: PRK13347 224914003500 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 224914003501 FeS/SAM binding site; other site 224914003502 HemN C-terminal region; Region: HemN_C; pfam06969 224914003503 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 224914003504 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 224914003505 ligand binding site; other site 224914003506 flexible hinge region; other site 224914003507 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 224914003508 putative switch regulator; other site 224914003509 non-specific DNA interactions; other site 224914003510 DNA binding site 224914003511 sequence specific DNA binding site; other site 224914003512 putative cAMP binding site; other site 224914003513 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914003514 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 224914003515 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 224914003516 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 224914003517 synthetase active site; other site 224914003518 NTP binding site; other site 224914003519 metal-binding site 224914003520 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named...; Region: TGS_RelA_SpoT; cd01668 224914003521 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 224914003522 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl00765 224914003523 LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback...; Region: LabA_like; cd06167 224914003524 putative metal binding site; other site 224914003525 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 224914003526 SmpB protein; Region: SmpB; cl00482 224914003527 Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue...; Region: DHDPS; cd00950 224914003528 dihydrodipicolinate synthase; Region: dapA; TIGR00674 224914003529 dimer interface; other site 224914003530 active site 224914003531 catalytic residue; other site 224914003532 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 224914003533 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914003534 N-acetyl-D-glucosamine binding site; other site 224914003535 catalytic residue; other site 224914003536 Uncharacterized conserved protein [Function unknown]; Region: COG3743 224914003537 Porin subfamily; Region: Porin_2; pfam02530 224914003538 Porin subfamily; Region: Porin_2; pfam02530 224914003539 Phage integrase family; Region: Phage_integrase; pfam00589 224914003540 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 224914003541 DNA binding site 224914003542 Int/Topo IB signature motif; other site 224914003543 active site 224914003544 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 224914003545 pyridoxal 5'-phosphate binding site; other site 224914003546 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 224914003547 pyridoxal 5'-phosphate binding pocket; other site 224914003548 catalytic residue; other site 224914003549 Protein of unknown function (DUF423); Region: DUF423; cl01008 224914003550 Uncharacterized conserved protein [Function unknown]; Region: COG1284 224914003551 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 224914003552 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; cl01951 224914003553 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen...; Region: GST_N_Ure2p_like; cd03048 224914003554 glutathione S-transferase; Provisional; Region: PRK13972 224914003555 C-terminal domain interface; other site 224914003556 GSH binding site (G-site); other site 224914003557 dimer interface; other site 224914003558 GST_C family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen...; Region: GST_C_Ure2p_like; cd03178 224914003559 dimer interface; other site 224914003560 N-terminal domain interface; other site 224914003561 putative substrate binding pocket (H-site); other site 224914003562 AMP nucleosidase; Provisional; Region: PRK08292 224914003563 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 224914003564 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 224914003565 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 224914003566 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 224914003567 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003568 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 224914003569 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 224914003570 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 224914003571 Major Facilitator Superfamily; Region: MFS_1; pfam07690 224914003572 putative substrate translocation pore; other site 224914003573 EamA-like transporter family; Region: EamA; cl01037 224914003574 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 224914003575 aminopeptidase N; Provisional; Region: pepN; PRK14015 224914003576 Peptidase family M1; Region: Peptidase_M1; pfam01433 224914003577 PAS fold; Region: PAS_3; pfam08447 224914003578 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 224914003579 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 224914003580 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914003581 dimer interface; other site 224914003582 phosphorylation site 224914003583 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 224914003584 ATP binding site; other site 224914003585 Mg2+ binding site; other site 224914003586 G-X-G motif; other site 224914003587 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 224914003588 O-Antigen ligase; Region: Wzy_C; cl04850 224914003589 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional; Region: PRK14108 224914003590 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 224914003591 metal binding triad; other site 224914003592 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 224914003593 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 224914003594 metal binding triad; other site 224914003595 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 224914003596 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 224914003597 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914003598 dimer interface; other site 224914003599 phosphorylation site 224914003600 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 224914003601 ATP binding site; other site 224914003602 Mg2+ binding site; other site 224914003603 G-X-G motif; other site 224914003604 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 224914003605 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 224914003606 active site 224914003607 phosphorylation site 224914003608 intermolecular recognition site; other site 224914003609 dimerization interface; other site 224914003610 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914003611 DNA binding site 224914003612 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 224914003613 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic...; Region: Tryp_SPc; cl00149 224914003614 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 224914003615 protein binding site; other site 224914003616 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-...; Region: PDZ_serine_protease; cd00987 224914003617 protein binding site; other site 224914003618 Cytochrome C biogenesis protein; Region: CcmH; cl01179 224914003619 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 224914003620 CcmE; Region: CcmE; cl00994 224914003621 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 224914003622 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 224914003623 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 224914003624 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 224914003625 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 224914003626 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 224914003627 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 224914003628 ATP binding site; other site 224914003629 Mg2+ binding site; other site 224914003630 G-X-G motif; other site 224914003631 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 224914003632 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 224914003633 active site 224914003634 phosphorylation site 224914003635 intermolecular recognition site; other site 224914003636 dimerization interface; other site 224914003637 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914003638 DNA binding site 224914003639 NlpC/P60 family; Region: NLPC_P60; cl11438 224914003640 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 224914003641 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 224914003642 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 224914003643 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 224914003644 Phage-related minor tail protein [Function unknown]; Region: COG5281 224914003645 Protein of unknown function (DUF3356); Region: DUF3356; pfam11836 224914003646 Phage major tail protein 2; Region: Phage_tail_2; cl11463 224914003647 Phage portal protein; Region: Phage_portal; cl01923 224914003648 phage portal protein, HK97 family; Region: portal_HK97; TIGR01537 224914003649 Uncharacterized conserved protein [Function unknown]; Region: COG5323 224914003650 Transglycosylase; Region: Transgly; cl07896 224914003651 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 224914003652 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 224914003653 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 224914003654 Protein of unknown function (DUF1254); Region: DUF1254; cl02257 224914003655 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5330 224914003656 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 224914003657 Protein of unknown function (DUF1491); Region: DUF1491; cl11568 224914003658 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914003659 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914003660 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 224914003661 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans...; Region: HisKA; cd00082 224914003662 dimer interface; other site 224914003663 phosphorylation site 224914003664 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 224914003665 ATP binding site; other site 224914003666 Mg2+ binding site; other site 224914003667 G-X-G motif; other site 224914003668 Flavin Reductases; Region: FlaRed; cl00801 224914003669 Fe-S metabolism associated domain; Region: SufE; cl00951 224914003670 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 224914003671 amidase; Provisional; Region: PRK07056 224914003672 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 224914003673 DnaA box-binding interface; other site 224914003674 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; cl11561 224914003675 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 224914003676 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914003677 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 224914003678 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 224914003679 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 224914003680 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914003681 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914003682 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 224914003683 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914003684 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 224914003685 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 224914003686 putative substrate translocation pore; other site 224914003687 Transcriptional regulators [Transcription]; Region: FadR; COG2186 224914003688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914003689 DNA binding site 224914003690 FCD domain; Region: FCD; cl11656 224914003691 CorA-like Mg2+ transporter protein; Region: CorA; cl00459 224914003692 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 224914003693 SpoVT / AbrB like domain; Region: SpoVT_AbrB; cl00877 224914003694 Fic/DOC family; Region: Fic; cl00960 224914003695 transcription elongation factor regulatory protein; Validated; Region: PRK06342 224914003696 C-term; Region: GreA_GreB; pfam01272 224914003697 L-asparaginase II; Region: Asparaginase_II; cl01842 224914003698 transcriptional regulator BetI; Validated; Region: PRK00767 224914003699 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914003700 choline dehydrogenase; Validated; Region: PRK02106 224914003701 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914003702 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914003703 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914003704 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 224914003705 NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1; Region: ALDH_F9_TMBADH; cd07090 224914003706 tetrameric interface; other site 224914003707 NAD binding site; other site 224914003708 catalytic residues; other site 224914003709 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 224914003710 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914003711 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 224914003712 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 224914003713 DNA binding site 224914003714 domain linker motif; other site 224914003715 Periplasmic sugar-binding domain of uncharacterized transport systems; Region: PBP1_uncharacterized_sugar_binding; cd06307 224914003716 putative ligand binding site; other site 224914003717 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 224914003718 D-xylulose kinase; Region: XylB; TIGR01312 224914003719 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 224914003720 L-rhamnose isomerase (RhaA); Region: RhaA; cl09945 224914003721 xylose isomerase; Region: PLN02923 224914003722 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914003723 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003724 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914003725 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 224914003726 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cl12060 224914003727 DNA interaction; other site 224914003728 Metal-binding active site; metal-binding site 224914003729 AP endonuclease family 2 C terminus; Region: AP_endonuc_2_N; pfam07582 224914003730 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 224914003731 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Region: PBP1_ABC_sugar_binding_like_3; cd06311 224914003732 putative ligand binding site; other site 224914003733 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914003734 TM-ABC transporter signature motif; other site 224914003735 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 224914003736 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914003737 Walker A/P-loop; other site 224914003738 ATP binding site; other site 224914003739 Q-loop/lid; other site 224914003740 ABC transporter signature motif; other site 224914003741 Walker B; other site 224914003742 D-loop; other site 224914003743 H-loop/switch region; other site 224914003744 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_II; cd03215 224914003745 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 224914003746 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule...; Region: GT1_like_4; cd03795 224914003747 putative ADP-binding pocket; other site 224914003748 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cd00249 224914003749 dimerization interface; other site 224914003750 putative active cleft; other site 224914003751 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 224914003752 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 224914003753 Substrate binding site; other site 224914003754 Cupin domain; Region: Cupin_2; cl09118 224914003755 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 224914003756 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 224914003757 active site 224914003758 substrate binding site; other site 224914003759 metal-binding site 224914003760 putative transposase OrfB; Reviewed; Region: PHA02517 224914003761 Integrase core domain; Region: rve; cl01316 224914003762 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003763 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003764 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003765 Integrase core domain; Region: rve; cl01316 224914003766 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003767 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003768 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 224914003769 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 224914003770 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003771 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003772 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003773 Integrase core domain; Region: rve; cl01316 224914003774 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003775 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003776 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003777 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 224914003778 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 224914003779 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 224914003780 inhibitor-cofactor binding pocket; inhibition site 224914003781 pyridoxal 5'-phosphate binding site; other site 224914003782 catalytic residue; other site 224914003783 ABC-2 type transporter; Region: ABC2_membrane; cl11417 224914003784 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 224914003785 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides...; Region: ABC_KpsT_Wzt; cd03220 224914003786 Walker A/P-loop; other site 224914003787 ATP binding site; other site 224914003788 Q-loop/lid; other site 224914003789 ABC transporter signature motif; other site 224914003790 Walker B; other site 224914003791 D-loop; other site 224914003792 H-loop/switch region; other site 224914003793 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 224914003794 Formyl transferase; Region: Formyl_trans_N; cl00395 224914003795 Integrase core domain; Region: rve; cl01316 224914003796 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003797 Integrase core domain; Region: rve; cl01316 224914003798 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914003799 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine...; Region: GT_WbpL_WbcO_like; cd06854 224914003800 Mg++ binding site; other site 224914003801 putative catalytic motif; other site 224914003802 putative substrate binding site; other site 224914003803 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 224914003804 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003805 Protein of unknown function (DUF2793); Region: DUF2793; pfam10983 224914003806 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU)...; Region: TLP_HIUase; cd05822 224914003807 active site 224914003808 homotetramer interface; other site 224914003809 Ureidoglycolate hydrolase [Nucleotide transport and metabolism]; Region: DAL3; COG3194 224914003810 Ureidoglycolate hydrolase; Region: Ureidogly_hydro; cl01250 224914003811 BioY family; Region: BioY; cl00560 224914003812 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 224914003813 Protein of unknown function (DUF1499); Region: DUF1499; cl01841 224914003814 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 224914003815 pyruvate phosphate dikinase; Provisional; Region: PRK09279 224914003816 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 224914003817 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 224914003818 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 224914003819 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914003820 Cation efflux family; Region: Cation_efflux; cl00316 224914003821 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 224914003822 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 224914003823 Walker A/P-loop; other site 224914003824 ATP binding site; other site 224914003825 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 224914003826 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 224914003827 ABC transporter signature motif; other site 224914003828 Walker B; other site 224914003829 D-loop; other site 224914003830 H-loop/switch region; other site 224914003831 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 224914003832 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 224914003833 Protein of unknown function (DUF721); Region: DUF721; cl02324 224914003834 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 224914003835 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 224914003836 minor groove reading motif; other site 224914003837 helix-hairpin-helix signature motif; other site 224914003838 substrate binding pocket; other site 224914003839 active site 224914003840 FES domain; Region: FES; smart00525 224914003841 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 224914003842 DNA binding and oxoG recognition site 224914003843 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 224914003844 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914003845 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914003846 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 224914003847 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 224914003848 Cl- selectivity filter; other site 224914003849 Cl- binding residues; other site 224914003850 pore gating glutamate residue; other site 224914003851 dimer interface; other site 224914003852 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair; cl10010 224914003853 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 224914003854 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 224914003855 active site 224914003856 motif I; other site 224914003857 motif II; other site 224914003858 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 224914003859 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 224914003860 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 224914003861 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants...; Region: Thr-synth_2; cd01560 224914003862 pyridoxal 5'-phosphate binding site; other site 224914003863 catalytic residue; other site 224914003864 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 224914003865 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 224914003866 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 224914003867 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 224914003868 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914003869 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 224914003870 PAS fold; Region: PAS_3; pfam08447 224914003871 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914003872 metal-binding site 224914003873 active site 224914003874 I-site; other site 224914003875 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 224914003876 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 224914003877 Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4233 224914003878 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 224914003879 catalytic triad; other site 224914003880 dimer interface; other site 224914003881 RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack...; Region: RnaseH; cd06222 224914003882 RNA/DNA hybrid binding site; other site 224914003883 active site 224914003884 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 224914003885 Phosphotransferase enzyme family; Region: APH; pfam01636 224914003886 putative active site; other site 224914003887 putative substrate binding site; other site 224914003888 ATP binding site; other site 224914003889 LytB protein; Region: LYTB; cl00507 224914003890 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 224914003891 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 224914003892 Protein of unknown function (DUF983); Region: DUF983; cl02211 224914003893 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 224914003894 Subunit III/VIIa interface; other site 224914003895 Phospholipid binding site; other site 224914003896 Subunit I/III interface; other site 224914003897 Subunit III/VIb interface; other site 224914003898 Subunit III/VIa interface; other site 224914003899 Subunit III/Vb interface; other site 224914003900 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 224914003901 UbiA prenyltransferase family; Region: UbiA; cl00337 224914003902 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 224914003903 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 224914003904 Subunit I/III interface; other site 224914003905 D-pathway; other site 224914003906 Subunit I/VIIc interface; other site 224914003907 Subunit I/IV interface; other site 224914003908 Subunit I/II interface; other site 224914003909 Low-spin heme (heme a) binding site; other site 224914003910 Subunit I/VIIa interface; other site 224914003911 Subunit I/VIa interface; other site 224914003912 Dimer interface; other site 224914003913 Putative water exit pathway; other site 224914003914 Binuclear center (heme a3/CuB); other site 224914003915 K-pathway; other site 224914003916 Subunit I/Vb interface; other site 224914003917 Putative proton exit pathway; other site 224914003918 Subunit I/VIb interface; other site 224914003919 Subunit I/VIc interface; other site 224914003920 Electron transfer pathway; other site 224914003921 Subunit I/VIIIb interface; other site 224914003922 Subunit I/VIIb interface; other site 224914003923 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 224914003924 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 224914003925 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl10078 224914003926 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 224914003927 Putative modulator of DNA gyrase; Region: PmbA_TldD; cl00398 224914003928 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and...; Region: GMPK; cd00071 224914003929 catalytic site; other site 224914003930 G-X2-G-X-G-K; other site 224914003931 hypothetical protein; Provisional; Region: PRK11820 224914003932 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 224914003933 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 224914003934 YceG-like family; Region: YceG; pfam02618 224914003935 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 224914003936 dimerization interface; other site 224914003937 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 224914003938 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 224914003939 dimer interface; other site 224914003940 active site 224914003941 Phosphopantetheine attachment site; Region: PP-binding; cl09936 224914003942 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003943 3-ketoacyl-(acyl-carrier-protein) reductase NodG; Reviewed; Region: PRK12936 224914003944 Acyl transferase domain; Region: Acyl_transf_1; cl08282 224914003945 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 224914003946 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 224914003947 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 224914003948 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 224914003949 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 224914003950 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 224914003951 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 224914003952 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 224914003953 S-adenosylmethionine binding site; other site 224914003954 replicative DNA helicase; Provisional; Region: PRK09165 224914003955 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 224914003956 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 224914003957 Walker A motif; other site 224914003958 ATP binding site; other site 224914003959 Walker B motif; other site 224914003960 DNA binding loops 224914003961 DNA repair protein RadA; Provisional; Region: PRK11823 224914003962 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 224914003963 Walker A motif/ATP binding site; other site 224914003964 ATP binding site; other site 224914003965 Walker B motif; other site 224914003966 Colicin V production protein; Region: Colicin_V; cl00567 224914003967 amidophosphoribosyltransferase; Provisional; Region: PRK09123 224914003968 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 224914003969 active site 224914003970 tetramer interface; other site 224914003971 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914003972 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914003973 short chain dehydrogenase; Provisional; Region: PRK08945 224914003974 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 224914003975 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 224914003976 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 224914003977 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914003978 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 224914003979 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 224914003980 Walker A/P-loop; other site 224914003981 ATP binding site; other site 224914003982 Q-loop/lid; other site 224914003983 ABC transporter signature motif; other site 224914003984 Walker B; other site 224914003985 D-loop; other site 224914003986 H-loop/switch region; other site 224914003987 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 224914003988 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cl00107 224914003989 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; cl01604 224914003990 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 224914003991 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 224914003992 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914003993 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 224914003994 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 224914003995 RNA binding surface; other site 224914003996 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 224914003997 S-adenosylmethionine binding site; other site 224914003998 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 224914003999 TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products with important pharmaceutical activity. DXS...; Region: TPP_DXS; cd02007 224914004000 TPP-binding site; other site 224914004001 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 224914004002 PYR/PP interface; other site 224914004003 dimer interface; other site 224914004004 TPP binding site; other site 224914004005 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 224914004006 Pirin-related protein [General function prediction only]; Region: COG1741 224914004007 Cupin domain; Region: Cupin_2; cl09118 224914004008 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 224914004009 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 224914004010 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 224914004011 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 224914004012 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 224914004013 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 224914004014 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 224914004015 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 224914004016 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 224914004017 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cl00522 224914004018 dimerization interface; other site 224914004019 active site 224914004020 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 224914004021 Tetramer interface; other site 224914004022 active site 224914004023 FMN-binding site; other site 224914004024 Protein of unknown function (DUF1344); Region: DUF1344; pfam07076 224914004025 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 224914004026 putative acyl-acceptor binding pocket; other site 224914004027 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 224914004028 DNA binding site 224914004029 RNA-binding motif; other site 224914004030 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 224914004031 catalytic core; other site 224914004032 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 224914004033 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004034 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 224914004035 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 224914004036 HSP70 interaction site; other site 224914004037 DnaJ C terminal region; Region: DnaJ_C; pfam01556 224914004038 DnaJ C terminal region; Region: DnaJ_C; pfam01556 224914004039 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 224914004040 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 224914004041 Pyridoxine 5'-phosphate oxidase C-terminal dimerization region; Region: PNPOx_C; pfam10590 224914004042 UbiA prenyltransferase family; Region: UbiA; cl00337 224914004043 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 224914004044 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 224914004045 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914004046 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 224914004047 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914004048 metal-binding site 224914004049 active site 224914004050 I-site; other site 224914004051 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914004052 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 224914004053 active site 224914004054 enoyl-CoA hydratase; Provisional; Region: PRK05980 224914004055 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 224914004056 substrate binding site; other site 224914004057 oxyanion hole (OAH) forming residues; other site 224914004058 trimer interface; other site 224914004059 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 224914004060 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 224914004061 FAD binding domain; Region: FAD_binding_4; cl10516 224914004062 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 224914004063 SUA5 domain; Region: SUA5; pfam03481 224914004064 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 224914004065 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 224914004066 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 224914004067 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 224914004068 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 224914004069 dimer interface; other site 224914004070 motif 1; other site 224914004071 active site 224914004072 motif 2; other site 224914004073 motif 3; other site 224914004074 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 224914004075 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 224914004076 binding surface 224914004077 TPR motif; other site 224914004078 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 224914004079 binding surface 224914004080 TPR motif; other site 224914004081 octaprenyl-diphosphate synthase; Region: PLN02857 224914004082 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 224914004083 substrate binding pocket; other site 224914004084 chain length determination region; other site 224914004085 substrate-Mg2+ binding site; other site 224914004086 catalytic residues; other site 224914004087 aspartate-rich region 1; other site 224914004088 active site lid residues 224914004089 aspartate-rich region 2; other site 224914004090 Protein of unknown function (DUF2007); Region: DUF2007; pfam09413 224914004091 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 224914004092 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914004093 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 224914004094 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 224914004095 tandem repeat interface; other site 224914004096 oligomer interface; other site 224914004097 active site residues 224914004098 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 224914004099 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 224914004100 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 224914004101 active site 224914004102 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 224914004103 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 224914004104 FeS/SAM binding site; other site 224914004105 bacterial Ribonuclease HII-like; Region: RNaseH_typeII_bacteria_HII_like; cd07182 224914004106 active site 224914004107 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 224914004108 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 224914004109 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 224914004110 ATP synthase subunit C; Region: ATP-synt_C; cl00466 224914004111 ATP synthase A chain; Region: ATP-synt_A; cl00413 224914004112 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 224914004113 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 224914004114 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 224914004115 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 224914004116 GTP-binding protein EngA; Reviewed; Region: engA; PRK00093 224914004117 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 224914004118 G1 box; other site 224914004119 GTP/Mg2+ binding site; other site 224914004120 Switch I region; other site 224914004121 G2 box; other site 224914004122 Switch II region; other site 224914004123 G3 box; other site 224914004124 G4 box; other site 224914004125 G5 box; other site 224914004126 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 224914004127 G1 box; other site 224914004128 GTP/Mg2+ binding site; other site 224914004129 Switch I region; other site 224914004130 G2 box; other site 224914004131 G3 box; other site 224914004132 Switch II region; other site 224914004133 G4 box; other site 224914004134 G5 box; other site 224914004135 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 224914004136 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 224914004137 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914004138 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 224914004139 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 224914004140 Predicted membrane protein [Function unknown]; Region: COG4129 224914004141 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 224914004142 putative catalytic residues; other site 224914004143 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 224914004144 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 224914004145 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914004146 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 224914004147 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 224914004148 DNA binding site 224914004149 active site 224914004150 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914004151 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914004152 NAD(P) binding site; other site 224914004153 catalytic residues; other site 224914004154 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a...; Region: DsbA_Com1_like; cd03023 224914004155 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 224914004156 catalytic residues; other site 224914004157 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 224914004158 metal binding site 2; metal-binding site 224914004159 putative DNA binding helix; other site 224914004160 metal binding site 1; metal-binding site 224914004161 dimer interface; other site 224914004162 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the...; Region: cbb3_Oxidase_I; cd01661 224914004163 Low-spin heme binding site; other site 224914004164 Putative water exit pathway; other site 224914004165 Binuclear center (active site); other site 224914004166 Putative proton exit pathway; other site 224914004167 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 224914004168 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 224914004169 Cytochrome c; Region: Cytochrom_C; cl11414 224914004170 Cytochrome c; Region: Cytochrom_C; cl11414 224914004171 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 224914004172 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 224914004173 FixH; Region: FixH; cl01254 224914004174 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 224914004175 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 224914004176 metal-binding site 224914004177 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 224914004178 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 224914004179 motif II; other site 224914004180 MOFRL family; Region: MOFRL; cl01013 224914004181 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 224914004182 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 224914004183 active site 224914004184 Predicted membrane protein [Function unknown]; Region: COG3748 224914004185 Protein of unknown function (DUF989); Region: DUF989; pfam06181 224914004186 Cytochrome c; Region: Cytochrom_C; cl11414 224914004187 transcriptional activator TtdR; Provisional; Region: PRK09801 224914004188 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004189 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 224914004190 putative effector binding pocket; other site 224914004191 dimerization interface; other site 224914004192 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 224914004193 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 224914004194 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 224914004195 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; pfam01315 224914004196 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 224914004197 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 224914004198 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 224914004199 FAD binding domain; Region: FAD_binding_4; cl10516 224914004200 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 224914004201 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 224914004202 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 224914004203 OHCU decarboxylase; Region: OHCU_decarbox; cl01251 224914004204 hypothetical protein; Provisional; Region: PRK11171 224914004205 Cupin domain; Region: Cupin_2; cl09118 224914004206 Cupin domain; Region: Cupin_2; cl09118 224914004207 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl00710 224914004208 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914004209 DctM-like transporters; Region: DctM; pfam06808 224914004210 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 224914004211 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 224914004212 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 224914004213 active site 224914004214 phosphorylation site 224914004215 intermolecular recognition site; other site 224914004216 dimerization interface; other site 224914004217 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914004218 DNA binding residues 224914004219 dimerization interface; other site 224914004220 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 224914004221 Cache domain; Region: Cache_2; pfam08269 224914004222 Histidine kinase; Region: HisKA_3; pfam07730 224914004223 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 224914004224 ATP binding site; other site 224914004225 Mg2+ binding site; other site 224914004226 G-X-G motif; other site 224914004227 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 224914004228 multidrug efflux protein; Reviewed; Region: PRK01766 224914004229 MatE; Region: MatE; pfam01554 224914004230 MatE; Region: MatE; pfam01554 224914004231 Proline racemase [Amino acid transport and metabolism]; Region: COG3938 224914004232 hydroxyproline-2-epimerase; Provisional; Region: PRK13971; cl11700 224914004233 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 224914004234 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004235 NAD(P) binding pocket; other site 224914004236 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 224914004237 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 224914004238 dimer interface; other site 224914004239 active site 224914004240 pyridoxal 5'-phosphate (PLP) binding site; other site 224914004241 catalytic residues; other site 224914004242 substrate binding site; other site 224914004243 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 224914004244 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 224914004245 FAD binding pocket; other site 224914004246 FAD binding motif; other site 224914004247 phosphate binding motif; other site 224914004248 beta-alpha-beta structure motif; other site 224914004249 NAD binding pocket; other site 224914004250 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 224914004251 active site 224914004252 oligomerization interface; other site 224914004253 metal-binding site 224914004254 pantoate--beta-alanine ligase; Region: panC; TIGR00018 224914004255 Pantoate-beta-alanine ligase; Region: PanC; cd00560 224914004256 active site 224914004257 ATP-binding site; other site 224914004258 pantoate-binding site; other site 224914004259 Alpha/beta hydrolase of unknown function (DUF900); Region: DUF900; cl09214 224914004260 LrgB-like family; Region: LrgB; cl00596 224914004261 LrgA family; Region: LrgA; cl00608 224914004262 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914004263 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004264 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 224914004265 putative dimerization interface; other site 224914004266 Glycosyltransferase family 29 (sialyltransferase); Region: Glyco_transf_29; pfam00777 224914004267 2-oxoacid ferredoxin oxidoreductase; Provisional; Region: PRK13030 224914004268 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 224914004269 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 224914004270 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 224914004271 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), 8-amino-7-...; Region: KBL_like; cd06454 224914004272 substrate-cofactor binding pocket; other site 224914004273 pyridoxal 5'-phosphate binding site; other site 224914004274 catalytic residue; other site 224914004275 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 224914004276 Sodium:solute symporter family; Region: SSF; cl00456 224914004277 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 224914004278 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cl00080 224914004279 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 224914004280 ATP binding site; other site 224914004281 Mg2+ binding site; other site 224914004282 G-X-G motif; other site 224914004283 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 224914004284 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 224914004285 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 224914004286 active site 224914004287 phosphorylation site 224914004288 intermolecular recognition site; other site 224914004289 dimerization interface; other site 224914004290 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914004291 DNA binding residues 224914004292 dimerization interface; other site 224914004293 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 224914004294 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914004295 Protein of unknown function (DUF952); Region: DUF952; cl01393 224914004296 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD...; Region: DHOD_2_like; cd04738 224914004297 quinone interaction residues; other site 224914004298 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 224914004299 active site 224914004300 catalytic residues; other site 224914004301 FMN binding site; other site 224914004302 substrate binding site; other site 224914004303 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 224914004304 MatE; Region: MatE; pfam01554 224914004305 MatE; Region: MatE; pfam01554 224914004306 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 224914004307 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 224914004308 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 224914004309 conserved cys residue; other site 224914004310 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 224914004311 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 224914004312 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 224914004313 O-succinylhomoserine sulfhydrylase; Reviewed; Region: PRK07504 224914004314 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 224914004315 homodimer interface; other site 224914004316 substrate-cofactor binding pocket; other site 224914004317 pyridoxal 5'-phosphate binding site; other site 224914004318 catalytic residue; other site 224914004319 Protein of unknown function (DUF525); Region: DUF525; cl01119 224914004320 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 224914004321 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 224914004322 dimerization interface; other site 224914004323 domain crossover interface; other site 224914004324 redox-dependent activation switch; other site 224914004325 ornithine carbamoyltransferase; Provisional; Region: PRK00779 224914004326 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 224914004327 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 224914004328 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 224914004329 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 224914004330 inhibitor-cofactor binding pocket; inhibition site 224914004331 pyridoxal 5'-phosphate binding site; other site 224914004332 catalytic residue; other site 224914004333 GcrA cell cycle regulator; Region: GcrA; cl11564 224914004334 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 224914004335 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914004336 dimer interface; other site 224914004337 phosphorylation site 224914004338 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 224914004339 ATP binding site; other site 224914004340 Mg2+ binding site; other site 224914004341 G-X-G motif; other site 224914004342 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 224914004343 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 224914004344 CESA_like_2 is a member of the cellulose synthase superfamily; Region: CESA_like_2; cd06427 224914004345 DXD motif; other site 224914004346 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 224914004347 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914004348 substrate binding pocket; other site 224914004349 membrane-bound complex binding site; other site 224914004350 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 224914004351 Protein export membrane protein; Region: SecD_SecF; cl14618 224914004352 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 224914004353 The M14 family of metallocarboxypeptidases (MCPs) are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key...; Region: Peptidase_M14_like; cl11393 224914004354 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 224914004355 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914004356 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 224914004357 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 224914004358 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914004359 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 224914004360 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 224914004361 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 224914004362 motif II; other site 224914004363 Predicted deacylase [General function prediction only]; Region: COG3608 224914004364 An uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the the M14 family of metallocarboxypeptidases. This subgroup includes Pseudomonas aeruginosa AotO and related proteins. ASTE...; Region: M14_PaAOTO_like; cd06250 224914004365 putative active site; other site 224914004366 Zn-binding site; other site 224914004367 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 224914004368 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 224914004369 active site 224914004370 dimer interface; other site 224914004371 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 224914004372 dimer interface; other site 224914004373 active site 224914004374 Polyketide cyclase / dehydrase and lipid transport; Region: Polyketide_cyc2; cl10449 224914004375 putative oxidoreductase; Provisional; Region: PRK11749 224914004376 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004377 dihydropyrimidine dehydrogenase; Validated; Region: PRK08318 224914004378 Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and...; Region: DHPD_FMN; cd02940 224914004379 homodimer interface; other site 224914004380 active site 224914004381 FMN binding site; other site 224914004382 substrate binding site; other site 224914004383 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl00255 224914004384 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_31; cd04690 224914004385 nudix motif; other site 224914004386 YcdC-like protein, C-terminal region; Region: TetR_C_3; pfam08362 224914004387 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914004388 allantoate amidohydrolase; Reviewed; Region: PRK12893 224914004389 Peptidase dimerization domain; Region: M20_dimer; cl09126 224914004390 phenylhydantoinase; Validated; Region: PRK08323 224914004391 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like...; Region: D-HYD; cd01314 224914004392 tetramer interface; other site 224914004393 active site 224914004394 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 224914004395 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914004396 sensory histidine kinase AtoS; Provisional; Region: PRK11360 224914004397 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 224914004398 ATP binding site; other site 224914004399 Mg2+ binding site; other site 224914004400 G-X-G motif; other site 224914004401 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914004402 UreF; Region: UreF; cl00531 224914004403 Urease accessory protein UreE [Posttranslational modification, protein turnover, chaperones]; Region: UreE; COG2371 224914004404 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-...; Region: UreE; cd00571 224914004405 dimer interface; other site 224914004406 catalytic residues; other site 224914004407 urease subunit alpha; Reviewed; Region: ureC; PRK13207 224914004408 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 224914004409 subunit interactions; other site 224914004410 active site 224914004411 flap region; other site 224914004412 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_beta; cd00407 224914004413 gamma-beta subunit interface; other site 224914004414 alpha-beta subunit interface; other site 224914004415 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 224914004416 alpha-gamma subunit interface; other site 224914004417 beta-gamma subunit interface; other site 224914004418 UreD urease accessory protein; Region: UreD; cl00530 224914004419 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 224914004420 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 224914004421 catalytic residues; other site 224914004422 catalytic nucleophile; other site 224914004423 Synaptic Antiparallel dimer interface; other site 224914004424 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 224914004425 DNA-binding interface; DNA binding site 224914004426 BRO family, N-terminal domain; Region: Bro-N; pfam02498 224914004427 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 224914004428 INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence...; Region: INT_SG2_C; cd01184 224914004429 Int/Topo IB signature motif; other site 224914004430 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 224914004431 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 224914004432 hinge; other site 224914004433 active site 224914004434 Protein of unknown function (DUF2948); Region: DUF2948; pfam11164 224914004435 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 224914004436 E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent oxidation of L-histidinol to L...; Region: Histidinol_dh; cd06572 224914004437 NAD binding site; other site 224914004438 dimerization interface; other site 224914004439 product binding site; other site 224914004440 substrate binding site; other site 224914004441 zinc binding site; other site 224914004442 catalytic residues; other site 224914004443 Uncharacterized protein family (UPF0262); Region: UPF0262; cl11489 224914004444 Low molecular weight phosphatase family; Region: LMWPc; cd00115 224914004445 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 224914004446 active site 224914004447 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 224914004448 rRNA binding site; other site 224914004449 predicted 30S ribosome binding site; other site 224914004450 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 224914004451 active site 224914004452 dimer interface; other site 224914004453 Domain of unknown function (DUF329); Region: DUF329; cl01144 224914004454 TIR domain; Region: TIR; cl02060 224914004455 GcrA cell cycle regulator; Region: GcrA; cl11564 224914004456 Domain of unknown function (DUF955); Region: DUF955; cl01076 224914004457 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; cl00743 224914004458 conjugative transfer relaxase protein TraI; Region: TraI_TIGR; TIGR02760 224914004459 DNA primase, catalytic core; Region: dnaG; TIGR01391 224914004460 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl01302 224914004461 integrase; Provisional; Region: PRK09692 224914004462 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 224914004463 Int/Topo IB signature motif; other site 224914004464 active site 224914004465 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 224914004466 Human rTS beta is encoded by the rTS gene which, through alternative RNA splicing, also encodes rTS alpha whose mRNA is complementary to thymidylate synthase mRNA. rTS beta expression is associated with the production of small molecules that appear to...; Region: rTSbeta_L-fuconate_dehydratase; cd03324 224914004467 putative active site pocket; other site 224914004468 metal-binding site 224914004469 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 224914004470 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 224914004471 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004472 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 224914004473 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914004474 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004475 Domain of unknown function (DUF718); Region: DUF718; cl01281 224914004476 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 224914004477 Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues...; Region: MR_like; cd03316 224914004478 active site pocket 224914004479 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 224914004480 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 224914004481 Walker A/P-loop; other site 224914004482 ATP binding site; other site 224914004483 Q-loop/lid; other site 224914004484 ABC transporter signature motif; other site 224914004485 Walker B; other site 224914004486 D-loop; other site 224914004487 H-loop/switch region; other site 224914004488 TOBE domain; Region: TOBE_2; cl01440 224914004489 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914004490 dimer interface; other site 224914004491 conserved gate region; other site 224914004492 putative PBP binding loops; other site 224914004493 ABC-ATPase subunit interface; other site 224914004494 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914004495 dimer interface; other site 224914004496 conserved gate region; other site 224914004497 putative PBP binding loops; other site 224914004498 ABC-ATPase subunit interface; other site 224914004499 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 224914004500 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914004501 Transcriptional regulator [Transcription]; Region: IclR; COG1414 224914004502 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004503 Bacterial transcriptional regulator; Region: IclR; pfam01614 224914004504 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 224914004505 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 224914004506 Sarcosine oxidase, gamma subunit family; Region: SoxG; cl01893 224914004507 sarcosine oxidase, alpha subunit family, heterotetrameric form; Region: soxA; TIGR01372 224914004508 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 224914004509 Sarcosine oxidase, delta subunit family; Region: SoxD; cl01767 224914004510 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004511 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 224914004512 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 224914004513 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 224914004514 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 224914004515 NAD(P) binding site; other site 224914004516 nitrobindin heme-binding domain; Region: nitrobindin; cl10502 224914004517 heme-binding site; other site 224914004518 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914004519 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 224914004520 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914004521 ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]; Region: OpuBA; COG1125 224914004522 OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family...; Region: ABC_OpuCA_Osmoprotection; cd03295 224914004523 Walker A/P-loop; other site 224914004524 ATP binding site; other site 224914004525 Q-loop/lid; other site 224914004526 ABC transporter signature motif; other site 224914004527 Walker B; other site 224914004528 D-loop; other site 224914004529 H-loop/switch region; other site 224914004530 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 224914004531 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914004532 dimer interface; other site 224914004533 conserved gate region; other site 224914004534 putative PBP binding loops; other site 224914004535 ABC-ATPase subunit interface; other site 224914004536 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 224914004537 DNA binding residues 224914004538 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 224914004539 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 224914004540 metal-binding site 224914004541 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 224914004542 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 224914004543 metal-binding site 224914004544 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 224914004545 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914004546 PAS domain S-box; Region: sensory_box; TIGR00229 224914004547 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 224914004548 PAS domain S-box; Region: sensory_box; TIGR00229 224914004549 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 224914004550 putative active site; other site 224914004551 heme pocket; other site 224914004552 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914004553 metal-binding site 224914004554 active site 224914004555 I-site; other site 224914004556 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 224914004557 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 224914004558 dimer interface; other site 224914004559 substrate binding site; other site 224914004560 ATP binding site; other site 224914004561 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004562 FAD dependent oxidoreductase; Region: DAO; pfam01266 224914004563 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004564 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 224914004565 thiS-thiF/thiG interaction site; other site 224914004566 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 224914004567 ThiS interaction site; other site 224914004568 putative active site; other site 224914004569 tetramer interface; other site 224914004570 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-...; Region: TMP_TenI; cd00564 224914004571 active site 224914004572 thiamine phosphate binding site; other site 224914004573 pyrophosphate binding site; other site 224914004574 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 224914004575 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914004576 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl00527 224914004577 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914004578 Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like; Region: ALDH_KGSADH-YcbD; cd07097 224914004579 NAD(P) binding site; other site 224914004580 catalytic residues; other site 224914004581 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914004582 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914004583 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14270 224914004584 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914004585 ATP binding site; other site 224914004586 Q-loop/lid; other site 224914004587 ABC transporter signature motif; other site 224914004588 Walker B; other site 224914004589 D-loop; other site 224914004590 H-loop/switch region; other site 224914004591 Transcriptional regulators [Transcription]; Region: PurR; COG1609 224914004592 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 224914004593 DNA binding site 224914004594 domain linker motif; other site 224914004595 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 224914004596 putative dimerization interface; other site 224914004597 putative ligand binding site; other site 224914004598 Protein of unknown function (DUF779); Region: DUF779; cl01432 224914004599 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 224914004600 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD3; cd08297 224914004601 NAD binding site; other site 224914004602 substrate binding site; other site 224914004603 catalytic Zn binding site; other site 224914004604 tetramer interface; other site 224914004605 structural Zn binding site; other site 224914004606 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 224914004607 Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like; Region: ALDH_ACDHII-AcoD; cd07116 224914004608 NAD(P) binding site; other site 224914004609 catalytic residues; other site 224914004610 GAF domain; Region: GAF; cl00853 224914004611 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 224914004612 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 224914004613 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004614 DNA-binding transcriptional repressor GlpR; Provisional; Region: PRK10906 224914004615 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004616 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 224914004617 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 224914004618 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914004619 DNA binding residues 224914004620 dimerization interface; other site 224914004621 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 224914004622 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 224914004623 ligand binding site; other site 224914004624 flexible hinge region; other site 224914004625 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004626 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 224914004627 active site 224914004628 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 224914004629 CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which...; Region: CysN_ATPS; cd04166 224914004630 CysD dimerization site; other site 224914004631 G1 box; other site 224914004632 putative GEF interaction site; other site 224914004633 GTP/Mg2+ binding site; other site 224914004634 Switch I region; other site 224914004635 G2 box; other site 224914004636 G3 box; other site 224914004637 Switch II region; other site 224914004638 G4 box; other site 224914004639 G5 box; other site 224914004640 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of...; Region: CysN_NodQ_II; cd03695 224914004641 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of...; Region: CysN_NoDQ_III; cd04095 224914004642 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation...; Region: APSK; cd02027 224914004643 ligand-binding site; other site 224914004644 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 224914004645 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 224914004646 Active Sites; active site 224914004647 aminotransferase; Provisional; Region: PRK06105 224914004648 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 224914004649 inhibitor-cofactor binding pocket; inhibition site 224914004650 pyridoxal 5'-phosphate binding site; other site 224914004651 catalytic residue; other site 224914004652 Autoinducer binding domain; Region: Autoind_bind; pfam03472 224914004653 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914004654 DNA binding residues 224914004655 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 224914004656 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]; Region: MHT1; cl14105 224914004657 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 224914004658 substrate binding pocket; other site 224914004659 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 224914004660 B12 binding site; other site 224914004661 cobalt ligand; other site 224914004662 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 224914004663 BA14K-like protein; Region: BA14K; pfam07886 224914004664 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 224914004665 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 224914004666 active site 224914004667 DNA binding site 224914004668 Stress responsive A/B Barrel Domain; Region: Dabb; pfam07876 224914004669 Bacterial protein of unknown function (DUF934); Region: DUF934; cl01526 224914004670 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 224914004671 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 224914004672 Active Sites; active site 224914004673 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 224914004674 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 224914004675 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 224914004676 Protein of unknown function (DUF2849); Region: DUF2849; pfam11011 224914004677 siroheme synthase, N-terminal domain; Region: cysG_Nterm; TIGR01470 224914004678 Sirohaem synthase dimerization region; Region: CysG_dimerizer; pfam10414 224914004679 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914004680 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 224914004681 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 224914004682 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 224914004683 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 224914004684 FeS/SAM binding site; other site 224914004685 HemN C-terminal region; Region: HemN_C; pfam06969 224914004686 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-...; Region: HAM1; cd00515 224914004687 active site 224914004688 dimerization interface; other site 224914004689 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914004690 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914004691 ribonuclease PH; Reviewed; Region: rph; PRK00173 224914004692 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 224914004693 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 224914004694 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 224914004695 HrcA protein C terminal domain; Region: HrcA; pfam01628 224914004696 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 224914004697 dimer interface; other site 224914004698 hsp70 (ATPase domain) interactions; other site 224914004699 Predicted membrane protein [Function unknown]; Region: COG2860 224914004700 UPF0126 domain; Region: UPF0126; pfam03458 224914004701 UPF0126 domain; Region: UPF0126; pfam03458 224914004702 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 224914004703 substrate binding site; other site 224914004704 ATP binding site; other site 224914004705 Protein of unknown function (DUF540); Region: DUF540; cl01126 224914004706 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 224914004707 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 224914004708 minor groove reading motif; other site 224914004709 helix-hairpin-helix signature motif; other site 224914004710 substrate binding pocket; other site 224914004711 active site 224914004712 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 224914004713 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 224914004714 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein...; Region: ACD_IbpA-B_like; cd06470 224914004715 putative dimer interface; other site 224914004716 Protein of unknown function (DUF1150); Region: DUF1150; cl11577 224914004717 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 224914004718 active site 224914004719 phosphorylation site 224914004720 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 224914004721 30S subunit binding site; other site 224914004722 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 224914004723 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 224914004724 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 224914004725 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 224914004726 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 224914004727 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 224914004728 Walker A/P-loop; other site 224914004729 ATP binding site; other site 224914004730 Q-loop/lid; other site 224914004731 ABC transporter signature motif; other site 224914004732 Walker B; other site 224914004733 D-loop; other site 224914004734 H-loop/switch region; other site 224914004735 OstA-like protein; Region: OstA; cl00844 224914004736 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 224914004737 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 224914004738 tandem repeat interface; other site 224914004739 oligomer interface; other site 224914004740 active site residues 224914004741 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher...; Region: HU_IHF; cd00591 224914004742 IHF dimer interface; other site 224914004743 IHF - DNA interface; other site 224914004744 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 224914004745 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 224914004746 S-adenosylmethionine binding site; other site 224914004747 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 224914004748 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 224914004749 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 224914004750 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 224914004751 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl00357 224914004752 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 224914004753 MutS domain I; Region: MutS_I; pfam01624 224914004754 MutS domain II; Region: MutS_II; pfam05188 224914004755 MutS domain III; Region: MutS_III; cl04977 224914004756 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 224914004757 Walker A/P-loop; other site 224914004758 ATP binding site; other site 224914004759 Q-loop/lid; other site 224914004760 ABC transporter signature motif; other site 224914004761 Walker B; other site 224914004762 D-loop; other site 224914004763 H-loop/switch region; other site 224914004764 Malic enzyme, N-terminal domain; Region: malic; pfam00390 224914004765 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 224914004766 putative NAD(P) binding site; other site 224914004767 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 224914004768 PII uridylyl-transferase; Provisional; Region: PRK05092 224914004769 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 224914004770 metal binding triad; other site 224914004771 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 224914004772 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 224914004773 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 224914004774 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 224914004775 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 224914004776 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 224914004777 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 224914004778 active site 224914004779 HIGH motif; other site 224914004780 dimer interface; other site 224914004781 KMSKS motif; other site 224914004782 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 224914004783 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 224914004784 NifU-like domain; Region: NifU; cl00484 224914004785 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914004786 Protein of unknown function (DUF1052); Region: DUF1052; cl02197 224914004787 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 224914004788 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 224914004789 active site 224914004790 phosphorylation site 224914004791 intermolecular recognition site; other site 224914004792 dimerization interface; other site 224914004793 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914004794 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914004795 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 224914004796 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 224914004797 ATP binding site; other site 224914004798 Mg2+ binding site; other site 224914004799 G-X-G motif; other site 224914004800 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 224914004801 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; cl12029 224914004802 ATP binding site; other site 224914004803 putative Mg++ binding site; other site 224914004804 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 224914004805 nucleotide binding region; other site 224914004806 ATP-binding site; other site 224914004807 Helicase associated domain (HA2); Region: HA2; cl04503 224914004808 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 224914004809 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 224914004810 substrate binding site; other site 224914004811 catalytic Zn binding site; other site 224914004812 NAD binding site; other site 224914004813 structural Zn binding site; other site 224914004814 dimer interface; other site 224914004815 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914004816 Protein of unknown function (DUF1345); Region: DUF1345; cl01753 224914004817 Predicted esterase [General function prediction only]; Region: COG0627 224914004818 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914004819 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 224914004820 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 224914004821 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 224914004822 anchoring element; other site 224914004823 dimer interface; other site 224914004824 ATP binding site; other site 224914004825 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of...; Region: TOPRIM_TopoIIA_GyrB; cd03366 224914004826 active site 224914004827 putative metal-binding site; other site 224914004828 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 224914004829 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 224914004830 DEAD-like helicases superfamily; Region: DEXDc; smart00487 224914004831 ATP binding site; other site 224914004832 Mg++ binding site; other site 224914004833 motif III; other site 224914004834 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 224914004835 nucleotide binding region; other site 224914004836 ATP-binding site; other site 224914004837 ATP-dependent helicase HepA; Validated; Region: PRK04914 224914004838 DbpA RNA binding domain; Region: DbpA; pfam03880 224914004839 DNA polymerase I; Provisional; Region: PRK05755 224914004840 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and...; Region: 53EXOc; cd00008 224914004841 metal binding site I; metal-binding site 224914004842 putative ssDNA interaction site; other site 224914004843 metal binding site II; metal-binding site 224914004844 The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E.coli-like Polymerase I (pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-...; Region: DNA_polA_I_Ecoli_like_exo; cd06139 224914004845 active site 224914004846 catalytic site; other site 224914004847 substrate binding site; other site 224914004848 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 224914004849 active site 224914004850 DNA binding site 224914004851 catalytic site; other site 224914004852 Peptidase dimerization domain; Region: M20_dimer; cl09126 224914004853 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 224914004854 Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and...; Region: RNaseD_exo; cd06142 224914004855 putative active site; other site 224914004856 catalytic site; other site 224914004857 putative substrate binding site; other site 224914004858 Surface antigen; Region: Surface_Ag_2; cl01155 224914004859 Surface antigen; Region: Surface_Ag_2; cl01155 224914004860 Transglycosylase; Region: Transgly; cl07896 224914004861 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 224914004862 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01039 224914004863 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914004864 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 224914004865 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 224914004866 putative substrate binding site; other site 224914004867 putative ATP binding site; other site 224914004868 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 224914004869 S-adenosylmethionine binding site; other site 224914004870 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 224914004871 hypothetical protein; Provisional; Region: PRK10281 224914004872 Nicotinic acid phosphoribosyltransferase [Coenzyme metabolism]; Region: PncB; COG1488 224914004873 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl12019 224914004874 active site 224914004875 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 224914004876 Protein of unknown function (DUF3131); Region: DUF3131; pfam11329 224914004877 Uncharacterized protein conserved in bacteria (DUF2329); Region: DUF2329; pfam10091 224914004878 Putative carbohydrate binding domain; Region: CBM_X; pfam06204 224914004879 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 224914004880 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 224914004881 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 224914004882 Putative carbohydrate binding domain; Region: CBM_X; pfam06204 224914004883 Glycosyltransferase family 36; Region: Glyco_transf_36; pfam06165 224914004884 Glycosyltransferase 36 associated family; Region: GT36_AF; pfam06205 224914004885 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 224914004886 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 224914004887 Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute...; Region: ABC_CysA_sulfate_importer; cd03296 224914004888 Walker A/P-loop; other site 224914004889 ATP binding site; other site 224914004890 Q-loop/lid; other site 224914004891 ABC transporter signature motif; other site 224914004892 Walker B; other site 224914004893 D-loop; other site 224914004894 H-loop/switch region; other site 224914004895 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914004896 dimer interface; other site 224914004897 conserved gate region; other site 224914004898 putative PBP binding loops; other site 224914004899 ABC-ATPase subunit interface; other site 224914004900 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914004901 dimer interface; other site 224914004902 conserved gate region; other site 224914004903 putative PBP binding loops; other site 224914004904 ABC-ATPase subunit interface; other site 224914004905 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914004906 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 224914004907 putative active site; other site 224914004908 Domain of Unknown Function (DUF930); Region: DUF930; pfam06059 224914004909 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004910 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; Region: REC; cl09944 224914004911 Dehydratase family; Region: ILVD_EDD; cl00340 224914004912 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 224914004913 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 224914004914 catalytic residues; other site 224914004915 central insert; other site 224914004916 Heme exporter protein D (CcmD); Region: CcmD; cl11475 224914004917 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 224914004918 CcmB protein; Region: CcmB; cl01016 224914004919 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 224914004920 CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH); Region: ABC_CcmA_heme_exporter; cd03231 224914004921 Walker A/P-loop; other site 224914004922 ATP binding site; other site 224914004923 Q-loop/lid; other site 224914004924 ABC transporter signature motif; other site 224914004925 Walker B; other site 224914004926 D-loop; other site 224914004927 H-loop/switch region; other site 224914004928 aconitate hydratase; Validated; Region: PRK09277 224914004929 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 224914004930 substrate binding site; other site 224914004931 ligand binding site; other site 224914004932 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 224914004933 substrate binding site; other site 224914004934 Protein of unknown function (DUF1223); Region: DUF1223; cl10501 224914004935 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 224914004936 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 224914004937 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914004938 Coenzyme A binding pocket; other site 224914004939 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cd06181 224914004940 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 224914004941 Predicted permease; Region: FtsX; cl11418 224914004942 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 224914004943 active site 224914004944 catalytic triad; other site 224914004945 oxyanion hole; other site 224914004946 switch loop; other site 224914004947 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 224914004948 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 224914004949 2',5' RNA ligase family; Region: 2_5_RNA_ligase; pfam02834 224914004950 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 224914004951 Low molecular weight phosphatase family; Region: LMWPc; cd00115 224914004952 active site 224914004953 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 224914004954 aromatic arch; other site 224914004955 DCoH dimer interaction site; other site 224914004956 DCoH /HNF-1 dimer interaction site; other site 224914004957 DCoH tetramer interaction site; other site 224914004958 substrate binding site; other site 224914004959 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 224914004960 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 224914004961 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl14056 224914004962 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 224914004963 LysE type translocator; Region: LysE; cl00565 224914004964 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 224914004965 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 224914004966 ANP binding site; other site 224914004967 Substrate Binding Site II; other site 224914004968 Substrate Binding Site I; other site 224914004969 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 224914004970 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 224914004971 YadA-like C-terminal region; Region: YadA; pfam03895 224914004972 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 224914004973 Cell division inhibitor SulA; Region: SulA; cl01880 224914004974 DNA Polymerase Y-family; Region: Pol_Y_like; cd03468 224914004975 active site 224914004976 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 224914004977 DNA binding site 224914004978 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 224914004979 DNA polymerase alpha chain like domain; Region: POLIIIAc; cl02625 224914004980 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 224914004981 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli...; Region: DnaE_OBF; cd04485 224914004982 generic binding surface II; other site 224914004983 generic binding surface I; other site 224914004984 Haemolysin-III related; Region: HlyIII; cl03831 224914004985 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914004986 N-acetyl-D-glucosamine binding site; other site 224914004987 catalytic residue; other site 224914004988 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 224914004989 ATPase; Provisional; Region: PRK13764 224914004990 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside...; Region: NK; cl11962 224914004991 active site 224914004992 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 224914004993 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914004994 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914004995 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914004996 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 224914004997 putative effector binding pocket; other site 224914004998 putative dimerization interface; other site 224914004999 phosphoglucomutase; Region: PLN02307 224914005000 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one...; Region: PGM1; cd03085 224914005001 substrate binding site; other site 224914005002 dimer interface; other site 224914005003 active site 224914005004 metal-binding site 224914005005 Domain of unknown function DUF59; Region: DUF59; cl00941 224914005006 putative ATPase; Provisional; Region: PRK11670 224914005007 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 224914005008 Walker A motif; other site 224914005009 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914005010 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914005011 Reeler-like domain of YcnI and similar proteins; Region: YcnI_like; cd08545 224914005012 Protein of unknown function (DUF461); Region: DUF461; cl01071 224914005013 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914005014 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 224914005015 Family of unknown function (DUF490); Region: DUF490; pfam04357 224914005016 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 224914005017 Surface antigen; Region: Bac_surface_Ag; cl03097 224914005018 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 224914005019 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 224914005020 Subunit I/III interface; other site 224914005021 Subunit III/IV interface; other site 224914005022 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 224914005023 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 224914005024 D-pathway; other site 224914005025 Putative ubiquinol binding site; other site 224914005026 Low-spin heme (heme b) binding site; other site 224914005027 Putative water exit pathway; other site 224914005028 Binuclear center (heme o3/CuB); other site 224914005029 K-pathway; other site 224914005030 Putative proton exit pathway; other site 224914005031 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 224914005032 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl10078 224914005033 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 224914005034 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 224914005035 putative MPT binding site; other site 224914005036 Cytochrome c; Region: Cytochrom_C; cl11414 224914005037 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 224914005038 Ligand binding site; other site 224914005039 oligomer interface; other site 224914005040 prephenate dehydratase; Provisional; Region: PRK11899 224914005041 Prephenate dehydratase; Region: PDT; pfam00800 224914005042 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 224914005043 putative L-Phe binding site; other site 224914005044 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 224914005045 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 224914005046 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 224914005047 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 224914005048 putative NADH binding site; other site 224914005049 putative active site; other site 224914005050 nudix motif; other site 224914005051 putative metal binding site; other site 224914005052 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the...; Region: HIT_like; cl00228 224914005053 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 224914005054 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914005055 Walker A motif; other site 224914005056 ATP binding site; other site 224914005057 Walker B motif; other site 224914005058 arginine finger; other site 224914005059 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 224914005060 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 224914005061 Uncharacterized BCR, YbaB family COG0718; Region: DUF149; cl00494 224914005062 recombination protein RecR; Reviewed; Region: recR; PRK00076 224914005063 RecR protein; Region: RecR; pfam02132 224914005064 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 224914005065 putative active site; other site 224914005066 putative metal-binding site; other site 224914005067 tetramer interface; other site 224914005068 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 224914005069 lytic murein transglycosylase; Region: MltB_2; TIGR02283 224914005070 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 224914005071 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914005072 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 224914005073 putative dimerization interface; other site 224914005074 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 224914005075 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 224914005076 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 224914005077 RNA binding site; other site 224914005078 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 224914005079 RNA binding site; other site 224914005080 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 224914005081 RNA binding site; other site 224914005082 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 224914005083 RNA binding site; other site 224914005084 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain...; Region: S1_like; cl09927 224914005085 RNA binding site; other site 224914005086 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec6; cd05691 224914005087 RNA binding site; other site 224914005088 cytidylate kinase; Provisional; Region: cmk; PRK00023 224914005089 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 224914005090 CMP-binding site; other site 224914005091 The sites determining sugar specificity; other site 224914005092 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 224914005093 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form 5-enolpyruvylshkimate-3-...; Region: EPSP_synthase; cd01556 224914005094 hinge; other site 224914005095 active site 224914005096 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 224914005097 Predicted acyltransferases [Lipid metabolism]; Region: COG1835; cl00792 224914005098 Acyltransferase family; Region: Acyl_transf_3; pfam01757 224914005099 CHRD domain; Region: CHRD; cl06473 224914005100 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 224914005101 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 224914005102 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914005103 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914005104 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 224914005105 isovaleryl-CoA dehydrogenase; Region: PLN02519 224914005106 substrate binding site; other site 224914005107 FAD binding site; other site 224914005108 catalytic base; other site 224914005109 3-methylcrotonyl-CoA carboxylase; Region: PLN02820 224914005110 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 224914005111 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 224914005112 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 224914005113 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914005114 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 224914005115 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 224914005116 carboxyltransferase (CT) interaction site; other site 224914005117 biotinylation site; other site 224914005118 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 224914005119 active site 224914005120 catalytic residues; other site 224914005121 metal-binding site 224914005122 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 224914005123 substrate binding site; other site 224914005124 oxyanion hole (OAH) forming residues; other site 224914005125 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 224914005126 trimer interface; other site 224914005127 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; cl11392 224914005128 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914005129 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 224914005130 dimerization interface; other site 224914005131 ligand binding site; other site 224914005132 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 224914005133 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_14; cd08497 224914005134 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 224914005135 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_14; cd08497 224914005136 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005137 dimer interface; other site 224914005138 conserved gate region; other site 224914005139 putative PBP binding loops; other site 224914005140 ABC-ATPase subunit interface; other site 224914005141 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005142 dimer interface; other site 224914005143 conserved gate region; other site 224914005144 putative PBP binding loops; other site 224914005145 ABC-ATPase subunit interface; other site 224914005146 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 224914005147 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914005148 Walker A/P-loop; other site 224914005149 ATP binding site; other site 224914005150 Q-loop/lid; other site 224914005151 ABC transporter signature motif; other site 224914005152 Walker B; other site 224914005153 D-loop; other site 224914005154 H-loop/switch region; other site 224914005155 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914005156 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914005157 Walker A/P-loop; other site 224914005158 ATP binding site; other site 224914005159 Q-loop/lid; other site 224914005160 ABC transporter signature motif; other site 224914005161 Walker B; other site 224914005162 D-loop; other site 224914005163 H-loop/switch region; other site 224914005164 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914005165 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 224914005166 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005167 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 224914005168 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of...; Region: ThiF_MoeB_HesA_family; cd00757 224914005169 ATP binding site; other site 224914005170 substrate interface; other site 224914005171 RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication...; Region: ABC_RecF; cd03242 224914005172 Walker A/P-loop; other site 224914005173 ATP binding site; other site 224914005174 Q-loop/lid; other site 224914005175 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005176 ABC transporter signature motif; other site 224914005177 Walker B; other site 224914005178 D-loop; other site 224914005179 H-loop/switch region; other site 224914005180 DNA polymerase III subunit beta; Validated; Region: PRK05643 224914005181 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the...; Region: beta_clamp; cd00140 224914005182 putative DNA binding surface; other site 224914005183 dimer interface; other site 224914005184 beta-clamp/clamp loader binding surface; other site 224914005185 beta-clamp/translesion DNA polymerase binding surface; other site 224914005186 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 224914005187 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005188 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 224914005189 DnaA box-binding interface; other site 224914005190 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 224914005191 enoyl-CoA hydratase; Provisional; Region: PRK05980 224914005192 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 224914005193 substrate binding site; other site 224914005194 oxyanion hole (OAH) forming residues; other site 224914005195 trimer interface; other site 224914005196 formamidopyrimidine-DNA glycosylase; Validated; Region: PRK01103 224914005197 Formamidopyrimidine-DNA glycosylase N-terminal domain; Region: Fapy_DNA_glyco; pfam01149 224914005198 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 224914005199 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 224914005200 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein...; Region: Peptidase_M17; cd00433 224914005201 interface (dimer of trimers); other site 224914005202 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 224914005203 Substrate-binding/catalytic site; other site 224914005204 Zn-binding sites; other site 224914005205 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914005206 NlpC/P60 family; Region: NLPC_P60; cl11438 224914005207 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 224914005208 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914005209 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 224914005210 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005211 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 224914005212 Bacterial SH3 domain; Region: SH3_3; cl02551 224914005213 Bacterial SH3 domain; Region: SH3_3; cl02551 224914005214 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914005215 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 224914005216 metal binding site 2; metal-binding site 224914005217 putative DNA binding helix; other site 224914005218 metal binding site 1; metal-binding site 224914005219 dimer interface; other site 224914005220 structural Zn2+ binding site; other site 224914005221 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 224914005222 active site 1 224914005223 dimer interface; other site 224914005224 active site 2 224914005225 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 224914005226 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 224914005227 dimer interface; other site 224914005228 active site 224914005229 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005230 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 224914005231 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914005232 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 224914005233 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914005234 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 224914005235 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 224914005236 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 224914005237 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 224914005238 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 224914005239 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 224914005240 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 224914005241 putative nucleic acid binding region; other site 224914005242 G-X-X-G motif; other site 224914005243 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 224914005244 RNA binding site; other site 224914005245 domain interface; other site 224914005246 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole...; Region: Ribosomal_S15p_S13e; cd00353 224914005247 16S/18S rRNA binding site; other site 224914005248 S13e-L30e interaction site; other site 224914005249 25S rRNA binding site; other site 224914005250 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 224914005251 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 224914005252 RNA binding site; other site 224914005253 active site 224914005254 Ribosome-binding factor A; Region: RBFA; cl00542 224914005255 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 224914005256 translation initiation factor IF-2; Region: IF-2; TIGR00487 224914005257 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 224914005258 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 224914005259 G1 box; other site 224914005260 putative GEF interaction site; other site 224914005261 GTP/Mg2+ binding site; other site 224914005262 Switch I region; other site 224914005263 G2 box; other site 224914005264 G3 box; other site 224914005265 Switch II region; other site 224914005266 G4 box; other site 224914005267 G5 box; other site 224914005268 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the...; Region: IF2_mtIF2_II; cd03702 224914005269 Translation-initiation factor 2; Region: IF-2; pfam11987 224914005270 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation...; Region: mtIF2_IVc; cd03692 224914005271 hypothetical protein; Provisional; Region: PRK09190 224914005272 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cd00279 224914005273 putative RNA binding cleft; other site 224914005274 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 224914005275 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 224914005276 NusA N-terminal domain; Region: NusA_N; pfam08529 224914005277 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and...; Region: S1_NusA; cd04455 224914005278 RNA binding site; other site 224914005279 homodimer interface; other site 224914005280 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 224914005281 G-X-X-G motif; other site 224914005282 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 224914005283 hypothetical protein; Reviewed; Region: PRK00092 224914005284 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 224914005285 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members...; Region: Sm_like; cl00259 224914005286 Sm1 motif; other site 224914005287 D3 - B interaction site; other site 224914005288 D1 - D2 interaction site; other site 224914005289 Hfq - Hfq interaction site; other site 224914005290 RNA binding pocket; other site 224914005291 Sm2 motif; other site 224914005292 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914005293 S-adenosylmethionine synthetase; Validated; Region: PRK05250 224914005294 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 224914005295 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 224914005296 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 224914005297 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 224914005298 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 224914005299 non-specific DNA binding site; other site 224914005300 salt bridge; other site 224914005301 sequence-specific DNA binding site; other site 224914005302 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 224914005303 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 224914005304 putative active site; other site 224914005305 catalytic triad; other site 224914005306 putative dimer interface; other site 224914005307 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 224914005308 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 224914005309 Transporter associated domain; Region: CorC_HlyC; pfam03471 224914005310 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 224914005311 PhoH-like protein; Region: PhoH; cl12134 224914005312 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 224914005313 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 224914005314 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 224914005315 FeS/SAM binding site; other site 224914005316 TRAM domain; Region: TRAM; cl01282 224914005317 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 224914005318 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 224914005319 putative acyl-acceptor binding pocket; other site 224914005320 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 224914005321 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00443 224914005322 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 224914005323 Ferritin-like domain; Region: Ferritin; pfam00210 224914005324 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 224914005325 dimerization interface; other site 224914005326 DPS ferroxidase diiron center; other site 224914005327 ion pore; other site 224914005328 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 224914005329 Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer membrane]; Region: SleB; COG3773 224914005330 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 224914005331 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 224914005332 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 224914005333 active site 224914005334 phosphorylation site 224914005335 intermolecular recognition site; other site 224914005336 dimerization interface; other site 224914005337 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914005338 DNA binding site 224914005339 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 224914005340 PhoU domain; Region: PhoU; pfam01895 224914005341 PhoU domain; Region: PhoU; pfam01895 224914005342 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 224914005343 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 224914005344 Walker A/P-loop; other site 224914005345 ATP binding site; other site 224914005346 Q-loop/lid; other site 224914005347 ABC transporter signature motif; other site 224914005348 Walker B; other site 224914005349 D-loop; other site 224914005350 H-loop/switch region; other site 224914005351 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 224914005352 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005353 dimer interface; other site 224914005354 conserved gate region; other site 224914005355 putative PBP binding loops; other site 224914005356 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914005357 ABC-ATPase subunit interface; other site 224914005358 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 224914005359 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914005360 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005361 dimer interface; other site 224914005362 conserved gate region; other site 224914005363 putative PBP binding loops; other site 224914005364 ABC-ATPase subunit interface; other site 224914005365 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914005366 Protein of unknown function (DUF454); Region: DUF454; cl01063 224914005367 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 224914005368 Bacterial protein of unknown function (DUF920); Region: DUF920; cl01479 224914005369 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914005370 Walker A motif; other site 224914005371 ATP binding site; other site 224914005372 Walker B motif; other site 224914005373 arginine finger; other site 224914005374 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 224914005375 glutathione synthetase; Provisional; Region: PRK05246 224914005376 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 224914005377 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 224914005378 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 224914005379 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 224914005380 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 224914005381 active site 224914005382 dimer interface; other site 224914005383 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914005384 chaperone protein DnaJ; Provisional; Region: PRK10767 224914005385 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of...; Region: DnaJ; cd06257 224914005386 HSP70 interaction site; other site 224914005387 DnaJ C terminal region; Region: DnaJ_C; pfam01556 224914005388 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 224914005389 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914005390 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005391 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914005392 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 224914005393 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 224914005394 putative tRNA-binding site; other site 224914005395 B3/4 domain; Region: B3_4; cl11458 224914005396 tRNA synthetase B5 domain; Region: B5; cl08394 224914005397 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 224914005398 dimer interface; other site 224914005399 motif 1; other site 224914005400 motif 3; other site 224914005401 motif 2; other site 224914005402 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 224914005403 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 224914005404 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 224914005405 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 224914005406 dimer interface; other site 224914005407 motif 1; other site 224914005408 active site 224914005409 motif 2; other site 224914005410 motif 3; other site 224914005411 Ribosomal protein L20; Region: Ribosomal_L20; cl00393 224914005412 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 224914005413 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 224914005414 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 224914005415 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 224914005416 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 224914005417 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914005418 Uncharacterized protein involved in benzoate metabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BenE; COG3135 224914005419 Benzoate membrane transport protein; Region: BenE; cl09308 224914005420 Protein of unknown function (DUF2852); Region: DUF2852; pfam11014 224914005421 Protein of unknown function (DUF2852); Region: DUF2852; pfam11014 224914005422 Protein of unknown function DUF45; Region: DUF45; cl00636 224914005423 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 224914005424 putative active site; other site 224914005425 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric...; Region: PRAI; cd00405 224914005426 active site 224914005427 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 224914005428 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 224914005429 pyridoxal 5'-phosphate binding site; other site 224914005430 catalytic residue; other site 224914005431 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are...; Region: Tryptophan_synthase_alpha; cd04724 224914005432 substrate binding site; other site 224914005433 active site 224914005434 catalytic residues; other site 224914005435 heterodimer interface; other site 224914005436 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 224914005437 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 224914005438 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 224914005439 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 224914005440 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 224914005441 catalytic residues; other site 224914005442 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 224914005443 UvrD/REP helicase; Region: UvrD-helicase; cl14126 224914005444 UvrD/REP helicase; Region: UvrD-helicase; cl14126 224914005445 Domain of unknown function DUF83; Region: Cas_Cas4; cl00641 224914005446 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 224914005447 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 224914005448 Domain of unknown function DUF83; Region: Cas_Cas4; cl00641 224914005449 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 224914005450 Substrate binding site; other site 224914005451 metal-binding site 224914005452 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 224914005453 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 224914005454 sensory histidine kinase AtoS; Provisional; Region: PRK11360 224914005455 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914005456 dimer interface; other site 224914005457 phosphorylation site 224914005458 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 224914005459 ATP binding site; other site 224914005460 Mg2+ binding site; other site 224914005461 G-X-G motif; other site 224914005462 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 224914005463 S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; Region: AdoHcyase; cd00401 224914005464 oligomerization interface; other site 224914005465 active site 224914005466 NAD+ binding site; other site 224914005467 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 224914005468 dimerization domain swap beta strand; other site 224914005469 regulatory protein interface; other site 224914005470 active site 224914005471 regulatory phosphorylation site; other site 224914005472 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_man; cd00006 224914005473 active pocket/dimerization site; other site 224914005474 active site 224914005475 phosphorylation site 224914005476 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-...; Region: HprK_C; cd01918 224914005477 Hpr binding site; other site 224914005478 active site 224914005479 homohexamer subunit interaction site; other site 224914005480 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 224914005481 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 224914005482 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914005483 dimer interface; other site 224914005484 phosphorylation site 224914005485 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 224914005486 ATP binding site; other site 224914005487 Mg2+ binding site; other site 224914005488 G-X-G motif; other site 224914005489 proteobacterial dedicated sortase system response regulator; Region: marine_sort_RR; TIGR03787 224914005490 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 224914005491 active site 224914005492 phosphorylation site 224914005493 intermolecular recognition site; other site 224914005494 dimerization interface; other site 224914005495 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914005496 DNA binding site 224914005497 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 224914005498 phosphoenolpyruvate carboxykinase; Provisional; Region: PRK09344 224914005499 active site 224914005500 substrate-binding site; other site 224914005501 metal-binding site 224914005502 ATP binding site; other site 224914005503 RF-1 domain; Region: RF-1; cl02875 224914005504 pantothenate kinase; Provisional; Region: PRK05439 224914005505 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 224914005506 ATP-binding site; other site 224914005507 CoA-binding site; other site 224914005508 Mg2+-binding site; other site 224914005509 Phosphoribosyl-ATP pyrophosphohydrolase; Region: PRA-PH; cl00345 224914005510 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-; Region: HisF; cd04731 224914005511 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 224914005512 substrate binding site; other site 224914005513 glutamase interaction surface; other site 224914005514 Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]; Region: HisA; COG0106 224914005515 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 224914005516 catalytic residues; other site 224914005517 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 224914005518 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 224914005519 putative active site; other site 224914005520 oxyanion strand; other site 224914005521 catalytic triad; other site 224914005522 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 224914005523 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 224914005524 putative active site pocket; other site 224914005525 4-fold oligomerization interface; other site 224914005526 metal binding residues; metal-binding site 224914005527 3-fold/trimer interface; other site 224914005528 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 224914005529 active site 224914005530 HslU subunit interaction site; other site 224914005531 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 224914005532 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914005533 Walker A motif; other site 224914005534 ATP binding site; other site 224914005535 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005536 Protein of unknown function (DUF1402); Region: DUF1402; pfam07182 224914005537 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 224914005538 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl09100 224914005539 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 224914005540 Smr domain; Region: Smr; cl02619 224914005541 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 224914005542 MltA specific insert domain; Region: MltA; pfam03562 224914005543 3D domain; Region: 3D; cl01439 224914005544 Tim44-like domain; Region: Tim44; cl09208 224914005545 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 224914005546 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 224914005547 SecA binding site; other site 224914005548 Preprotein binding site; other site 224914005549 Proteobacterial; Region: dnaQ_proteo; TIGR01406 224914005550 This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (polIII) and similar proteins. PolIII is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten...; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 224914005551 active site 224914005552 substrate binding site; other site 224914005553 catalytic site; other site 224914005554 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 224914005555 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 224914005556 CoA-binding site; other site 224914005557 ATP-binding; other site 224914005558 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 224914005559 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 224914005560 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 224914005561 shikimate binding site; other site 224914005562 NAD(P) binding site; other site 224914005563 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 224914005564 active site 224914005565 dimer interface; other site 224914005566 Domain of unknown function (DUF299); Region: DUF299; cl00780 224914005567 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 224914005568 ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: ModC; COG4148 224914005569 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005570 Walker A/P-loop; other site 224914005571 ATP binding site; other site 224914005572 Q-loop/lid; other site 224914005573 ABC transporter signature motif; other site 224914005574 Walker B; other site 224914005575 D-loop; other site 224914005576 H-loop/switch region; other site 224914005577 TOBE domain; Region: TOBE_2; cl01440 224914005578 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005579 dimer interface; other site 224914005580 conserved gate region; other site 224914005581 putative PBP binding loops; other site 224914005582 ABC-ATPase subunit interface; other site 224914005583 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914005584 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 224914005585 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 224914005586 active site residue 224914005587 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 224914005588 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 224914005589 KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best...; Region: KDPG_aldolase; cd00452 224914005590 active site 224914005591 intersubunit interface; other site 224914005592 catalytic residue; other site 224914005593 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 224914005594 Peptidase M15; Region: Peptidase_M15_3; cl01194 224914005595 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 224914005596 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 224914005597 active site 224914005598 phosphorylation site 224914005599 intermolecular recognition site; other site 224914005600 dimerization interface; other site 224914005601 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914005602 Walker A motif; other site 224914005603 ATP binding site; other site 224914005604 Walker B motif; other site 224914005605 Bacterial regulatory protein, Fis family; Region: HTH_8; cl01091 224914005606 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 224914005607 Oligopeptidase F; Region: Peptidase_M3_N; pfam08439 224914005608 Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad...; Region: M3B_Oligoendopeptidase_F; cd06459 224914005609 active site 224914005610 zinc binding site; other site 224914005611 aminodeoxychorismate synthase; Provisional; Region: PRK07508 224914005612 chorismate binding enzyme; Region: Chorismate_bind; cl10555 224914005613 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 224914005614 Aminotransferase class IV; Region: Aminotran_4; pfam01063 224914005615 substrate-cofactor binding pocket; other site 224914005616 pyridoxal 5'-phosphate binding site; other site 224914005617 homodimer interface; other site 224914005618 catalytic residue; other site 224914005619 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 224914005620 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 224914005621 ferrochelatase; Reviewed; Region: hemH; PRK00035 224914005622 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 224914005623 C-terminal domain interface; other site 224914005624 active site 224914005625 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 224914005626 active site 224914005627 N-terminal domain interface; other site 224914005628 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 224914005629 NfeD-like; Region: NfeD; cl00686 224914005630 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 224914005631 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-...; Region: SIS_Kpsf; cd05014 224914005632 putative active site; other site 224914005633 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 224914005634 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; cl12051 224914005635 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 224914005636 active site 224914005637 tetramer interface; other site 224914005638 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases...; Region: lysozyme_like; cl00222 224914005639 lytic murein transglycosylase; Region: MltB_2; TIGR02283 224914005640 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914005641 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914005642 N-acetyl-D-glucosamine binding site; other site 224914005643 catalytic residue; other site 224914005644 TrbC/VIRB2 family; Region: TrbC; cl01583 224914005645 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 224914005646 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 224914005647 VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 224914005648 Type IV secretion system proteins; Region: T4SS; cl06849 224914005649 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 224914005650 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 224914005651 VirB8 protein; Region: VirB8; cl01500 224914005652 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 224914005653 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 224914005654 VirB7 interaction site; other site 224914005655 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 224914005656 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 224914005657 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial...; Region: VirB11-like_ATPase; cd01130 224914005658 Walker A motif; other site 224914005659 hexamer interface; other site 224914005660 ATP binding site; other site 224914005661 Walker B motif; other site 224914005662 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 224914005663 ligand binding site; other site 224914005664 SGNH_peri2; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known...; Region: SGNH_hydrolase_peri2; cd01829 224914005665 active site 224914005666 catalytic triad; other site 224914005667 oxyanion hole; other site 224914005668 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 224914005669 Amino acid permease; Region: AA_permease; pfam00324 224914005670 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 224914005671 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005672 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 224914005673 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-...; Region: GltS; cd00713 224914005674 active site 224914005675 dimer interface; other site 224914005676 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 224914005677 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant...; Region: GltS_FMN; cd02808 224914005678 active site 224914005679 FMN binding site; other site 224914005680 substrate binding site; other site 224914005681 3Fe-4S cluster binding site; other site 224914005682 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 224914005683 domain interface; other site 224914005684 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 224914005685 tetramer interface; other site 224914005686 pyridoxal 5'-phosphate binding site; other site 224914005687 catalytic residue; other site 224914005688 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 224914005689 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein...; Region: ACD_IbpA-B_like; cd06470 224914005690 putative dimer interface; other site 224914005691 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 224914005692 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914005693 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914005694 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates; Region: Bacterial_IMPase_like_1; cd01641 224914005695 active site 224914005696 N-formylglutamate amidohydrolase; Region: FGase; cl01522 224914005697 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 224914005698 active site 224914005699 phosphorylation site 224914005700 intermolecular recognition site; other site 224914005701 dimerization interface; other site 224914005702 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 224914005703 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 224914005704 active site 224914005705 phosphorylation site 224914005706 intermolecular recognition site; other site 224914005707 dimerization interface; other site 224914005708 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914005709 dimerization interface; other site 224914005710 DNA binding residues 224914005711 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans...; Region: HisKA; cd00082 224914005712 dimer interface; other site 224914005713 phosphorylation site 224914005714 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 224914005715 ATP binding site; other site 224914005716 Mg2+ binding site; other site 224914005717 G-X-G motif; other site 224914005718 MgtC family; Region: MgtC; pfam02308 224914005719 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 224914005720 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 224914005721 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 224914005722 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914005723 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 224914005724 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 224914005725 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 224914005726 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 224914005727 shikimate binding site; other site 224914005728 NAD(P) binding site; other site 224914005729 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 224914005730 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 224914005731 E3 interaction surface; other site 224914005732 lipoyl attachment site; other site 224914005733 e3 binding domain; Region: E3_binding; pfam02817 224914005734 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 224914005735 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 224914005736 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 224914005737 tetramer interface; other site 224914005738 TPP-binding site; other site 224914005739 heterodimer interface; other site 224914005740 phosphorylation loop region 224914005741 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 224914005742 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 224914005743 alpha subunit interface; other site 224914005744 TPP binding site; other site 224914005745 heterodimer interface; other site 224914005746 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 224914005747 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005748 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005749 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 224914005750 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914005751 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914005752 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914005753 Walker A/P-loop; other site 224914005754 ATP binding site; other site 224914005755 Q-loop/lid; other site 224914005756 ABC transporter signature motif; other site 224914005757 Walker B; other site 224914005758 D-loop; other site 224914005759 H-loop/switch region; other site 224914005760 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 224914005761 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 224914005762 Walker A/P-loop; other site 224914005763 ATP binding site; other site 224914005764 Q-loop/lid; other site 224914005765 ABC transporter signature motif; other site 224914005766 Walker B; other site 224914005767 D-loop; other site 224914005768 H-loop/switch region; other site 224914005769 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 224914005770 TM-ABC transporter signature motif; other site 224914005771 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 224914005772 TM-ABC transporter signature motif; other site 224914005773 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914005774 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914005775 Transcriptional regulators [Transcription]; Region: FadR; COG2186 224914005776 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914005777 DNA binding site 224914005778 FCD domain; Region: FCD; cl11656 224914005779 RNA polymerase sigma factor; Provisional; Region: PRK12539 224914005780 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 224914005781 Protein of unknown function (DUF1109); Region: DUF1109; cl02071 224914005782 pentapeptide MXKDX repeat protein; Region: penta_MxKDx; TIGR02953 224914005783 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 224914005784 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 224914005785 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 224914005786 Moco binding site; other site 224914005787 metal coordination site; other site 224914005788 Condensation domain; Region: Condensation; cl09290 224914005789 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 224914005790 chorismate binding enzyme; Region: Chorismate_bind; cl10555 224914005791 enterobactin synthase subunit E; Provisional; Region: entE; PRK10946 224914005792 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914005793 Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in...; Region: isochorismatase; cd01013 224914005794 hydrophobic substrate binding pocket; other site 224914005795 Isochorismatase family; Region: Isochorismatase; pfam00857 224914005796 active site 224914005797 conserved cis-peptide bond; other site 224914005798 Phosphopantetheine attachment site; Region: PP-binding; cl09936 224914005799 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914005800 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 224914005801 Phosphopantetheinyl transferase component of siderophore synthetase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: EntD; COG2977 224914005802 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 224914005803 Bacterial protein of unknown function (DUF922); Region: DUF922; cl02415 224914005804 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914005805 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914005806 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 224914005807 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914005808 Walker A/P-loop; other site 224914005809 ATP binding site; other site 224914005810 Q-loop/lid; other site 224914005811 ABC transporter signature motif; other site 224914005812 Walker B; other site 224914005813 D-loop; other site 224914005814 H-loop/switch region; other site 224914005815 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_II; cd03215 224914005816 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 224914005817 TM-ABC transporter signature motif; other site 224914005818 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 224914005819 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 224914005820 TM-ABC transporter signature motif; other site 224914005821 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 224914005822 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 224914005823 active site 224914005824 tetramer interface; other site 224914005825 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of...; Region: ribokinase; cd01174 224914005826 substrate binding site; other site 224914005827 dimer interface; other site 224914005828 ATP binding site; other site 224914005829 replication initiation protein RepC; Provisional; Region: PRK13824 224914005830 Replication protein C N-terminal domain; Region: RP-C; pfam03428 224914005831 Replication protein C C-terminal region; Region: RP-C_C; pfam11800 224914005832 plasmid partitioning protein RepB; Region: partition_RepB; TIGR03454 224914005833 ParB-like nuclease domain; Region: ParBc; cl02129 224914005834 plasmid partitioning protein RepA; Region: partition_RepA; TIGR03453 224914005835 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 224914005836 P-loop; other site 224914005837 Magnesium ion binding site; other site 224914005838 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following...; Region: ParA; cd02042 224914005839 P-loop; other site 224914005840 Magnesium ion binding site; other site 224914005841 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 224914005842 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 224914005843 FeS/SAM binding site; other site 224914005844 HemN C-terminal region; Region: HemN_C; pfam06969 224914005845 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 224914005846 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 224914005847 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914005848 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914005849 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914005850 Walker A/P-loop; other site 224914005851 ATP binding site; other site 224914005852 Q-loop/lid; other site 224914005853 ABC transporter signature motif; other site 224914005854 Walker B; other site 224914005855 D-loop; other site 224914005856 H-loop/switch region; other site 224914005857 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005858 Q-loop/lid; other site 224914005859 ABC transporter signature motif; other site 224914005860 Walker B; other site 224914005861 D-loop; other site 224914005862 H-loop/switch region; other site 224914005863 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005864 spermidine/putrescine ABC transporter ATP-binding subunit; Region: potA; TIGR01187 224914005865 Walker A/P-loop; other site 224914005866 ATP binding site; other site 224914005867 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 224914005868 TM-ABC transporter signature motif; other site 224914005869 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 224914005870 TM-ABC transporter signature motif; other site 224914005871 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914005872 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_5; cd06338 224914005873 putative ligand binding site; other site 224914005874 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 224914005875 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914005876 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 224914005877 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 224914005878 N-terminal plug; other site 224914005879 ligand-binding site; other site 224914005880 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 224914005881 ROK family; Region: ROK; cl09121 224914005882 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005883 dimer interface; other site 224914005884 conserved gate region; other site 224914005885 putative PBP binding loops; other site 224914005886 ABC-ATPase subunit interface; other site 224914005887 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 224914005888 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 224914005889 Walker A/P-loop; other site 224914005890 ATP binding site; other site 224914005891 Q-loop/lid; other site 224914005892 ABC transporter signature motif; other site 224914005893 Walker B; other site 224914005894 D-loop; other site 224914005895 H-loop/switch region; other site 224914005896 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 224914005897 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914005898 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 224914005899 Sulfatase; Region: Sulfatase; cl10460 224914005900 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 224914005901 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 224914005902 active site 224914005903 metal-binding site 224914005904 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 224914005905 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914005906 Walker A/P-loop; other site 224914005907 ATP binding site; other site 224914005908 Q-loop/lid; other site 224914005909 ABC transporter signature motif; other site 224914005910 Walker B; other site 224914005911 D-loop; other site 224914005912 H-loop/switch region; other site 224914005913 TOBE domain; Region: TOBE_2; cl01440 224914005914 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914005915 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914005916 dimer interface; other site 224914005917 conserved gate region; other site 224914005918 putative PBP binding loops; other site 224914005919 ABC-ATPase subunit interface; other site 224914005920 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 224914005921 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914005922 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 224914005923 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914005924 DNA binding site 224914005925 UTRA domain; Region: UTRA; cl06649 224914005926 Sulfite exporter TauE/SafE; Region: TauE; cl00498 224914005927 Protein of unknown function (DUF1634); Region: DUF1634; cl01741 224914005928 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914005929 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914005930 Walker A/P-loop; other site 224914005931 ATP binding site; other site 224914005932 Q-loop/lid; other site 224914005933 ABC transporter signature motif; other site 224914005934 Walker B; other site 224914005935 D-loop; other site 224914005936 H-loop/switch region; other site 224914005937 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 224914005938 TM-ABC transporter signature motif; other site 224914005939 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 224914005940 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 224914005941 Walker A/P-loop; other site 224914005942 ATP binding site; other site 224914005943 Q-loop/lid; other site 224914005944 ABC transporter signature motif; other site 224914005945 Walker B; other site 224914005946 D-loop; other site 224914005947 H-loop/switch region; other site 224914005948 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 224914005949 TM-ABC transporter signature motif; other site 224914005950 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914005951 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_7; cd06341 224914005952 putative ligand binding site; other site 224914005953 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 224914005954 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 224914005955 active site 224914005956 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914005957 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914005958 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 224914005959 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914005960 Transcriptional regulator [Transcription]; Region: IclR; COG1414 224914005961 Bacterial transcriptional regulator; Region: IclR; pfam01614 224914005962 Uncharacterized protein family (UPF0261); Region: UPF0261; cl02262 224914005963 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 224914005964 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 224914005965 motif II; other site 224914005966 hypothetical protein; Provisional; Region: PRK07481 224914005967 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 224914005968 inhibitor-cofactor binding pocket; inhibition site 224914005969 pyridoxal 5'-phosphate binding site; other site 224914005970 catalytic residue; other site 224914005971 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 224914005972 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 224914005973 inhibitor-cofactor binding pocket; inhibition site 224914005974 pyridoxal 5'-phosphate binding site; other site 224914005975 catalytic residue; other site 224914005976 Phosphotransferase enzyme family; Region: APH; pfam01636 224914005977 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 224914005978 active site 224914005979 ATP binding site; other site 224914005980 substrate binding site; other site 224914005981 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914005982 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 224914005983 putative substrate binding pocket; other site 224914005984 trimer interface; other site 224914005985 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 224914005986 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 224914005987 NAD binding site; other site 224914005988 catalytic residues; other site 224914005989 3,4-dihydroxyphenylacetate 2,3-dioxygenase; Region: HpaD; TIGR02295 224914005990 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914005991 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914005992 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 224914005993 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 224914005994 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Carbohydrate transport and metabolism]; Region: HpcH; COG3836 224914005995 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 224914005996 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914005997 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914005998 NAD(P) binding site; other site 224914005999 catalytic residues; other site 224914006000 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914006001 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 224914006002 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914006003 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006004 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006005 TM-ABC transporter signature motif; other site 224914006006 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 224914006007 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914006008 Walker A/P-loop; other site 224914006009 ATP binding site; other site 224914006010 Q-loop/lid; other site 224914006011 ABC transporter signature motif; other site 224914006012 Walker B; other site 224914006013 D-loop; other site 224914006014 H-loop/switch region; other site 224914006015 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 224914006016 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 224914006017 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 224914006018 putative ligand binding site; other site 224914006019 Uncharacterized conserved protein [Function unknown]; Region: COG3268 224914006020 autotransporter-associated beta strand repeat; Region: autotrns_rpt; TIGR02601 224914006021 autotransporter-associated beta strand repeat; Region: autotrns_rpt; TIGR02601 224914006022 adhesin; Provisional; Region: PRK09752 224914006023 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43...; Region: PL2_Passenger_AT; cd01344 224914006024 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 224914006025 Autotransporter beta-domain; Region: Autotransporter; cl02365 224914006026 adhesin; Provisional; Region: PRK09752 224914006027 flagellin; Reviewed; Region: PRK12687 224914006028 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 224914006029 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 224914006030 Flagellar basal body M-ring protein [Cell motility and secretion]; Region: fliF; COG1766 224914006031 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 224914006032 flagellar motor protein MotB; Validated; Region: motB; PRK05996 224914006033 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 224914006034 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 224914006035 ligand binding site; other site 224914006036 chemotaxis protein; Reviewed; Region: PRK12798 224914006037 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 224914006038 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 224914006039 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 224914006040 N-acetyl-D-glucosamine binding site; other site 224914006041 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 224914006042 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914006043 DNA binding site 224914006044 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 224914006045 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 224914006046 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 224914006047 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 224914006048 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 224914006049 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07521 224914006050 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 224914006051 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK06008 224914006052 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 224914006053 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 224914006054 Flagellar protein FlaF; Region: FlaF; cl11454 224914006055 Flagellar protein FlbT; Region: FlbT; cl11455 224914006056 Flagellar hook capping protein; Region: FlgD; cl04347 224914006057 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 224914006058 FHIPEP family; Region: FHIPEP; cl07980 224914006059 FHIPEP family; Region: FHIPEP; cl07980 224914006060 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 224914006061 Rod binding protein; Region: Rod-binding; cl01626 224914006062 FlgN protein; Region: FlgN; cl09176 224914006063 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 224914006064 metal binding site 2; metal-binding site 224914006065 putative DNA binding helix; other site 224914006066 metal binding site 1; metal-binding site 224914006067 dimer interface; other site 224914006068 structural Zn2+ binding site; other site 224914006069 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 224914006070 ABC-ATPase subunit interface; other site 224914006071 dimer interface; other site 224914006072 putative PBP binding regions; other site 224914006073 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 224914006074 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-...; Region: ABC_Metallic_Cations; cd03235 224914006075 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 224914006076 metal-binding site 224914006077 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 224914006078 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914006079 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 224914006080 rrf2 family protein (putative transcriptional regulator); Region: rrf2_super; TIGR00738 224914006081 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006082 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 224914006083 ROK family; Region: ROK; cl09121 224914006084 putative transposase OrfB; Reviewed; Region: PHA02517 224914006085 Integrase core domain; Region: rve; cl01316 224914006086 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 224914006087 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 224914006088 PemK-like protein; Region: PemK; cl00995 224914006089 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 224914006090 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 224914006091 intersubunit interface; other site 224914006092 active site 224914006093 Zn2+ binding site; other site 224914006094 Glutamate-1-semialdehyde aminotransferase [Coenzyme metabolism]; Region: HemL; COG0001 224914006095 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 224914006096 pyridoxal 5'-phosphate binding pocket; other site 224914006097 catalytic residue; other site 224914006098 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 224914006099 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914006100 Walker A/P-loop; other site 224914006101 ATP binding site; other site 224914006102 Q-loop/lid; other site 224914006103 ABC transporter signature motif; other site 224914006104 Walker B; other site 224914006105 D-loop; other site 224914006106 H-loop/switch region; other site 224914006107 TOBE domain; Region: TOBE_2; cl01440 224914006108 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006109 dimer interface; other site 224914006110 conserved gate region; other site 224914006111 putative PBP binding loops; other site 224914006112 ABC-ATPase subunit interface; other site 224914006113 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006114 dimer interface; other site 224914006115 conserved gate region; other site 224914006116 putative PBP binding loops; other site 224914006117 ABC-ATPase subunit interface; other site 224914006118 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914006119 amidase; Provisional; Region: PRK07486 224914006120 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 224914006121 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 224914006122 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 224914006123 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006124 Walker A/P-loop; other site 224914006125 ATP binding site; other site 224914006126 Q-loop/lid; other site 224914006127 ABC transporter signature motif; other site 224914006128 Walker B; other site 224914006129 D-loop; other site 224914006130 H-loop/switch region; other site 224914006131 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006132 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 224914006133 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006134 Walker A/P-loop; other site 224914006135 ATP binding site; other site 224914006136 Q-loop/lid; other site 224914006137 ABC transporter signature motif; other site 224914006138 Walker B; other site 224914006139 D-loop; other site 224914006140 H-loop/switch region; other site 224914006141 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006142 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006143 dimer interface; other site 224914006144 conserved gate region; other site 224914006145 putative PBP binding loops; other site 224914006146 ABC-ATPase subunit interface; other site 224914006147 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006148 dimer interface; other site 224914006149 conserved gate region; other site 224914006150 putative PBP binding loops; other site 224914006151 ABC-ATPase subunit interface; other site 224914006152 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 224914006153 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 224914006154 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006155 FCD domain; Region: FCD; cl11656 224914006156 ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]; Region: AppF; COG4608 224914006157 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006158 Walker A/P-loop; other site 224914006159 ATP binding site; other site 224914006160 Q-loop/lid; other site 224914006161 ABC transporter signature motif; other site 224914006162 Walker B; other site 224914006163 D-loop; other site 224914006164 H-loop/switch region; other site 224914006165 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006166 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 224914006167 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006168 Walker A/P-loop; other site 224914006169 ATP binding site; other site 224914006170 Q-loop/lid; other site 224914006171 ABC transporter signature motif; other site 224914006172 Walker B; other site 224914006173 D-loop; other site 224914006174 H-loop/switch region; other site 224914006175 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006176 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006177 putative PBP binding loops; other site 224914006178 dimer interface; other site 224914006179 ABC-ATPase subunit interface; other site 224914006180 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914006181 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006182 dimer interface; other site 224914006183 conserved gate region; other site 224914006184 putative PBP binding loops; other site 224914006185 ABC-ATPase subunit interface; other site 224914006186 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 224914006187 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_16; cd08502 224914006188 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 224914006189 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 224914006190 Penicillin amidase; Region: Penicil_amidase; pfam01804 224914006191 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-...; Region: Ntn_hydrolase; cl00467 224914006192 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-...; Region: Ntn_PGA_like; cd03747 224914006193 active site 224914006194 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914006195 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 224914006196 active site 224914006197 enoyl-CoA hydratase; Provisional; Region: PRK05980 224914006198 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 224914006199 substrate binding site; other site 224914006200 oxyanion hole (OAH) forming residues; other site 224914006201 trimer interface; other site 224914006202 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 224914006203 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006204 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 224914006205 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 224914006206 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 224914006207 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 224914006208 tetramer interface; other site 224914006209 TPP-binding site; other site 224914006210 heterodimer interface; other site 224914006211 phosphorylation loop region 224914006212 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 224914006213 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 224914006214 alpha subunit interface; other site 224914006215 TPP binding site; other site 224914006216 heterodimer interface; other site 224914006217 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 224914006218 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_7; cd08512 224914006219 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 224914006220 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 224914006221 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 224914006222 E3 interaction surface; other site 224914006223 lipoyl attachment site; other site 224914006224 e3 binding domain; Region: E3_binding; pfam02817 224914006225 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914006226 Transcriptional regulator [Transcription]; Region: IclR; COG1414 224914006227 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006228 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006229 dimer interface; other site 224914006230 conserved gate region; other site 224914006231 putative PBP binding loops; other site 224914006232 ABC-ATPase subunit interface; other site 224914006233 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914006234 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914006235 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 224914006236 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006237 Walker A/P-loop; other site 224914006238 ATP binding site; other site 224914006239 Q-loop/lid; other site 224914006240 ABC transporter signature motif; other site 224914006241 Walker B; other site 224914006242 D-loop; other site 224914006243 H-loop/switch region; other site 224914006244 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006245 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 224914006246 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006247 Walker A/P-loop; other site 224914006248 ATP binding site; other site 224914006249 Q-loop/lid; other site 224914006250 ABC transporter signature motif; other site 224914006251 Walker B; other site 224914006252 D-loop; other site 224914006253 H-loop/switch region; other site 224914006254 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006255 CoA-transferase family III; Region: CoA_transf_3; cl00778 224914006256 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 224914006257 tetramerization interface; other site 224914006258 NAD(P) binding site; other site 224914006259 catalytic residues; other site 224914006260 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914006261 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914006262 DNA binding site 224914006263 FCD domain; Region: FCD; cl11656 224914006264 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 224914006265 putative transposase OrfB; Reviewed; Region: PHA02517 224914006266 Integrase core domain; Region: rve; cl01316 224914006267 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 224914006268 SlyX; Region: SlyX; cl01090 224914006269 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 224914006270 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 224914006271 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 224914006272 S-adenosylmethionine binding site; other site 224914006273 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 224914006274 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 224914006275 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 224914006276 ATP binding site; other site 224914006277 active site 224914006278 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 224914006279 Flavoprotein; Region: Flavoprotein; cl08021 224914006280 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 224914006281 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 224914006282 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 224914006283 G1 box; other site 224914006284 putative GEF interaction site; other site 224914006285 GTP/Mg2+ binding site; other site 224914006286 Switch I region; other site 224914006287 G2 box; other site 224914006288 G3 box; other site 224914006289 Switch II region; other site 224914006290 G4 box; other site 224914006291 G5 box; other site 224914006292 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 224914006293 Uncharacterized conserved protein [Function unknown]; Region: HdeD; cl01277 224914006294 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 224914006295 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 224914006296 active site 224914006297 signature motif; other site 224914006298 Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of...; Region: PLDc; cd00138 224914006299 active site 224914006300 signature motif; other site 224914006301 Endonuclease/Exonuclease/phosphatase family; Region: Exo_endo_phos; cl00490 224914006302 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914006303 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 224914006304 NAD(P) binding site; other site 224914006305 catalytic residues; other site 224914006306 YhhN-like protein; Region: YhhN; cl01505 224914006307 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 224914006308 Ligand Binding Site; other site 224914006309 Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD...; Region: BluB; cd02145 224914006310 putative FMN binding site; other site 224914006311 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 224914006312 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 224914006313 active site 224914006314 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 224914006315 catalytic core; other site 224914006316 dihydrodipicolinate reductase; Provisional; Region: PRK00048 224914006317 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006318 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 224914006319 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 224914006320 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914006321 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 224914006322 Walker A/P-loop; other site 224914006323 ATP binding site; other site 224914006324 Q-loop/lid; other site 224914006325 ABC transporter signature motif; other site 224914006326 Walker B; other site 224914006327 D-loop; other site 224914006328 H-loop/switch region; other site 224914006329 ROK family; Region: ROK; cl09121 224914006330 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 224914006331 active site 224914006332 dimer interfaces; other site 224914006333 catalytic residues; other site 224914006334 Murein endopeptidase [Cell envelope biogenesis, outer membrane]; Region: MepA; COG3770 224914006335 Penicillin-insensitive murein endopeptidase; Region: Peptidase_M74; cl01538 224914006336 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 224914006337 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006338 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 224914006339 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 224914006340 HEAT repeat; Region: HEAT; pfam02985 224914006341 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 224914006342 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 224914006343 Glutathione S-transferase (GST) family, C-terminal alpha helical 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...; Region: GST_C_family; cd00299 224914006344 N-terminal domain interface; other site 224914006345 dimer interface; other site 224914006346 substrate binding pocket (H-site); other site 224914006347 Bacitracin resistance protein BacA; Region: BacA; cl00858 224914006348 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 224914006349 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006350 GTP-binding protein LepA; Provisional; Region: PRK05433 224914006351 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 224914006352 G1 box; other site 224914006353 putative GEF interaction site; other site 224914006354 GTP/Mg2+ binding site; other site 224914006355 Switch I region; other site 224914006356 G2 box; other site 224914006357 G3 box; other site 224914006358 Switch II region; other site 224914006359 G4 box; other site 224914006360 G5 box; other site 224914006361 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-...; Region: lepA_II; cd03699 224914006362 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 224914006363 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 224914006364 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 224914006365 Rdx family; Region: Rdx; cl01407 224914006366 RmuC family; Region: RmuC; pfam02646 224914006367 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe...; Region: Pep_deformylase; cd00487 224914006368 active site 224914006369 catalytic residues; other site 224914006370 metal-binding site 224914006371 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 224914006372 Formyl transferase; Region: Formyl_trans_N; cl00395 224914006373 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 224914006374 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 224914006375 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 224914006376 dimerization interface 3.5A; other site 224914006377 active site 224914006378 Peptidase dimerization domain; Region: M20_dimer; cl09126 224914006379 succinyl-diaminopimelate desuccinylase, proteobacterial clade; Region: dapE_proteo; TIGR01246 224914006380 Bacterial protein of unknown function (DUF920); Region: DUF920; cl01479 224914006381 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 224914006382 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 224914006383 trimer interface; other site 224914006384 active site 224914006385 substrate binding site; other site 224914006386 CoA binding site; other site 224914006387 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 224914006388 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 224914006389 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914006390 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using...; Region: AAK_NAGK-C; cd04250 224914006391 feedback inhibition sensing region; other site 224914006392 homohexameric interface; other site 224914006393 nucleotide binding site; other site 224914006394 N-acetyl-L-glutamate binding site; other site 224914006395 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 224914006396 G1 box; other site 224914006397 GTP/Mg2+ binding site; other site 224914006398 Switch I region; other site 224914006399 G2 box; other site 224914006400 G3 box; other site 224914006401 Switch II region; other site 224914006402 G4 box; other site 224914006403 G5 box; other site 224914006404 putative inner membrane protein translocase component YidC; Provisional; Region: PRK01318 224914006405 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 224914006406 Ribonuclease P; Region: Ribonuclease_P; cl00457 224914006407 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 224914006408 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 224914006409 homotrimer interaction site; other site 224914006410 putative active site; other site 224914006411 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 224914006412 Major Facilitator Superfamily; Region: MFS_1; pfam07690 224914006413 putative substrate translocation pore; other site 224914006414 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 224914006415 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914006416 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914006417 DNA binding site 224914006418 FCD domain; Region: FCD; cl11656 224914006419 1-pyrroline-5-carboxylate dehydrogenase; Provisional; Region: PRK03137 224914006420 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 224914006421 NAD(P) binding site; other site 224914006422 catalytic residues; other site 224914006423 catalytic residues; other site 224914006424 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 224914006425 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006426 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_6; cd08494 224914006427 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 224914006428 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006429 dimer interface; other site 224914006430 conserved gate region; other site 224914006431 putative PBP binding loops; other site 224914006432 ABC-ATPase subunit interface; other site 224914006433 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006434 dimer interface; other site 224914006435 conserved gate region; other site 224914006436 putative PBP binding loops; other site 224914006437 ABC-ATPase subunit interface; other site 224914006438 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 224914006439 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006440 Walker A/P-loop; other site 224914006441 ATP binding site; other site 224914006442 Q-loop/lid; other site 224914006443 ABC transporter signature motif; other site 224914006444 Walker B; other site 224914006445 D-loop; other site 224914006446 H-loop/switch region; other site 224914006447 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006448 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 224914006449 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006450 Walker A/P-loop; other site 224914006451 ATP binding site; other site 224914006452 Q-loop/lid; other site 224914006453 ABC transporter signature motif; other site 224914006454 Walker B; other site 224914006455 D-loop; other site 224914006456 H-loop/switch region; other site 224914006457 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914006458 amidase; Provisional; Region: PRK07042 224914006459 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 224914006460 DNA polymerase III subunit epsilon; Validated; Region: PRK09182 224914006461 DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved...; Region: DEDDh; cd06127 224914006462 active site 224914006463 substrate binding site; other site 224914006464 catalytic site; other site 224914006465 Predicted dehydrogenase [General function prediction only]; Region: COG0579 224914006466 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006467 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914006468 metal-binding site 224914006469 active site 224914006470 I-site; other site 224914006471 Protein of unknown function (DUF2778); Region: DUF2778; pfam10908 224914006472 glutathionine S-transferase; Provisional; Region: PRK10542 224914006473 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 224914006474 C-terminal domain interface; other site 224914006475 GSH binding site (G-site); other site 224914006476 dimer interface; other site 224914006477 GST_C 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_C_Beta; cd03188 224914006478 dimer interface; other site 224914006479 N-terminal domain interface; other site 224914006480 substrate binding pocket (H-site); other site 224914006481 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914006482 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 224914006483 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 224914006484 N-terminal plug; other site 224914006485 ligand-binding site; other site 224914006486 Transcriptional regulator [Transcription]; Region: IclR; COG1414 224914006487 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006488 Bacterial transcriptional regulator; Region: IclR; pfam01614 224914006489 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914006490 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 224914006491 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914006492 Walker A/P-loop; other site 224914006493 ATP binding site; other site 224914006494 Q-loop/lid; other site 224914006495 ABC transporter signature motif; other site 224914006496 Walker B; other site 224914006497 D-loop; other site 224914006498 H-loop/switch region; other site 224914006499 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 224914006500 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006501 TM-ABC transporter signature motif; other site 224914006502 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006503 TM-ABC transporter signature motif; other site 224914006504 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 224914006505 homotrimer interaction site; other site 224914006506 putative active site; other site 224914006507 Ferric reductase like transmembrane component; Region: Ferric_reduct; cl01043 224914006508 YedY_like molybdopterin cofactor (Moco) binding domain, a subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. Escherichia coli YedY has been propsed to form a heterodimer, consisting of a soluble catalytic subunit termed YedY...; Region: YedY_like_Moco; cd02107 224914006509 Moco binding site; other site 224914006510 metal coordination site; other site 224914006511 Predicted esterase [General function prediction only]; Region: COG0400 224914006512 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914006513 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues...; Region: WD40; cl02567 224914006514 structural tetrad; other site 224914006515 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 224914006516 P-loop, Walker A motif; other site 224914006517 Base recognition motif; other site 224914006518 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 224914006519 Creatinine amidohydrolase; Region: Creatininase; cl00618 224914006520 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006521 transcriptional regulator SlyA; Provisional; Region: PRK03573 224914006522 Transcriptional regulators [Transcription]; Region: PurR; COG1609 224914006523 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 224914006524 DNA binding site 224914006525 domain linker motif; other site 224914006526 Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; Region: PBP1_MalI_like; cd06289 224914006527 putative dimerization interface; other site 224914006528 putative ligand binding site; other site 224914006529 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 224914006530 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006531 Peptidase C26; Region: Peptidase_C26; pfam07722 224914006532 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 224914006533 catalytic triad; other site 224914006534 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 224914006535 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006536 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914006537 metal-binding site 224914006538 active site 224914006539 I-site; other site 224914006540 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 224914006541 Beta-lactamase; Region: Beta-lactamase; cl01009 224914006542 Beta-lactamase; Region: Beta-lactamase; cl01009 224914006543 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 224914006544 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 224914006545 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; pfam05222 224914006546 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 224914006547 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 224914006548 NAD(P) transhydrogenase beta subunit; Region: PNTB; cl00566 224914006549 Predicted homoserine dehydrogenase [Amino acid transport and metabolism]; Region: COG4091 224914006550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006551 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 224914006552 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 224914006553 motif II; other site 224914006554 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 224914006555 putative active site; other site 224914006556 putative catalytic site; other site 224914006557 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 224914006558 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 224914006559 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 224914006560 binding surface 224914006561 TPR motif; other site 224914006562 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 224914006563 binding surface 224914006564 TPR motif; other site 224914006565 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 224914006566 binding surface 224914006567 TPR motif; other site 224914006568 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914006569 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006570 dimer interface; other site 224914006571 conserved gate region; other site 224914006572 ABC-ATPase subunit interface; other site 224914006573 ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]; Region: AbcC; COG1135 224914006574 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein; Region: ABC_MetN_methionine_transporter; cd03258 224914006575 Walker A/P-loop; other site 224914006576 ATP binding site; other site 224914006577 Q-loop/lid; other site 224914006578 ABC transporter signature motif; other site 224914006579 Walker B; other site 224914006580 D-loop; other site 224914006581 H-loop/switch region; other site 224914006582 NIL domain; Region: NIL; pfam09383 224914006583 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914006584 choline dehydrogenase; Validated; Region: PRK02106 224914006585 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006586 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914006587 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914006588 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 224914006589 TM-ABC transporter signature motif; other site 224914006590 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 224914006591 TM-ABC transporter signature motif; other site 224914006592 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914006593 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914006594 Walker A/P-loop; other site 224914006595 ATP binding site; other site 224914006596 Q-loop/lid; other site 224914006597 ABC transporter signature motif; other site 224914006598 Walker B; other site 224914006599 D-loop; other site 224914006600 H-loop/switch region; other site 224914006601 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 224914006602 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 224914006603 Walker A/P-loop; other site 224914006604 ATP binding site; other site 224914006605 Q-loop/lid; other site 224914006606 ABC transporter signature motif; other site 224914006607 Walker B; other site 224914006608 D-loop; other site 224914006609 H-loop/switch region; other site 224914006610 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914006611 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 224914006612 putative ligand binding site; other site 224914006613 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914006614 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006615 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914006616 dimerization interface; other site 224914006617 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914006618 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006619 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 224914006620 active site 224914006621 substrate binding site; other site 224914006622 Phosphotransferase enzyme family; Region: APH; pfam01636 224914006623 ATP binding site; other site 224914006624 Peptidase family M23; Region: Peptidase_M23; pfam01551 224914006625 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]; Region: GabT; COG0160 224914006626 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 224914006627 inhibitor-cofactor binding pocket; inhibition site 224914006628 pyridoxal 5'-phosphate binding site; other site 224914006629 catalytic residue; other site 224914006630 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 224914006631 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914006632 substrate binding pocket; other site 224914006633 membrane-bound complex binding site; other site 224914006634 hinge residues; other site 224914006635 D-aminopeptidase; Reviewed; Region: PRK13128 224914006636 Beta-lactamase; Region: Beta-lactamase; cl01009 224914006637 D-aminopeptidase, domain B; Region: DAP_B; pfam07930 224914006638 D-aminopeptidase, domain C; Region: DAP_C; pfam07932 224914006639 thiamine pyrophosphate protein; Validated; Region: PRK08199 224914006640 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 224914006641 PYR/PP interface; other site 224914006642 dimer interface; other site 224914006643 TPP binding site; other site 224914006644 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 224914006645 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...; Region: TPP_enzymes; cd00568 224914006646 TPP-binding site; other site 224914006647 Transcriptional regulators [Transcription]; Region: FadR; COG2186 224914006648 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914006649 DNA binding site 224914006650 FCD domain; Region: FCD; cl11656 224914006651 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 224914006652 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 224914006653 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914006654 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006655 Dehydratase family; Region: ILVD_EDD; cl00340 224914006656 dihydroxy-acid dehydratase; Region: ilvD; TIGR00110 224914006657 2-keto-3-deoxy-galactonokinase; Region: DGOK; cl01517 224914006658 Entner-Doudoroff aldolase; Region: eda; TIGR01182 224914006659 KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best...; Region: KDPG_aldolase; cd00452 224914006660 active site 224914006661 intersubunit interface; other site 224914006662 catalytic residue; other site 224914006663 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914006664 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 224914006665 putative ligand binding site; other site 224914006666 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 224914006667 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914006668 Walker A/P-loop; other site 224914006669 ATP binding site; other site 224914006670 Q-loop/lid; other site 224914006671 ABC transporter signature motif; other site 224914006672 Walker B; other site 224914006673 D-loop; other site 224914006674 H-loop/switch region; other site 224914006675 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 224914006676 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006677 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006678 TM-ABC transporter signature motif; other site 224914006679 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and D-...; Region: D-AAT_like; cd01558 224914006680 homodimer interface; other site 224914006681 substrate-cofactor binding pocket; other site 224914006682 pyridoxal 5'-phosphate binding site; other site 224914006683 Aminotransferase class IV; Region: Aminotran_4; pfam01063 224914006684 catalytic residue; other site 224914006685 HutD; Region: HutD; cl01532 224914006686 urocanate hydratase; Provisional; Region: PRK05414 224914006687 urocanate hydratase; Region: hutU; TIGR01228 224914006688 N-formylglutamate amidohydrolase; Region: FGase; cl01522 224914006689 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 224914006690 tetramer interface; other site 224914006691 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 224914006692 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria...; Region: Imidazolone-5PH; cd01296 224914006693 active site 224914006694 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 224914006695 active sites 224914006696 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 224914006697 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_E; cd01313 224914006698 active site 224914006699 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 224914006700 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914006701 DNA binding site 224914006702 UTRA domain; Region: UTRA; cl06649 224914006703 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 224914006704 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 224914006705 inhibitor-cofactor binding pocket; inhibition site 224914006706 pyridoxal 5'-phosphate binding site; other site 224914006707 catalytic residue; other site 224914006708 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 224914006709 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 224914006710 non-specific DNA binding site; other site 224914006711 salt bridge; other site 224914006712 sequence-specific DNA binding site; other site 224914006713 Cupin domain; Region: Cupin_2; cl09118 224914006714 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006715 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 224914006716 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 224914006717 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 224914006718 active site 224914006719 pyridoxal 5'-phosphate (PLP) binding site; other site 224914006720 dimer interface; other site 224914006721 substrate binding site; other site 224914006722 catalytic residues; other site 224914006723 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914006724 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006725 Surface antigen; Region: Surface_Ag_2; cl01155 224914006726 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 224914006727 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 224914006728 phosphate binding site; other site 224914006729 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 224914006730 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 224914006731 putative molybdopterin cofactor binding site; other site 224914006732 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT)...; Region: MopB_CT_ydeP; cd02787 224914006733 putative molybdopterin cofactor binding site; other site 224914006734 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914006735 putative membrane fusion protein; Region: TIGR02828 224914006736 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914006737 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 224914006738 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 224914006739 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914006740 DNA binding site 224914006741 UTRA domain; Region: UTRA; cl06649 224914006742 Predicted phosphosugar isomerases [Cell envelope biogenesis, outer membrane]; Region: AgaS; COG2222 224914006743 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 224914006744 dimer interface; other site 224914006745 active site 224914006746 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 224914006747 dimer interface; other site 224914006748 active site 224914006749 N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to...; Region: NagA; cd00854 224914006750 active site 224914006751 dimer interface; other site 224914006752 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 224914006753 putative active site; other site 224914006754 formyltetrahydrofolate deformylase; Reviewed; Region: PRK13011 224914006755 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 224914006756 Formyl transferase; Region: Formyl_trans_N; cl00395 224914006757 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 224914006758 tetrameric interface; other site 224914006759 NAD binding site; other site 224914006760 catalytic residues; other site 224914006761 Protein of unknown function (DUF1338); Region: DUF1338; cl02226 224914006762 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 224914006763 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006764 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914006765 dimerization interface; other site 224914006766 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006767 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 224914006768 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 224914006769 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 224914006770 Uncharacterized protein family (UPF0081); Region: UPF0081; cl00525 224914006771 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl11430 224914006772 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin...; Region: S1_Tex; cd05685 224914006773 RNA binding site; other site 224914006774 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 224914006775 dimerization interface; other site 224914006776 putative DNA binding site; other site 224914006777 putative Zn2+ binding site; other site 224914006778 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 224914006779 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 224914006780 FMN binding site; other site 224914006781 active site 224914006782 substrate binding site; other site 224914006783 catalytic residue; other site 224914006784 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914006785 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006786 Arginase family; Region: Arginase; cl00306 224914006787 ornithine cyclodeaminase; Validated; Region: PRK07589 224914006788 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006789 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is...; Region: Trunc_globin; cd00454 224914006790 apolar tunnel; other site 224914006791 heme binding site; other site 224914006792 dimerization interface; other site 224914006793 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 224914006794 putative deacylase active site; other site 224914006795 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 224914006796 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 224914006797 catalytic residues; other site 224914006798 Found in ATP-dependent protease La (LON); Region: LON; cl01056 224914006799 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 224914006800 Trm112p-like protein; Region: Trm112p; cl01066 224914006801 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 224914006802 isocitrate dehydrogenase; Validated; Region: PRK06451 224914006803 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 224914006804 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 224914006805 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 224914006806 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 224914006807 DNA binding site 224914006808 active site 224914006809 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 224914006810 putative substrate translocation pore; other site 224914006811 metabolite-proton symporter; Region: 2A0106; TIGR00883 224914006812 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 224914006813 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006814 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 224914006815 Transcriptional regulators [Transcription]; Region: MarR; COG1846 224914006816 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006817 OsmC-like protein; Region: OsmC; cl00767 224914006818 Domain of unknown function (DUF1025); Region: DUF1025; cl01577 224914006819 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-...; Region: IPMI_Swivel; cd01577 224914006820 substrate binding site; other site 224914006821 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 224914006822 Domain of unknown function (DUF1737); Region: DUF1737; cl10503 224914006823 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914006824 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 224914006825 Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and...; Region: M3A_DCP_Oligopeptidase_A; cd06456 224914006826 active site 224914006827 zinc binding site; other site 224914006828 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 224914006829 MgtE intracellular N domain; Region: MgtE_N; pfam03448 224914006830 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 224914006831 Divalent cation transporter; Region: MgtE; cl00786 224914006832 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 224914006833 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 224914006834 G1 box; other site 224914006835 putative GEF interaction site; other site 224914006836 GTP/Mg2+ binding site; other site 224914006837 Switch I region; other site 224914006838 G2 box; other site 224914006839 G3 box; other site 224914006840 Switch II region; other site 224914006841 G4 box; other site 224914006842 G5 box; other site 224914006843 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 224914006844 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a...; Region: BipA_TypA_C; cd03710 224914006845 Uncharacterized conserved protein [Function unknown]; Region: COG1739 224914006846 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 224914006847 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 224914006848 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-...; Region: FBPase; cd00354 224914006849 AMP binding site; other site 224914006850 metal-binding site 224914006851 active site 224914006852 tagatose-bisphosphate aldolase; Reviewed; Region: gatY; PRK09195 224914006853 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose...; Region: TBP_aldolase_IIB; cd00947 224914006854 intersubunit interface; other site 224914006855 active site 224914006856 zinc binding site; other site 224914006857 Na+ binding site; other site 224914006858 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 224914006859 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 224914006860 substrate binding site; other site 224914006861 dimer interface; other site 224914006862 catalytic triad; other site 224914006863 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 224914006864 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006865 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 224914006866 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 224914006867 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 224914006868 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 224914006869 glycerol-3-phosphate dehydrogenase; Provisional; Region: PRK13369 224914006870 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006871 Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; Region: XylB; COG1070 224914006872 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 224914006873 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 224914006874 Predicted periplasmic lipoprotein (DUF2291); Region: DUF2291; cl02395 224914006875 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 224914006876 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914006877 Walker A/P-loop; other site 224914006878 ATP binding site; other site 224914006879 Q-loop/lid; other site 224914006880 ABC transporter signature motif; other site 224914006881 Walker B; other site 224914006882 D-loop; other site 224914006883 H-loop/switch region; other site 224914006884 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses...; Region: ABC_Carb_Monos_II; cd03215 224914006885 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914006886 TM-ABC transporter signature motif; other site 224914006887 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 224914006888 ligand binding site; other site 224914006889 dimerization interface; other site 224914006890 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 224914006891 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914006892 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 224914006893 hypothetical protein; Validated; Region: PRK08238 224914006894 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others...; Region: HAD_like; cl11391 224914006895 UbiA prenyltransferase family; Region: UbiA; cl00337 224914006896 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 224914006897 FAD binding domain; Region: FAD_binding_4; cl10516 224914006898 hypothetical protein; Provisional; Region: PRK02971 224914006899 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 224914006900 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914006901 Ornithine/acetylornithine aminotransferase [Amino acid transport and metabolism]; Region: ArgD; COG4992 224914006902 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 224914006903 inhibitor-cofactor binding pocket; inhibition site 224914006904 pyridoxal 5'-phosphate binding site; other site 224914006905 catalytic residue; other site 224914006906 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914006907 Protein of unknown function DUF91; Region: DUF91; cl00709 224914006908 Uncharacterized conserved protein [Function unknown]; Region: COG3586 224914006909 Protein of unknown function DUF45; Region: DUF45; cl00636 224914006910 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 224914006911 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl01057 224914006912 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 224914006913 ATP binding site; other site 224914006914 putative Mg++ binding site; other site 224914006915 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; cl12029 224914006916 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 224914006917 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 224914006918 HsdM N-terminal domain; Region: HsdM_N; pfam12161 224914006919 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914006920 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 224914006921 Uncharacterized phage-associated protein [Function unknown]; Region: GepA; COG3600 224914006922 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 224914006923 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 224914006924 FMN binding site; other site 224914006925 substrate binding site; other site 224914006926 putative catalytic residue; other site 224914006927 Lhr-like helicases [General function prediction only]; Region: Lhr; COG1201 224914006928 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 224914006929 ATP binding site; other site 224914006930 putative Mg++ binding site; other site 224914006931 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 224914006932 nucleotide binding region; other site 224914006933 ATP-binding site; other site 224914006934 DEAD/H associated; Region: DEAD_assoc; pfam08494 224914006935 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 224914006936 putative active site; other site 224914006937 putative metal binding site; other site 224914006938 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; cl09826 224914006939 Sulfite exporter TauE/SafE; Region: TauE; cl00498 224914006940 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 224914006941 Sel1 repeat; Region: Sel1; cl02723 224914006942 Sel1 repeat; Region: Sel1; cl02723 224914006943 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 224914006944 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 224914006945 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 224914006946 DNA binding residues 224914006947 putative dimer interface; other site 224914006948 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 224914006949 CrcB-like protein; Region: CRCB; cl09114 224914006950 CrcB-like protein; Region: CRCB; cl09114 224914006951 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914006952 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 224914006953 mannonate dehydratase; Provisional; Region: PRK03906 224914006954 mannonate dehydratase; Region: uxuA; TIGR00695 224914006955 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914006956 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914006957 DNA binding site 224914006958 FCD domain; Region: FCD; cl11656 224914006959 Glucuronate isomerase; Region: UxaC; cl00829 224914006960 Glucuronate isomerase; Region: UxaC; cl00829 224914006961 Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]; Region: MtlD; COG0246 224914006962 Mannitol dehydrogenase Rossmann domain; Region: Mannitol_dh; pfam01232 224914006963 Mannitol dehydrogenase C-terminal domain; Region: Mannitol_dh_C; pfam08125 224914006964 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG4134 224914006965 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914006966 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 224914006967 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914006968 Walker A/P-loop; other site 224914006969 ATP binding site; other site 224914006970 Q-loop/lid; other site 224914006971 ABC transporter signature motif; other site 224914006972 Walker B; other site 224914006973 D-loop; other site 224914006974 H-loop/switch region; other site 224914006975 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006976 putative PBP binding loops; other site 224914006977 ABC-ATPase subunit interface; other site 224914006978 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914006979 SAF domain; Region: SAF; cl00555 224914006980 nickel responsive regulator; Provisional; Region: PRK02967 224914006981 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 224914006982 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 224914006983 The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA; cd08489 224914006984 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 224914006985 substrate binding site; other site 224914006986 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006987 dimer interface; other site 224914006988 conserved gate region; other site 224914006989 putative PBP binding loops; other site 224914006990 ABC-ATPase subunit interface; other site 224914006991 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914006992 dimer interface; other site 224914006993 conserved gate region; other site 224914006994 putative PBP binding loops; other site 224914006995 ABC-ATPase subunit interface; other site 224914006996 nickel transporter ATP-binding protein NikD; Provisional; Region: nikD; PRK10418 224914006997 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914006998 Walker A/P-loop; other site 224914006999 ATP binding site; other site 224914007000 Q-loop/lid; other site 224914007001 ABC transporter signature motif; other site 224914007002 Walker B; other site 224914007003 D-loop; other site 224914007004 H-loop/switch region; other site 224914007005 nickel transporter ATP-binding protein NikE; Provisional; Region: nikE; PRK10419 224914007006 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914007007 Walker A/P-loop; other site 224914007008 ATP binding site; other site 224914007009 Q-loop/lid; other site 224914007010 ABC transporter signature motif; other site 224914007011 Walker B; other site 224914007012 D-loop; other site 224914007013 H-loop/switch region; other site 224914007014 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914007015 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 224914007016 active site 224914007017 The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold; Region: PBP2_Nac; cd08433 224914007018 putative dimerization interface; other site 224914007019 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 224914007020 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914007021 Putative acyl-CoA dehydrogenases similar to fadE5; Region: ACAD_fadE5; cd01153 224914007022 FAD binding site; other site 224914007023 substrate binding site; other site 224914007024 catalytic residues; other site 224914007025 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 224914007026 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 224914007027 dimer interface; other site 224914007028 active site 224914007029 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 224914007030 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 224914007031 substrate binding site; other site 224914007032 oxyanion hole (OAH) forming residues; other site 224914007033 trimer interface; other site 224914007034 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl11406 224914007035 LDH/MDH dimer interface; other site 224914007036 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 224914007037 Predicted transcriptional regulator [Transcription]; Region: COG2932 224914007038 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA...; Region: S24_LexA-like; cd06529 224914007039 Catalytic site; other site 224914007040 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 224914007041 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 224914007042 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914007043 active site 224914007044 nucleotide binding site; other site 224914007045 HIGH motif; other site 224914007046 KMSKS motif; other site 224914007047 tellurite resistance protein terB; Region: terB; cd07176 224914007048 putative metal binding site; other site 224914007049 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 224914007050 active site clefts 224914007051 zinc binding site; other site 224914007052 dimer interface; other site 224914007053 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 224914007054 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_13; cd08517 224914007055 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007056 dimer interface; other site 224914007057 conserved gate region; other site 224914007058 putative PBP binding loops; other site 224914007059 ABC-ATPase subunit interface; other site 224914007060 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007061 dimer interface; other site 224914007062 conserved gate region; other site 224914007063 putative PBP binding loops; other site 224914007064 ABC-ATPase subunit interface; other site 224914007065 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 224914007066 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914007067 Walker A/P-loop; other site 224914007068 ATP binding site; other site 224914007069 Q-loop/lid; other site 224914007070 ABC transporter signature motif; other site 224914007071 Walker B; other site 224914007072 D-loop; other site 224914007073 H-loop/switch region; other site 224914007074 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 224914007075 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914007076 Walker A/P-loop; other site 224914007077 ATP binding site; other site 224914007078 Q-loop/lid; other site 224914007079 ABC transporter signature motif; other site 224914007080 Walker B; other site 224914007081 D-loop; other site 224914007082 H-loop/switch region; other site 224914007083 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914007084 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 224914007085 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007086 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 224914007087 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 224914007088 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 224914007089 homodimer interface; other site 224914007090 NADP binding site; other site 224914007091 substrate binding site; other site 224914007092 Dehydratase family; Region: ILVD_EDD; cl00340 224914007093 6-phosphogluconate dehydratase; Region: edd; TIGR01196 224914007094 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 224914007095 putative active site; other site 224914007096 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 224914007097 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 224914007098 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 224914007099 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 224914007100 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007101 drug efflux system protein MdtG; Provisional; Region: PRK09874 224914007102 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 224914007103 putative substrate translocation pore; other site 224914007104 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 224914007105 AzlC protein; Region: AzlC; cl00570 224914007106 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 224914007107 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007108 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007109 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 224914007110 S23 ribosomal protein; Region: Ribosomal_S23p; cl05287 224914007111 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 224914007112 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 224914007113 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914007114 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007115 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007116 dimerization interface; other site 224914007117 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 224914007118 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-...; Region: ExoVII_LU_OBF; cd04489 224914007119 generic binding surface II; other site 224914007120 generic binding surface I; other site 224914007121 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 224914007122 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 224914007123 Transcriptional regulators [Transcription]; Region: MarR; COG1846 224914007124 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007125 Fusaric acid resistance protein family; Region: FUSC; pfam04632 224914007126 Bacterial protein of unknown function (DUF939); Region: DUF939; cl12136 224914007127 Protein of unknown function (DUF1656); Region: DUF1656; cl11658 224914007128 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 224914007129 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 224914007130 Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and...; Region: TroA_a; cd01148 224914007131 putative ligand binding residues; other site 224914007132 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 224914007133 ABC-ATPase subunit interface; other site 224914007134 dimer interface; other site 224914007135 putative PBP binding regions; other site 224914007136 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 224914007137 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 224914007138 Walker A/P-loop; other site 224914007139 ATP binding site; other site 224914007140 Q-loop/lid; other site 224914007141 ABC transporter signature motif; other site 224914007142 Walker B; other site 224914007143 D-loop; other site 224914007144 H-loop/switch region; other site 224914007145 Uncharacterized conserved protein [Function unknown]; Region: COG5476 224914007146 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 224914007147 MlrC C-terminus; Region: MlrC_C; pfam07171 224914007148 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 224914007149 homotrimer interaction site; other site 224914007150 putative active site; other site 224914007151 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007152 dimer interface; other site 224914007153 conserved gate region; other site 224914007154 putative PBP binding loops; other site 224914007155 ABC-ATPase subunit interface; other site 224914007156 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 224914007157 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007158 3-ketoacyl-(acyl-carrier-protein) reductase; Reviewed; Region: PRK12826 224914007159 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007160 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 224914007161 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 224914007162 Walker A/P-loop; other site 224914007163 ATP binding site; other site 224914007164 Q-loop/lid; other site 224914007165 ABC transporter signature motif; other site 224914007166 Walker B; other site 224914007167 D-loop; other site 224914007168 H-loop/switch region; other site 224914007169 TOBE domain; Region: TOBE_2; cl01440 224914007170 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 224914007171 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 224914007172 putative active site; other site 224914007173 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 224914007174 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like; Region: PLPDE_III_LS_D-TA_like; cd06820 224914007175 dimer interface; other site 224914007176 active site 224914007177 pyridoxal 5'-phosphate (PLP) binding site; other site 224914007178 substrate binding site; other site 224914007179 catalytic residue; other site 224914007180 ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]; Region: ProV; COG4175 224914007181 This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these...; Region: ABC_Pro_Gly_Bertaine; cd03294 224914007182 Walker A/P-loop; other site 224914007183 ATP binding site; other site 224914007184 Q-loop/lid; other site 224914007185 ABC transporter signature motif; other site 224914007186 Walker B; other site 224914007187 D-loop; other site 224914007188 H-loop/switch region; other site 224914007189 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so...; Region: CBS_pair; cl10010 224914007190 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007191 dimer interface; other site 224914007192 conserved gate region; other site 224914007193 putative PBP binding loops; other site 224914007194 ABC-ATPase subunit interface; other site 224914007195 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914007196 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 224914007197 EamA-like transporter family; Region: EamA; cl01037 224914007198 BA14K-like protein; Region: BA14K; pfam07886 224914007199 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 224914007200 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 224914007201 putative active site; other site 224914007202 metal-binding site 224914007203 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 224914007204 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 224914007205 N-formylglutamate amidohydrolase; Region: FGase; cl01522 224914007206 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 224914007207 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 224914007208 putative active site; other site 224914007209 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 224914007210 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007211 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 224914007212 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 224914007213 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 224914007214 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-...; Region: GCS_H; cd06848 224914007215 lipoyl attachment site; other site 224914007216 glycine dehydrogenase; Provisional; Region: PRK05367 224914007217 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 224914007218 pyridoxal 5'-phosphate binding pocket; other site 224914007219 catalytic residue; other site 224914007220 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...; Region: GDC-P; cd00613 224914007221 tetramer interface; other site 224914007222 pyridoxal 5'-phosphate binding site; other site 224914007223 catalytic residue; other site 224914007224 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 224914007225 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007226 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 224914007227 Proline dehydrogenase; Region: Pro_dh; cl03282 224914007228 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 224914007229 Glutamate binding site; other site 224914007230 NAD binding site; other site 224914007231 catalytic residues; other site 224914007232 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein; Region: PhnS; TIGR03227 224914007233 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007234 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 224914007235 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007236 dimer interface; other site 224914007237 conserved gate region; other site 224914007238 putative PBP binding loops; other site 224914007239 ABC-ATPase subunit interface; other site 224914007240 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007241 dimer interface; other site 224914007242 conserved gate region; other site 224914007243 putative PBP binding loops; other site 224914007244 ABC-ATPase subunit interface; other site 224914007245 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 224914007246 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914007247 Walker A/P-loop; other site 224914007248 ATP binding site; other site 224914007249 Q-loop/lid; other site 224914007250 ABC transporter signature motif; other site 224914007251 Walker B; other site 224914007252 D-loop; other site 224914007253 H-loop/switch region; other site 224914007254 TOBE domain; Region: TOBE_2; cl01440 224914007255 Bacterial family of Mg++ dependent phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate inositol monophosphate or similar substrates; Region: Bacterial_IMPase_like_2; cd01643 224914007256 active site 224914007257 KduI/IolB family; Region: KduI; cl01508 224914007258 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 224914007259 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 224914007260 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 224914007261 PYR/PP interface; other site 224914007262 dimer interface; other site 224914007263 TPP binding site; other site 224914007264 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 224914007265 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...; Region: TPP_enzymes; cl01629 224914007266 TPP-binding site; other site 224914007267 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 224914007268 substrate binding site; other site 224914007269 ATP binding site; other site 224914007270 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 224914007271 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 224914007272 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose...; Region: SIS_RpiR; cd05013 224914007273 putative active site; other site 224914007274 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007275 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914007276 Protein of unknown function (DUF1612); Region: DUF1612; pfam07756 224914007277 HTH DNA binding domain; Region: HTH_13; pfam11972 224914007278 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 224914007279 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007280 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 224914007281 dimerization interface; other site 224914007282 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 224914007283 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic...; Region: PRX_Typ2cys; cd03015 224914007284 dimer interface; other site 224914007285 decamer (pentamer of dimers) interface; other site 224914007286 catalytic triad; other site 224914007287 peroxidatic and resolving cysteines; other site 224914007288 Uncharacterized conserved protein [Function unknown]; Region: COG2128 224914007289 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 224914007290 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 224914007291 metabolite-proton symporter; Region: 2A0106; TIGR00883 224914007292 putative substrate translocation pore; other site 224914007293 multicopper oxidase; Provisional; Region: PRK10965 224914007294 Multicopper oxidase; Region: Cu-oxidase; cl11412 224914007295 Multicopper oxidase; Region: Cu-oxidase; cl11412 224914007296 Multicopper oxidase; Region: Cu-oxidase; cl11412 224914007297 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 224914007298 E-class dimer interface; other site 224914007299 P-class dimer interface; other site 224914007300 active site 224914007301 Cu2+ binding site; other site 224914007302 Zn2+ binding site; other site 224914007303 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007304 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 224914007305 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 224914007306 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 224914007307 Walker A/P-loop; other site 224914007308 ATP binding site; other site 224914007309 Q-loop/lid; other site 224914007310 ABC transporter signature motif; other site 224914007311 Walker B; other site 224914007312 D-loop; other site 224914007313 H-loop/switch region; other site 224914007314 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 224914007315 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007316 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 224914007317 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007318 dimer interface; other site 224914007319 conserved gate region; other site 224914007320 putative PBP binding loops; other site 224914007321 ABC-ATPase subunit interface; other site 224914007322 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (; Region: PTPc; cl00053 224914007323 FdhD/NarQ family; Region: FdhD-NarQ; cl00659 224914007324 6,7-dimethyl-8-ribityllumazine synthase; Region: DMRL_synthase; cl00317 224914007325 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 224914007326 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007327 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007328 dimer interface; other site 224914007329 conserved gate region; other site 224914007330 putative PBP binding loops; other site 224914007331 ABC-ATPase subunit interface; other site 224914007332 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007333 dimer interface; other site 224914007334 conserved gate region; other site 224914007335 putative PBP binding loops; other site 224914007336 ABC-ATPase subunit interface; other site 224914007337 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 224914007338 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 224914007339 Walker A/P-loop; other site 224914007340 ATP binding site; other site 224914007341 Q-loop/lid; other site 224914007342 ABC transporter signature motif; other site 224914007343 Walker B; other site 224914007344 D-loop; other site 224914007345 H-loop/switch region; other site 224914007346 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 224914007347 multidrug efflux system protein MdtE; Provisional; Region: PRK10504 224914007348 putative substrate translocation pore; other site 224914007349 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 224914007350 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914007351 exopolyphosphatase; Region: exo_poly_only; TIGR03706 224914007352 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 224914007353 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 224914007354 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914007355 Walker A/P-loop; other site 224914007356 ATP binding site; other site 224914007357 Q-loop/lid; other site 224914007358 ABC transporter signature motif; other site 224914007359 Walker B; other site 224914007360 D-loop; other site 224914007361 H-loop/switch region; other site 224914007362 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007363 dimer interface; other site 224914007364 conserved gate region; other site 224914007365 putative PBP binding loops; other site 224914007366 ABC-ATPase subunit interface; other site 224914007367 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 224914007368 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 224914007369 substrate binding pocket; other site 224914007370 membrane-bound complex binding site; other site 224914007371 hinge residues; other site 224914007372 5-oxoprolinase; Region: PLN02666 224914007373 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 224914007374 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 224914007375 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 224914007376 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]; Region: COG5631 224914007377 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 224914007378 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 224914007379 Walker A/P-loop; other site 224914007380 ATP binding site; other site 224914007381 Q-loop/lid; other site 224914007382 ABC transporter signature motif; other site 224914007383 Walker B; other site 224914007384 D-loop; other site 224914007385 H-loop/switch region; other site 224914007386 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cl00462 224914007387 ABC-ATPase subunit interface; other site 224914007388 dimer interface; other site 224914007389 putative PBP binding regions; other site 224914007390 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 224914007391 ABC-ATPase subunit interface; other site 224914007392 dimer interface; other site 224914007393 putative PBP binding regions; other site 224914007394 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 224914007395 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 224914007396 putative ligand binding residues; other site 224914007397 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 224914007398 NAD binding site; other site 224914007399 catalytic residues; other site 224914007400 Protein of unknown function (DUF3775); Region: DUF3775; pfam12616 224914007401 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007402 Sulfite exporter TauE/SafE; Region: TauE; cl00498 224914007403 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 224914007404 substrate-cofactor binding pocket; other site 224914007405 pyridoxal 5'-phosphate binding site; other site 224914007406 catalytic residue; other site 224914007407 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cl00224 224914007408 EamA-like transporter family; Region: EamA; cl01037 224914007409 Protein of unknown function (DUF2938); Region: DUF2938; pfam11158 224914007410 Permease family; Region: Xan_ur_permease; cl00967 224914007411 Permease family; Region: Xan_ur_permease; cl00967 224914007412 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 224914007413 nucleoside/Zn binding site; other site 224914007414 dimer interface; other site 224914007415 catalytic motif; other site 224914007416 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914007417 transmembrane helices; other site 224914007418 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914007419 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]; Region: COG0490 224914007420 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914007421 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 224914007422 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 224914007423 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 224914007424 Walker A/P-loop; other site 224914007425 ATP binding site; other site 224914007426 Q-loop/lid; other site 224914007427 ABC transporter signature motif; other site 224914007428 Walker B; other site 224914007429 D-loop; other site 224914007430 H-loop/switch region; other site 224914007431 TOBE domain; Region: TOBE_2; cl01440 224914007432 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007433 dimer interface; other site 224914007434 conserved gate region; other site 224914007435 ABC-ATPase subunit interface; other site 224914007436 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914007437 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914007438 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 224914007439 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007440 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics...; Region: rDP_like; cd01301 224914007441 active site 224914007442 dimer interface; other site 224914007443 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 224914007444 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 224914007445 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen...; Region: AdeC; cd01295 224914007446 active site 224914007447 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 224914007448 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914007449 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914007450 Walker A/P-loop; other site 224914007451 ATP binding site; other site 224914007452 Q-loop/lid; other site 224914007453 ABC transporter signature motif; other site 224914007454 Walker B; other site 224914007455 D-loop; other site 224914007456 H-loop/switch region; other site 224914007457 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 224914007458 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 224914007459 Walker A/P-loop; other site 224914007460 ATP binding site; other site 224914007461 Q-loop/lid; other site 224914007462 ABC transporter signature motif; other site 224914007463 Walker B; other site 224914007464 D-loop; other site 224914007465 H-loop/switch region; other site 224914007466 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 224914007467 TM-ABC transporter signature motif; other site 224914007468 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 224914007469 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 224914007470 TM-ABC transporter signature motif; other site 224914007471 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914007472 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914007473 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 224914007474 tetramer interface; other site 224914007475 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 224914007476 Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_alpha; cd03463 224914007477 heterodimer interface; other site 224914007478 active site 224914007479 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl01383 224914007480 active site 224914007481 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 224914007482 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 224914007483 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914007484 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 224914007485 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007486 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007487 dimerization interface; other site 224914007488 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007489 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 224914007490 4-hydroxyphenylacetate catabolism regulatory protein HpaA; Region: HpaA; TIGR02297 224914007491 Cupin domain; Region: Cupin_2; cl09118 224914007492 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914007493 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 224914007494 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007495 Bacterial transcriptional regulator; Region: IclR; pfam01614 224914007496 Coenzyme A transferase; Region: CoA_trans; cl00773 224914007497 Coenzyme A transferase; Region: CoA_trans; cl00773 224914007498 Coenzyme A transferase; Region: CoA_trans; cl00773 224914007499 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 224914007500 active site 224914007501 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914007502 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 224914007503 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914007504 DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved...; Region: DEDDh; cd06127 224914007505 active site 224914007506 substrate binding site; other site 224914007507 catalytic site; other site 224914007508 Pyrimidine dimer DNA glycosylase; Region: Pyr_excise; cl12126 224914007509 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914007510 metal-binding site 224914007511 active site 224914007512 I-site; other site 224914007513 Uncharacterized conserved protein [Function unknown]; Region: COG3391 224914007514 DNA polymerase IV; Provisional; Region: PRK02794 224914007515 DNA Polymerase IV/Kappa; Region: Pol_IV_kappa; cd03586 224914007516 active site 224914007517 DNA binding site 224914007518 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 224914007519 Protein of unknown function (DUF3572); Region: DUF3572; pfam12096 224914007520 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 224914007521 active site 224914007522 phosphorylation site 224914007523 intermolecular recognition site; other site 224914007524 dimerization interface; other site 224914007525 response regulator PleD; Reviewed; Region: pleD; PRK09581 224914007526 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 224914007527 active site 224914007528 phosphorylation site 224914007529 intermolecular recognition site; other site 224914007530 dimerization interface; other site 224914007531 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 224914007532 active site 224914007533 phosphorylation site 224914007534 intermolecular recognition site; other site 224914007535 dimerization interface; other site 224914007536 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914007537 metal-binding site 224914007538 active site 224914007539 I-site; other site 224914007540 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 224914007541 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 224914007542 putative substrate translocation pore; other site 224914007543 Protein of unknown function (DUF983); Region: DUF983; cl02211 224914007544 ribonuclease R; Region: RNase_R; TIGR02063 224914007545 RNB domain; Region: RNB; pfam00773 224914007546 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an...; Region: S1_RNase_R; cd04471 224914007547 RNA binding site; other site 224914007548 DNA topoisomerase I; Validated; Region: PRK09138 224914007549 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in...; Region: TOPRIM_TopoIA_TopoI; cd03363 224914007550 active site 224914007551 interdomain interaction site; other site 224914007552 putative metal-binding site; other site 224914007553 nucleotide binding site; other site 224914007554 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded...; Region: TOP1Ac; cd00186 224914007555 domain I; other site 224914007556 DNA binding groove 224914007557 phosphate binding site; other site 224914007558 domain II; other site 224914007559 domain III; other site 224914007560 nucleotide binding site; other site 224914007561 catalytic site; other site 224914007562 domain IV; other site 224914007563 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 224914007564 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 224914007565 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 224914007566 Domain of unknown function (DUF205); Region: DUF205; cl00410 224914007567 dihydroorotase; Validated; Region: PRK09059 224914007568 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 224914007569 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 224914007570 active site 224914007571 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 224914007572 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 224914007573 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 224914007574 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 224914007575 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914007576 active site 224914007577 Uncharacterized protein family (UPF0081); Region: UPF0081; cl00525 224914007578 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 224914007579 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 224914007580 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 224914007581 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 224914007582 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 224914007583 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 224914007584 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 224914007585 anchoring element; other site 224914007586 dimer interface; other site 224914007587 ATP binding site; other site 224914007588 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 224914007589 active site 224914007590 metal-binding site 224914007591 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 224914007592 EamA-like transporter family; Region: EamA; cl01037 224914007593 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 224914007594 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 224914007595 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 224914007596 PAS fold; Region: PAS_3; pfam08447 224914007597 putative active site; other site 224914007598 heme pocket; other site 224914007599 PAS fold; Region: PAS_3; pfam08447 224914007600 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 224914007601 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 224914007602 Histidine kinase; Region: HisKA_2; cl06527 224914007603 Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]; Region: VirJ; COG3946 224914007604 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 224914007605 Predicted integral membrane protein [Function unknown]; Region: COG0392 224914007606 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 224914007607 Uncharacterized conserved protein [Function unknown]; Region: COG2898 224914007608 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 224914007609 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl00515 224914007610 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 224914007611 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 224914007612 Substrate binding site; other site 224914007613 Mg++ binding site; other site 224914007614 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 224914007615 active site 224914007616 substrate binding site; other site 224914007617 CoA binding site; other site 224914007618 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 224914007619 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate...; Region: GFAT; cd00714 224914007620 glutaminase active site; other site 224914007621 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 224914007622 dimer interface; other site 224914007623 active site 224914007624 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 224914007625 dimer interface; other site 224914007626 active site 224914007627 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 224914007628 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-...; Region: RecG_wedge_OBF; cd04488 224914007629 generic binding surface II; other site 224914007630 ssDNA binding site; other site 224914007631 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 224914007632 ATP binding site; other site 224914007633 putative Mg++ binding site; other site 224914007634 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 224914007635 nucleotide binding region; other site 224914007636 ATP-binding site; other site 224914007637 Protein of unknown function (DUF339); Region: Sdh5; cl01110 224914007638 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 224914007639 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 224914007640 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 224914007641 ATP binding site; other site 224914007642 putative Mg++ binding site; other site 224914007643 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 224914007644 nucleotide binding region; other site 224914007645 ATP-binding site; other site 224914007646 TRCF domain; Region: TRCF; pfam03461 224914007647 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914007648 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 224914007649 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 224914007650 catalytic residues; other site 224914007651 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 224914007652 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_14; cd08497 224914007653 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 224914007654 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; cl01548 224914007655 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07494 224914007656 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007657 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 224914007658 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 224914007659 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 224914007660 NADP binding site; other site 224914007661 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 224914007662 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 224914007663 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 224914007664 Walker A/P-loop; other site 224914007665 ATP binding site; other site 224914007666 Q-loop/lid; other site 224914007667 ABC transporter signature motif; other site 224914007668 Walker B; other site 224914007669 D-loop; other site 224914007670 H-loop/switch region; other site 224914007671 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 224914007672 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette...; Region: TM_PBP1_transp_TpRbsC_like; cd06580 224914007673 TM-ABC transporter signature motif; other site 224914007674 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 224914007675 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette...; Region: TM_PBP1_transp_TpRbsC_like; cd06580 224914007676 TM-ABC transporter signature motif; other site 224914007677 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 224914007678 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 224914007679 putative ligand binding site; other site 224914007680 MiaB-like tRNA modifying enzyme YliG, TIGR01125; Region: TIGR01125 224914007681 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 224914007682 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl14056 224914007683 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 224914007684 Ferritin-like domain; Region: Ferritin; pfam00210 224914007685 heme binding site; other site 224914007686 ferroxidase pore; other site 224914007687 ferroxidase diiron center; other site 224914007688 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 224914007689 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007690 Predicted transcriptional regulator [Transcription]; Region: COG1959 224914007691 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 224914007692 putative deacylase active site; other site 224914007693 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914007694 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 224914007695 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 224914007696 Integrase core domain; Region: rve; cl01316 224914007697 Integrase core domain; Region: rve; cl01316 224914007698 Uncharacterized protein family (UPF0149); Region: UPF0149; cl01173 224914007699 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914007700 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914007701 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3293 224914007702 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 224914007703 Protein of unknown function (DUF995); Region: DUF995; pfam06191 224914007704 Glycosyl hydrolase family 26; Region: Glyco_hydro_26; cl09200 224914007705 Protein of unknown function (DUF995); Region: DUF995; pfam06191 224914007706 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 224914007707 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007708 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 224914007709 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 224914007710 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 224914007711 UDP-glucose:1,4-beta-D-glucan 4-beta-D-glucosyltransferase; Region: PLN02638 224914007712 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 224914007713 active site 224914007714 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 224914007715 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007716 UDP-glucuronate decarboxylase; Region: PLN02206 224914007717 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007718 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 224914007719 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 224914007720 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 224914007721 peptide binding site; other site 224914007722 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 224914007723 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 224914007724 peptide binding site; other site 224914007725 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007726 dimer interface; other site 224914007727 conserved gate region; other site 224914007728 putative PBP binding loops; other site 224914007729 ABC-ATPase subunit interface; other site 224914007730 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007731 dimer interface; other site 224914007732 conserved gate region; other site 224914007733 ABC-ATPase subunit interface; other site 224914007734 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 224914007735 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914007736 Walker A/P-loop; other site 224914007737 ATP binding site; other site 224914007738 Q-loop/lid; other site 224914007739 ABC transporter signature motif; other site 224914007740 Walker B; other site 224914007741 D-loop; other site 224914007742 H-loop/switch region; other site 224914007743 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914007744 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914007745 Walker A/P-loop; other site 224914007746 ATP binding site; other site 224914007747 Q-loop/lid; other site 224914007748 ABC transporter signature motif; other site 224914007749 Walker B; other site 224914007750 D-loop; other site 224914007751 H-loop/switch region; other site 224914007752 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914007753 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; cl01206 224914007754 benzoate transport; Region: 2A0115; TIGR00895 224914007755 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 224914007756 putative substrate translocation pore; other site 224914007757 L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active...; Region: DmpA; cd02253 224914007758 homodimer interface; other site 224914007759 homotetramer interface; other site 224914007760 active site pocket 224914007761 cleavage site 224914007762 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914007763 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 224914007764 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 224914007765 Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; Region: Pyr_redox_dim; pfam02852 224914007766 dihydrolipoamide dehydrogenase; Validated; Region: PRK05976 224914007767 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007768 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 224914007769 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 224914007770 E3 interaction surface; other site 224914007771 lipoyl attachment site; other site 224914007772 e3 binding domain; Region: E3_binding; pfam02817 224914007773 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 224914007774 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 224914007775 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 224914007776 alpha subunit interface; other site 224914007777 TPP binding site; other site 224914007778 heterodimer interface; other site 224914007779 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 224914007780 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal; Region: OxoDH_E1alpha_N; pfam12573 224914007781 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 224914007782 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 224914007783 tetramer interface; other site 224914007784 TPP-binding site; other site 224914007785 heterodimer interface; other site 224914007786 phosphorylation loop region 224914007787 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 224914007788 The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two...; Region: ABC_MalK_N; cd03301 224914007789 Walker A/P-loop; other site 224914007790 ATP binding site; other site 224914007791 Q-loop/lid; other site 224914007792 ABC transporter signature motif; other site 224914007793 Walker B; other site 224914007794 D-loop; other site 224914007795 H-loop/switch region; other site 224914007796 TOBE domain; Region: TOBE_2; cl01440 224914007797 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914007798 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007799 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007800 dimer interface; other site 224914007801 conserved gate region; other site 224914007802 putative PBP binding loops; other site 224914007803 ABC-ATPase subunit interface; other site 224914007804 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007805 dimer interface; other site 224914007806 conserved gate region; other site 224914007807 putative PBP binding loops; other site 224914007808 ABC-ATPase subunit interface; other site 224914007809 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007810 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914007811 Predicted N-acetylglucosamine kinase [Carbohydrate transport and metabolism]; Region: COG2971 224914007812 ROK family; Region: ROK; cl09121 224914007813 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 224914007814 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914007815 DNA binding site 224914007816 UTRA domain; Region: UTRA; cl06649 224914007817 Membrane bound YbgT-like protein; Region: YbgT_YccB; cl02039 224914007818 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 224914007819 cytochrome d oxidase, subunit II (cydB); Region: cydB; TIGR00203 224914007820 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 224914007821 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 224914007822 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 224914007823 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914007824 Walker A/P-loop; other site 224914007825 ATP binding site; other site 224914007826 Q-loop/lid; other site 224914007827 ABC transporter signature motif; other site 224914007828 Walker B; other site 224914007829 D-loop; other site 224914007830 H-loop/switch region; other site 224914007831 ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydD; COG4988 224914007832 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914007833 The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with...; Region: ABCC_MRP_Like; cd03228 224914007834 Walker A/P-loop; other site 224914007835 ATP binding site; other site 224914007836 Q-loop/lid; other site 224914007837 ABC transporter signature motif; other site 224914007838 Walker B; other site 224914007839 D-loop; other site 224914007840 H-loop/switch region; other site 224914007841 Predicted transcriptional regulators [Transcription]; Region: COG1510 224914007842 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 224914007843 dimerization interface; other site 224914007844 putative DNA binding site; other site 224914007845 putative Zn2+ binding site; other site 224914007846 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 224914007847 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 224914007848 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 224914007849 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12666 224914007850 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 224914007851 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 224914007852 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12648 224914007853 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 224914007854 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 224914007855 NADH-ubiquinone/plastoquinone oxidoreductase chain 6; Region: Oxidored_q3; cl00676 224914007856 NADH-ubiquinone/plastoquinone oxidoreductase chain 6; Region: Oxidored_q3; cl00676 224914007857 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4529 224914007858 hypothetical protein; Provisional; Region: PRK09897 224914007859 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_4; cd02140 224914007860 dimer interface; other site 224914007861 FMN binding site; other site 224914007862 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 224914007863 MPT binding site; other site 224914007864 trimer interface; other site 224914007865 Biotin synthase and related enzymes [Coenzyme metabolism]; Region: BioB; COG0502 224914007866 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 224914007867 FeS/SAM binding site; other site 224914007868 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 224914007869 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 224914007870 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 224914007871 pyridoxal 5'-phosphate binding pocket; other site 224914007872 catalytic residue; other site 224914007873 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: PLN02974 224914007874 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914007875 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 224914007876 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 224914007877 inhibitor-cofactor binding pocket; inhibition site 224914007878 pyridoxal 5'-phosphate binding site; other site 224914007879 catalytic residue; other site 224914007880 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK05963 224914007881 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 224914007882 dimer interface; other site 224914007883 active site 224914007884 CoA binding pocket; other site 224914007885 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 224914007886 proposed active site lysine; other site 224914007887 conserved cys residue; other site 224914007888 Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell envelope biogenesis, outer membrane]; Region: Acm; COG3757 224914007889 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the...; Region: GH25_muramidase_1; cd06413 224914007890 active site 224914007891 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 224914007892 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914007893 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; cl00411 224914007894 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007895 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 224914007896 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007897 Protein of unknown function, DUF488; Region: DUF488; cl01246 224914007898 osmolarity response regulator; Provisional; Region: ompR; PRK09468 224914007899 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 224914007900 active site 224914007901 phosphorylation site 224914007902 intermolecular recognition site; other site 224914007903 dimerization interface; other site 224914007904 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914007905 DNA binding site 224914007906 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 224914007907 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 224914007908 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914007909 dimer interface; other site 224914007910 phosphorylation site 224914007911 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 224914007912 ATP binding site; other site 224914007913 Mg2+ binding site; other site 224914007914 G-X-G motif; other site 224914007915 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 224914007916 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 224914007917 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 224914007918 putative substrate translocation pore; other site 224914007919 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007920 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 224914007921 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914007922 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 224914007923 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 224914007924 Walker A/P-loop; other site 224914007925 ATP binding site; other site 224914007926 Q-loop/lid; other site 224914007927 ABC transporter signature motif; other site 224914007928 Walker B; other site 224914007929 D-loop; other site 224914007930 H-loop/switch region; other site 224914007931 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914007932 dimer interface; other site 224914007933 conserved gate region; other site 224914007934 putative PBP binding loops; other site 224914007935 ABC-ATPase subunit interface; other site 224914007936 Cupin domain; Region: Cupin_2; cl09118 224914007937 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 224914007938 ABC-2 type transporter; Region: ABC2_membrane; cl11417 224914007939 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 224914007940 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 224914007941 Walker A/P-loop; other site 224914007942 ATP binding site; other site 224914007943 Q-loop/lid; other site 224914007944 ABC transporter signature motif; other site 224914007945 Walker B; other site 224914007946 D-loop; other site 224914007947 H-loop/switch region; other site 224914007948 hypothetical protein; Provisional; Region: PRK03598 224914007949 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11552 224914007950 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914007951 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 224914007952 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 224914007953 Domain of unknown function DUF20; Region: UPF0118; cl00465 224914007954 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914007955 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914007956 DNA binding site 224914007957 FCD domain; Region: FCD; cl11656 224914007958 YeeE/YedE family (DUF395); Region: DUF395; cl01018 224914007959 YeeE/YedE family (DUF395); Region: DUF395; cl01018 224914007960 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 224914007961 dimerization interface; other site 224914007962 putative DNA binding site; other site 224914007963 putative Zn2+ binding site; other site 224914007964 Protein of unknown function (DUF808); Region: DUF808; cl01002 224914007965 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe...; Region: Pep_deformylase; cd00487 224914007966 active site 224914007967 catalytic residues; other site 224914007968 metal-binding site 224914007969 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 224914007970 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007971 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 224914007972 L-serine binding site; other site 224914007973 ACT domain interface; other site 224914007974 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 224914007975 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914007976 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 224914007977 Acyl-protein synthetase, LuxE; Region: LuxE; cl10450 224914007978 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 224914007979 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914007980 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 224914007981 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 224914007982 dimer interface; other site 224914007983 active site 224914007984 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914007985 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 224914007986 active site 224914007987 SelR domain; Region: SelR; cl00369 224914007988 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 224914007989 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914007990 The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold; Region: PBP2_BudR; cd08451 224914007991 putative dimerization interface; other site 224914007992 putative substrate binding pocket; other site 224914007993 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 224914007994 putative substrate translocation pore; other site 224914007995 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 224914007996 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 224914007997 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 224914007998 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 224914007999 Permease family; Region: Xan_ur_permease; cl00967 224914008000 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 224914008001 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 224914008002 active site 224914008003 C-methyltransferase; Region: Methyltransf_14; pfam08484 224914008004 Hypothetical methyltransferase; Region: Methyltransf_13; pfam08421 224914008005 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914008006 Cupin domain; Region: Cupin_2; cl09118 224914008007 Uncharacterized protein conserved in bacteria with an aminopeptidase-like domain [General function prediction only]; Region: COG4310 224914008008 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 224914008009 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008010 glutamate-1-semialdehyde 2,1-aminomutase; Provisional; Region: PRK06209 224914008011 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 224914008012 pyridoxal 5'-phosphate binding pocket; other site 224914008013 catalytic residue; other site 224914008014 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 224914008015 Polysaccharide pyruvyl transferase; Region: PS_pyruv_trans; cl09156 224914008016 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 224914008017 active site 224914008018 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 224914008019 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 224914008020 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 224914008021 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 224914008022 Mg++ binding site; other site 224914008023 putative catalytic motif; other site 224914008024 substrate binding site; other site 224914008025 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 224914008026 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 224914008027 putative metal binding site; other site 224914008028 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 224914008029 putative active site; other site 224914008030 wcaF-like: This group is composed of the protein product of the E. coli wcaF gene and similar proteins. WcaF is part of the gene cluster responsible for the biosynthesis of the extracellular polysaccharide colanic acid. The wcaF protein is predicted to...; Region: LbH_wcaF_like; cd05825 224914008031 putative trimer interface; other site 224914008032 putative active site; other site 224914008033 putative substrate binding site; other site 224914008034 putative CoA binding site; other site 224914008035 Surface antigen; Region: Surface_Ag_2; cl01155 224914008036 This family is most closely related to the GT1 family of glycosyltransferases. Bme6 in Brucella melitensis has been shown to be involved in the biosynthesis of a polysaccharide; Region: GT1_Bme6_like; cd03821 224914008037 putative ADP-binding pocket; other site 224914008038 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 224914008039 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 224914008040 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 224914008041 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 224914008042 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 224914008043 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 224914008044 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 224914008045 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 224914008046 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 224914008047 Chain length determinant protein; Region: Wzz; cl01623 224914008048 cellulose synthase operon protein YhjQ; Region: cellulose_yhjQ; TIGR03371 224914008049 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 224914008050 G3 box; other site 224914008051 Switch II region; other site 224914008052 G4 box; other site 224914008053 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 224914008054 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914008055 DNA binding residues 224914008056 dimerization interface; other site 224914008057 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 224914008058 ligand binding site; other site 224914008059 flexible hinge region; other site 224914008060 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008061 putative switch regulator; other site 224914008062 non-specific DNA interactions; other site 224914008063 DNA binding site 224914008064 sequence specific DNA binding site; other site 224914008065 putative cAMP binding site; other site 224914008066 N-acetylneuraminic acid mutarotase; Provisional; Region: PRK14131 224914008067 Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]; Region: NanE; COG3010 224914008068 N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family...; Region: NanE; cd04729 224914008069 putative active site cavity; other site 224914008070 N-acetylmannosamine kinase; Provisional; Region: PRK05082 224914008071 ROK family; Region: ROK; cl09121 224914008072 Transcriptional regulators [Transcription]; Region: FadR; COG2186 224914008073 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914008074 DNA binding site 224914008075 FCD domain; Region: FCD; cl11656 224914008076 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 224914008077 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 224914008078 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008079 dimer interface; other site 224914008080 conserved gate region; other site 224914008081 putative PBP binding loops; other site 224914008082 ABC-ATPase subunit interface; other site 224914008083 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008084 dimer interface; other site 224914008085 conserved gate region; other site 224914008086 putative PBP binding loops; other site 224914008087 ABC-ATPase subunit interface; other site 224914008088 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 224914008089 Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family...; Region: DHDPS-like; cd00408 224914008090 inhibitor site; inhibition site 224914008091 active site 224914008092 dimer interface; other site 224914008093 catalytic residue; other site 224914008094 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 224914008095 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914008096 Walker A/P-loop; other site 224914008097 ATP binding site; other site 224914008098 Q-loop/lid; other site 224914008099 ABC transporter signature motif; other site 224914008100 Walker B; other site 224914008101 D-loop; other site 224914008102 H-loop/switch region; other site 224914008103 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914008104 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 224914008105 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 224914008106 Walker A/P-loop; other site 224914008107 ATP binding site; other site 224914008108 Q-loop/lid; other site 224914008109 ABC transporter signature motif; other site 224914008110 Walker B; other site 224914008111 D-loop; other site 224914008112 H-loop/switch region; other site 224914008113 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 224914008114 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008115 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914008116 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914008117 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008118 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 224914008119 Zinc-dependent alcohol dehydrogenases (ADH) and class III ADG (AKA formaldehyde dehydrogenase); Region: liver_ADH_like1; cd08281 224914008120 NAD binding site; other site 224914008121 catalytic Zn binding site; other site 224914008122 substrate binding site; other site 224914008123 structural Zn binding site; other site 224914008124 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914008125 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914008126 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 224914008127 tetramerization interface; other site 224914008128 NAD(P) binding site; other site 224914008129 catalytic residues; other site 224914008130 choline dehydrogenase; Validated; Region: PRK02106 224914008131 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 224914008132 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 224914008133 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 224914008134 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 224914008135 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 224914008136 shikimate binding site; other site 224914008137 NAD(P) binding site; other site 224914008138 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 224914008139 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008140 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 224914008141 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 224914008142 Walker A/P-loop; other site 224914008143 ATP binding site; other site 224914008144 Q-loop/lid; other site 224914008145 ABC transporter signature motif; other site 224914008146 Walker B; other site 224914008147 D-loop; other site 224914008148 H-loop/switch region; other site 224914008149 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 224914008150 TM-ABC transporter signature motif; other site 224914008151 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 224914008152 TM-ABC transporter signature motif; other site 224914008153 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 224914008154 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E...; Region: ABC_Mj1267_LivG_branched; cd03219 224914008155 Walker A/P-loop; other site 224914008156 ATP binding site; other site 224914008157 Q-loop/lid; other site 224914008158 ABC transporter signature motif; other site 224914008159 Walker B; other site 224914008160 D-loop; other site 224914008161 H-loop/switch region; other site 224914008162 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 224914008163 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 224914008164 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 224914008165 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 224914008166 NAD(P) binding site; other site 224914008167 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914008168 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914008169 DNA binding site 224914008170 FCD domain; Region: FCD; cl11656 224914008171 Cytochrome P450; Region: p450; cl12078 224914008172 Acetokinase family; Region: Acetate_kinase; cl01029 224914008173 putative phosphoketolase; Provisional; Region: PRK05261 224914008174 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 224914008175 TPP-binding site; other site 224914008176 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; Region: XFP; pfam03894 224914008177 XFP C-terminal domain; Region: XFP_C; pfam09363 224914008178 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 224914008179 Iron permease FTR1 family; Region: FTR1; cl00475 224914008180 Fe2+ transport protein; Region: Iron_transport; cl01377 224914008181 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 224914008182 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 224914008183 AMP/PPi binding site; other site 224914008184 candidate oxyanion hole; other site 224914008185 catalytic triad; other site 224914008186 potential glutamine specificity residues; other site 224914008187 GMP synthase, PP-ATPase domain/subunit [Nucleotide transport and metabolism]; Region: GuaA; COG0519 224914008188 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 224914008189 ATP Binding subdomain; other site 224914008190 Ligand Binding sites; other site 224914008191 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 224914008192 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 224914008193 CoenzymeA binding site; other site 224914008194 subunit interaction site; other site 224914008195 PHB binding site; other site 224914008196 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 224914008197 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 224914008198 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 224914008199 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 224914008200 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 224914008201 tetramer interface; other site 224914008202 heme binding pocket; other site 224914008203 NADPH binding site; other site 224914008204 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 224914008205 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008206 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 224914008207 dimerization interface; other site 224914008208 Cytochrome c [Energy production and conversion]; Region: COG3258 224914008209 Cytochrome c; Region: Cytochrom_C; cl11414 224914008210 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 224914008211 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 224914008212 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 224914008213 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the...; Region: IMPDH; cd00381 224914008214 active site 224914008215 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 224914008216 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 224914008217 putative ion selectivity filter; other site 224914008218 putative pore gating glutamate residue; other site 224914008219 putative H+/Cl- coupling transport residue; other site 224914008220 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly...; Region: nylC_like; cd02252 224914008221 putative active site pocket; other site 224914008222 cleavage site 224914008223 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 224914008224 ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In...; Region: ManB; cd03088 224914008225 active site 224914008226 substrate binding site; other site 224914008227 metal-binding site 224914008228 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 224914008229 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 224914008230 Substrate binding site; other site 224914008231 Cupin domain; Region: Cupin_2; cl09118 224914008232 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914008233 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914008234 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]; Region: COG4943 224914008235 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 224914008236 hns-dependent expression protein A (HdeA); Region: HdeA; cl05752 224914008237 Glutaminase; Region: Glutaminase; cl00907 224914008238 Glutaminase; Region: Glutaminase; cl00907 224914008239 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 224914008240 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 224914008241 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 224914008242 pyridoxal 5'-phosphate binding pocket; other site 224914008243 catalytic residue; other site 224914008244 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 224914008245 Protein of unknown function (DUF1269); Region: DUF1269; cl01978 224914008246 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 224914008247 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 224914008248 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 224914008249 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008250 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008251 dimer interface; other site 224914008252 conserved gate region; other site 224914008253 putative PBP binding loops; other site 224914008254 ABC-ATPase subunit interface; other site 224914008255 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008256 dimer interface; other site 224914008257 conserved gate region; other site 224914008258 putative PBP binding loops; other site 224914008259 ABC-ATPase subunit interface; other site 224914008260 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 224914008261 PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues...; Region: ABC_PotA_N; cd03300 224914008262 Walker A/P-loop; other site 224914008263 ATP binding site; other site 224914008264 Q-loop/lid; other site 224914008265 ABC transporter signature motif; other site 224914008266 Walker B; other site 224914008267 D-loop; other site 224914008268 H-loop/switch region; other site 224914008269 TOBE domain; Region: TOBE_2; cl01440 224914008270 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 224914008271 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914008272 Domain of unknown function (DUF3597); Region: DUF3597; pfam12200 224914008273 Septum formation topological specificity factor MinE; Region: MinE; cl00538 224914008274 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 224914008275 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...; Region: MinD; cd02036 224914008276 Switch I; other site 224914008277 Switch II; other site 224914008278 ADP binding residues; other site 224914008279 septum formation inhibitor; Reviewed; Region: minC; PRK05177 224914008280 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 224914008281 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 224914008282 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 224914008283 dimer interface; other site 224914008284 putative radical transfer pathway; other site 224914008285 diiron center; other site 224914008286 tyrosyl radical; other site 224914008287 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08188 224914008288 Ribonucleotide reductase N-terminal; Region: RNR_N; pfam08343 224914008289 Class I ribonucleotide reductase; Region: RNR_I; cd01679 224914008290 active site 224914008291 dimer interface; other site 224914008292 catalytic residues; other site 224914008293 effector binding site; other site 224914008294 R2 peptide binding site; other site 224914008295 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 224914008296 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide...; Region: NrdH; cd02976 224914008297 catalytic residues; other site 224914008298 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 224914008299 Bacterial protein of unknown function (DUF894); Region: DUF894; pfam05977 224914008300 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 224914008301 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914008302 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008303 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914008304 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 224914008305 conserved cys residue; other site 224914008306 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008307 ABC transporter signature motif; other site 224914008308 Walker B; other site 224914008309 D-loop; other site 224914008310 H-loop/switch region; other site 224914008311 TOBE domain; Region: TOBE_2; cl01440 224914008312 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008313 Walker A/P-loop; other site 224914008314 ATP binding site; other site 224914008315 Q-loop/lid; other site 224914008316 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008317 dimer interface; other site 224914008318 conserved gate region; other site 224914008319 putative PBP binding loops; other site 224914008320 ABC-ATPase subunit interface; other site 224914008321 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008322 putative PBP binding loops; other site 224914008323 dimer interface; other site 224914008324 ABC-ATPase subunit interface; other site 224914008325 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 224914008326 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 224914008327 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914008328 Transcriptional regulators [Transcription]; Region: PurR; COG1609 224914008329 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 224914008330 DNA binding site 224914008331 domain linker motif; other site 224914008332 Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_AglR_RafR_like; cd06271 224914008333 ligand binding site; other site 224914008334 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 224914008335 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 224914008336 ligand binding site; other site 224914008337 flexible hinge region; other site 224914008338 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008339 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 224914008340 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 224914008341 putative substrate translocation pore; other site 224914008342 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 224914008343 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_Nitrate-R-NarG-like; cd02750 224914008344 [4Fe-4S] binding site; other site 224914008345 molybdopterin cofactor binding site; other site 224914008346 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 224914008347 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 224914008348 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 224914008349 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-...; Region: Molybdopterin-Binding; cl09928 224914008350 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 224914008351 molybdopterin cofactor binding site; other site 224914008352 nitrate reductase, beta subunit; Region: narH; TIGR01660 224914008353 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cl00470 224914008354 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 224914008355 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 224914008356 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 224914008357 PPIC-type PPIASE domain; Region: Rotamase; cl08278 224914008358 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008359 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 224914008360 Flavoprotein; Region: Flavoprotein; cl08021 224914008361 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 224914008362 SCP-2 sterol transfer family; Region: SCP2; cl01225 224914008363 Peptidase family U32; Region: Peptidase_U32; pfam01136 224914008364 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 224914008365 Peptidase family U32; Region: Peptidase_U32; pfam01136 224914008366 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 224914008367 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars...; Region: ABC_NrtD_SsuB_transporters; cd03293 224914008368 Walker A/P-loop; other site 224914008369 ATP binding site; other site 224914008370 Q-loop/lid; other site 224914008371 ABC transporter signature motif; other site 224914008372 Walker B; other site 224914008373 D-loop; other site 224914008374 H-loop/switch region; other site 224914008375 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008376 dimer interface; other site 224914008377 conserved gate region; other site 224914008378 putative PBP binding loops; other site 224914008379 ABC-ATPase subunit interface; other site 224914008380 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 224914008381 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914008382 NnrS protein; Region: NnrS; cl01258 224914008383 Multicopper oxidase; Region: Cu-oxidase; cl11412 224914008384 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 224914008385 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008386 ApbE family; Region: ApbE; cl00643 224914008387 NosL; Region: NosL; cl01769 224914008388 ABC-2 type transporter; Region: ABC2_membrane; cl11417 224914008389 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 224914008390 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008391 Walker A/P-loop; other site 224914008392 ATP binding site; other site 224914008393 Q-loop/lid; other site 224914008394 ABC transporter signature motif; other site 224914008395 Walker B; other site 224914008396 D-loop; other site 224914008397 H-loop/switch region; other site 224914008398 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 224914008399 Periplasmic copper-binding protein (NosD); Region: NosD; pfam05048 224914008400 nitrous-oxide reductase; Validated; Region: PRK02888 224914008401 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl10078 224914008402 nitrous-oxide reductase; Validated; Region: PRK02888 224914008403 FMN-binding domain; Region: FMN_bind; cl01081 224914008404 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 224914008405 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 224914008406 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 224914008407 Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed...; Region: ABCD_peroxisomal_ALDP; cd03223 224914008408 Protein of unknown function (DUF2384); Region: DUF2384; pfam09722 224914008409 RES domain; Region: RES; cl02411 224914008410 Ribulose kinase [Energy production and conversion]; Region: AraB; COG1069 224914008411 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; pfam00370 224914008412 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 224914008413 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008414 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 224914008415 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 224914008416 TM-ABC transporter signature motif; other site 224914008417 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 224914008418 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008419 Walker A/P-loop; other site 224914008420 ATP binding site; other site 224914008421 Q-loop/lid; other site 224914008422 ABC transporter signature motif; other site 224914008423 Walker B; other site 224914008424 D-loop; other site 224914008425 H-loop/switch region; other site 224914008426 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 224914008427 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 224914008428 putative ligand binding site; other site 224914008429 Transcriptional regulators [Transcription]; Region: PurR; COG1609 224914008430 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cl02583 224914008431 Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs; Region: PBP1_FruR; cd06274 224914008432 dimerization interface; other site 224914008433 ligand binding site; other site 224914008434 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 224914008435 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 224914008436 ligand binding site; other site 224914008437 flexible hinge region; other site 224914008438 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 224914008439 putative switch regulator; other site 224914008440 non-specific DNA interactions; other site 224914008441 DNA binding site 224914008442 sequence specific DNA binding site; other site 224914008443 putative cAMP binding site; other site 224914008444 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; cl00556 224914008445 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 224914008446 Multicopper oxidase; Region: Cu-oxidase; cl11412 224914008447 Multicopper oxidase; Region: Cu-oxidase; cl11412 224914008448 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 224914008449 Isoprenylcysteine carboxyl methyltransferase (ICMT) family; Region: ICMT; cl00763 224914008450 Domain of unknown function DUF59; Region: DUF59; cl00941 224914008451 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cl00436 224914008452 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cl00436 224914008453 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-...; Region: SirA_YedF_YeeD; cl00436 224914008454 Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]; Region: NorD; COG4548 224914008455 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 224914008456 metal ion-dependent adhesion site (MIDAS); other site 224914008457 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes...; Region: AAA; cd00009 224914008458 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 224914008459 Walker A motif; other site 224914008460 ATP binding site; other site 224914008461 Walker B motif; other site 224914008462 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 224914008463 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily...; Region: Heme_Cu_Oxidase_I; cl00275 224914008464 D-pathway; other site 224914008465 K-pathway; other site 224914008466 Binuclear center (active site); other site 224914008467 Putative proton exit pathway; other site 224914008468 Cytochrome c; Region: Cytochrom_C; cl11414 224914008469 NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits...; Region: NorE_like; cd02862 224914008470 Uncharacterized conserved protein [Function unknown]; Region: COG3945 224914008471 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 224914008472 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 224914008473 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 224914008474 Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family...; Region: DHDPS-like; cd00408 224914008475 inhibitor site; inhibition site 224914008476 active site 224914008477 dimer interface; other site 224914008478 catalytic residue; other site 224914008479 Transcriptional regulators [Transcription]; Region: GntR; COG1802 224914008480 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914008481 DNA binding site 224914008482 FCD domain; Region: FCD; cl11656 224914008483 EamA-like transporter family; Region: EamA; cl01037 224914008484 EamA-like transporter family; Region: EamA; cl01037 224914008485 GAF domain; Region: GAF; cl00853 224914008486 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 224914008487 metal-binding site 224914008488 active site 224914008489 I-site; other site 224914008490 ApbE family; Region: ApbE; cl00643 224914008491 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 224914008492 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 224914008493 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR_like2; cd06201 224914008494 FAD binding pocket; other site 224914008495 FAD binding motif; other site 224914008496 catalytic residues; other site 224914008497 NAD binding pocket; other site 224914008498 phosphate binding motif; other site 224914008499 beta-alpha-beta structure motif; other site 224914008500 Predicted periplasmic protein (DUF2271); Region: DUF2271; cl01469 224914008501 Uncharacterized conserved protein [Function unknown]; Region: COG5591 224914008502 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 224914008503 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 224914008504 active site 224914008505 phosphorylation site 224914008506 intermolecular recognition site; other site 224914008507 dimerization interface; other site 224914008508 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase...; Region: trans_reg_C; cd00383 224914008509 DNA binding site 224914008510 sensor protein QseC; Provisional; Region: PRK10337 224914008511 Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The...; Region: HAMP; cl01054 224914008512 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-...; Region: HisKA; cd00082 224914008513 dimer interface; other site 224914008514 phosphorylation site 224914008515 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 224914008516 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 224914008517 potential catalytic triad; other site 224914008518 conserved cys residue; other site 224914008519 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg7; cd04786 224914008520 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 224914008521 DNA binding residues 224914008522 putative dimer interface; other site 224914008523 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 224914008524 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 224914008525 putative active site; other site 224914008526 putative FMN binding site; other site 224914008527 putative substrate binding site; other site 224914008528 putative catalytic residue; other site 224914008529 CoA-transferase family III; Region: CoA_transf_3; cl00778 224914008530 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 224914008531 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008532 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 224914008533 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 224914008534 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 224914008535 enoyl-CoA hydratase; Provisional; Region: PRK05980 224914008536 substrate binding site; other site 224914008537 oxyanion hole (OAH) forming residues; other site 224914008538 trimer interface; other site 224914008539 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008540 Transcriptional regulator [Transcription]; Region: IclR; COG1414 224914008541 Bacterial transcriptional regulator; Region: IclR; pfam01614 224914008542 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 224914008543 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 224914008544 active site 224914008545 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 224914008546 putative substrate translocation pore; other site 224914008547 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 224914008548 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 224914008549 ATP binding site; other site 224914008550 Mg2+ binding site; other site 224914008551 G-X-G motif; other site 224914008552 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 224914008553 ATP binding site; other site 224914008554 MutL C terminal dimerization domain; Region: MutL_C; cl07336 224914008555 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; cl11535 224914008556 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 224914008557 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 224914008558 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 224914008559 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 224914008560 Glycosyl transferases group 1; Region: Glycos_transf_1; cl12012 224914008561 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 224914008562 putative acyl-acceptor binding pocket; other site 224914008563 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 224914008564 active site 224914008565 Putative modulator of DNA gyrase; Region: PmbA_TldD; cl00398 224914008566 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 224914008567 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 224914008568 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008569 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 224914008570 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 224914008571 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 224914008572 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 224914008573 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 224914008574 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 224914008575 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 224914008576 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 224914008577 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 224914008578 S-adenosylmethionine binding site; other site 224914008579 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 224914008580 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 224914008581 RNA binding surface; other site 224914008582 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 224914008583 active site 224914008584 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 224914008585 nucleoside/Zn binding site; other site 224914008586 dimer interface; other site 224914008587 catalytic motif; other site 224914008588 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 224914008589 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 224914008590 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 224914008591 HIGH motif; other site 224914008592 active site 224914008593 nucleotide binding site; other site 224914008594 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 224914008595 active site 224914008596 KMSKS motif; other site 224914008597 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 224914008598 tRNA binding surface; other site 224914008599 anticodon binding site; other site 224914008600 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 224914008601 riboflavin kinase, C-terminal domain of the bifunctional riboflavin biosynthesis protein; Region: Flavokinase_C; cd02064 224914008602 active site 224914008603 Riboflavin kinase; Region: Flavokinase; pfam01687 224914008604 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 224914008605 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 224914008606 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts...; Region: cpn10; cd00320 224914008607 oligomerisation interface; other site 224914008608 mobile loop; other site 224914008609 roof hairpin; other site 224914008610 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 224914008611 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 224914008612 ring oligomerisation interface; other site 224914008613 ATP/Mg binding site; other site 224914008614 stacking interactions; other site 224914008615 hinge regions; other site 224914008616 fumarate hydratase; Reviewed; Region: fumC; PRK00485 224914008617 Class II fumarases; Region: Fumarase_classII; cd01362 224914008618 active site 224914008619 tetramer interface; other site 224914008620 DoxX; Region: DoxX; cl00976 224914008621 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 224914008622 putative substrate translocation pore; other site 224914008623 glucose/galactose transporter; Region: gluP; TIGR01272 224914008624 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cl11400 224914008625 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12295 224914008626 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 224914008627 motif 1; other site 224914008628 dimer interface; other site 224914008629 active site 224914008630 motif 2; other site 224914008631 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 224914008632 active site 224914008633 motif 3; other site 224914008634 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 224914008635 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 224914008636 dimer interface; other site 224914008637 motif 1; other site 224914008638 motif 2; other site 224914008639 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 224914008640 active site 224914008641 motif 3; other site 224914008642 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 224914008643 anticodon binding site; other site 224914008644 LysE type translocator; Region: LysE; cl00565 224914008645 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 224914008646 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 224914008647 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 224914008648 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and...; Region: Aldo_ket_red; cd06660 224914008649 active site 224914008650 catalytic tetrad; other site 224914008651 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 224914008652 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-; Region: HCP_like; cl00255 224914008653 Cysteine-rich domain; Region: CCG; pfam02754 224914008654 Cysteine-rich domain; Region: CCG; pfam02754 224914008655 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 224914008656 FAD binding domain; Region: FAD_binding_4; cl10516 224914008657 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 224914008658 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 224914008659 FAD binding domain; Region: FAD_binding_4; cl10516 224914008660 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008661 transcriptional activator TtdR; Provisional; Region: PRK09801 224914008662 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 224914008663 putative effector binding pocket; other site 224914008664 dimerization interface; other site 224914008665 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 224914008666 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 224914008667 DNA binding site 224914008668 FCD domain; Region: FCD; cl11656 224914008669 Protein of unknown function (DUF465); Region: DUF465; cl01070 224914008670 Cytochrome c; Region: Cytochrom_C; cl11414 224914008671 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43...; Region: PL2_Passenger_AT; cd01344 224914008672 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 224914008673 Autotransporter beta-domain; Region: Autotransporter; cl02365 224914008674 autotransporter-associated beta strand repeat; Region: autotrns_rpt; TIGR02601 224914008675 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 224914008676 Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their...; Region: malate_synt; cl09155 224914008677 Uncharacterized conserved protein [Function unknown]; Region: COG3777 224914008678 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 224914008679 active site 2 224914008680 active site 1 224914008681 CoA-transferase family III; Region: CoA_transf_3; cl00778 224914008682 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914008683 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008684 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 224914008685 putative dimerization interface; other site 224914008686 Uncharacterized protein conserved in bacteria (DUF2195); Region: DUF2195; cl02042 224914008687 FliP family; Region: FliP; cl00593 224914008688 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 224914008689 Flagellar L-ring protein; Region: FlgH; cl00905 224914008690 Uncharacterized conserved protein [Function unknown]; Region: COG3334 224914008691 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 224914008692 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 224914008693 SAF domain; Region: SAF; cl00555 224914008694 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 224914008695 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 224914008696 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 224914008697 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK12782 224914008698 Domain of unknown function (DUF1078); Region: DUF1078; pfam06429 224914008699 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06003 224914008700 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 224914008701 Protein of unknown function, DUF1537; Region: DUF1537; cl01345 224914008702 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 224914008703 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cl12060 224914008704 Metal-binding active site; metal-binding site 224914008705 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 224914008706 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008707 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 224914008708 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 224914008709 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008710 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 224914008711 intersubunit interface; other site 224914008712 active site 224914008713 Zn2+ binding site; other site 224914008714 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 224914008715 d-galactonate transporter; Region: 2A0114; TIGR00893 224914008716 putative substrate translocation pore; other site 224914008717 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl01116 224914008718 DNA-binding transcriptional activator FeaR; Provisional; Region: PRK09685 224914008719 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 224914008720 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl01961 224914008721 YdjC-like protein; Region: YdjC; cl01344 224914008722 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 224914008723 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 224914008724 Ligand binding site; other site 224914008725 Putative Catalytic site; other site 224914008726 DXD motif; other site 224914008727 Peptidase family M48; Region: Peptidase_M48; cl12018 224914008728 PAP2_like proteins, Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS), the major...; Region: PAP2_lipid_A_1_phosphatase; cd03389 224914008729 active site 224914008730 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008731 Walker A motif; other site 224914008732 ATP binding site; other site 224914008733 Walker B motif; other site 224914008734 flagellum-specific ATP synthase; Validated; Region: fliI; PRK06002 224914008735 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12642 224914008736 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 224914008737 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 224914008738 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 224914008739 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 224914008740 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 224914008741 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 224914008742 Flagellar motor switch protein [Cell motility and secretion]; Region: FliM; COG1868 224914008743 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 224914008744 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 224914008745 Flagellar motor switch protein [Cell motility and secretion]; Region: FliG; COG1536 224914008746 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; cl12017 224914008747 FlhB HrpN YscU SpaS Family; Region: Bac_export_2; pfam01312 224914008748 Autoinducer binding domain; Region: Autoind_bind; pfam03472 224914008749 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors...; Region: LuxR_C_like; cd06170 224914008750 DNA binding residues 224914008751 dimerization interface; other site 224914008752 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 224914008753 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 224914008754 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 224914008755 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 224914008756 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 224914008757 putative substrate translocation pore; other site 224914008758 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 224914008759 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 224914008760 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008761 dimer interface; other site 224914008762 conserved gate region; other site 224914008763 putative PBP binding loops; other site 224914008764 ABC-ATPase subunit interface; other site 224914008765 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cd06261 224914008766 dimer interface; other site 224914008767 conserved gate region; other site 224914008768 putative PBP binding loops; other site 224914008769 ABC-ATPase subunit interface; other site 224914008770 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 224914008771 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 224914008772 Walker A/P-loop; other site 224914008773 ATP binding site; other site 224914008774 Q-loop/lid; other site 224914008775 ABC transporter signature motif; other site 224914008776 Walker B; other site 224914008777 D-loop; other site 224914008778 H-loop/switch region; other site 224914008779 TOBE domain; Region: TOBE_2; cl01440 224914008780 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008781 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 224914008782 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 224914008783 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914008784 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008785 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; cl11611 224914008786 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 224914008787 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 224914008788 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 224914008789 O-Antigen ligase; Region: Wzy_C; cl04850 224914008790 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 224914008791 active site 224914008792 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp1; TIGR03087 224914008793 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 224914008794 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 224914008795 Chain length determinant protein; Region: Wzz; cl01623 224914008796 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 224914008797 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 224914008798 dimer interface; other site 224914008799 active site 224914008800 pyridoxal 5'-phosphate (PLP) binding site; other site 224914008801 catalytic residues; other site 224914008802 substrate binding site; other site 224914008803 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 224914008804 Transcriptional regulator [Transcription]; Region: LysR; COG0583 224914008805 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 224914008806 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 224914008807 putative effector binding pocket; other site 224914008808 dimerization interface; other site 224914008809 Protein of unknown function (DUF1007); Region: DUF1007; cl01487 224914008810 High-affinity nickel-transport protein; Region: NicO; cl00964