-- dump date 20140618_184440 -- class Genbank::misc_feature -- table misc_feature_note -- id note 591001000001 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001000002 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 591001000003 Walker A motif; other site 591001000004 ATP binding site [chemical binding]; other site 591001000005 Walker B motif; other site 591001000006 arginine finger; other site 591001000007 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 591001000008 DnaA box-binding interface [nucleotide binding]; other site 591001000009 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 591001000010 DnaA N-terminal domain; Region: DnaA_N; pfam11638 591001000011 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001000012 Walker A motif; other site 591001000013 ATP binding site [chemical binding]; other site 591001000014 Walker B motif; other site 591001000015 arginine finger; other site 591001000016 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 591001000017 DnaA box-binding interface [nucleotide binding]; other site 591001000018 DNA polymerase III subunit beta; Validated; Region: PRK05643 591001000019 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 591001000020 putative DNA binding surface [nucleotide binding]; other site 591001000021 dimer interface [polypeptide binding]; other site 591001000022 beta-clamp/clamp loader binding surface; other site 591001000023 beta-clamp/translesion DNA polymerase binding surface; other site 591001000024 recombination protein F; Reviewed; Region: recF; PRK00064 591001000025 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001000026 Walker A/P-loop; other site 591001000027 ATP binding site [chemical binding]; other site 591001000028 Q-loop/lid; other site 591001000029 Walker B; other site 591001000030 D-loop; other site 591001000031 H-loop/switch region; other site 591001000032 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001000033 ABC transporter signature motif; other site 591001000034 Walker B; other site 591001000035 D-loop; other site 591001000036 H-loop/switch region; other site 591001000037 Protein of unknown function (DUF721); Region: DUF721; pfam05258 591001000038 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 591001000039 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 591001000040 ATP binding site [chemical binding]; other site 591001000041 Mg2+ binding site [ion binding]; other site 591001000042 G-X-G motif; other site 591001000043 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 591001000044 anchoring element; other site 591001000045 dimer interface [polypeptide binding]; other site 591001000046 ATP binding site [chemical binding]; other site 591001000047 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 591001000048 active site 591001000049 putative metal-binding site [ion binding]; other site 591001000050 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 591001000051 Thiamine pyrophosphokinase; Region: TPK; cd07995 591001000052 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 591001000053 active site 591001000054 dimerization interface [polypeptide binding]; other site 591001000055 thiamine binding site [chemical binding]; other site 591001000056 hypothetical protein; Provisional; Region: PRK10621 591001000057 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 591001000058 DNA gyrase subunit A; Validated; Region: PRK05560 591001000059 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 591001000060 CAP-like domain; other site 591001000061 active site 591001000062 primary dimer interface [polypeptide binding]; other site 591001000063 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 591001000064 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 591001000065 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 591001000066 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 591001000067 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 591001000068 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 591001000069 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000070 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000071 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 591001000072 dimerization interface [polypeptide binding]; other site 591001000073 malate dehydrogenase; Provisional; Region: PRK13529 591001000074 Malic enzyme, N-terminal domain; Region: malic; pfam00390 591001000075 NAD(P) binding domain of malic enzyme (ME), subgroup 1; Region: NAD_bind_1_malic_enz; cd05312 591001000076 NAD(P) binding site [chemical binding]; other site 591001000077 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 591001000078 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_12; cd06347 591001000079 putative ligand binding site [chemical binding]; other site 591001000080 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 591001000081 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 591001000082 TM-ABC transporter signature motif; other site 591001000083 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 591001000084 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 591001000085 TM-ABC transporter signature motif; other site 591001000086 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 591001000087 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 591001000088 Walker A/P-loop; other site 591001000089 ATP binding site [chemical binding]; other site 591001000090 Q-loop/lid; other site 591001000091 ABC transporter signature motif; other site 591001000092 Walker B; other site 591001000093 D-loop; other site 591001000094 H-loop/switch region; other site 591001000095 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 591001000096 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 591001000097 Walker A/P-loop; other site 591001000098 ATP binding site [chemical binding]; other site 591001000099 Q-loop/lid; other site 591001000100 ABC transporter signature motif; other site 591001000101 Walker B; other site 591001000102 D-loop; other site 591001000103 H-loop/switch region; other site 591001000104 FOG: CBS domain [General function prediction only]; Region: COG0517 591001000105 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce...; Region: CBS_pair_ACT_assoc2; cd04585 591001000106 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 591001000107 Bacterial protein of unknown function (DUF951); Region: DUF951; pfam06107 591001000108 Protein of unknown function (DUF805); Region: DUF805; pfam05656 591001000109 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 591001000110 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001000111 Zn2+ binding site [ion binding]; other site 591001000112 Mg2+ binding site [ion binding]; other site 591001000113 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 591001000114 Ferritin-like domain; Region: Ferritin; pfam00210 591001000115 ferroxidase diiron center [ion binding]; other site 591001000116 Hantavirus glycoprotein G1; Region: Hanta_G1; pfam01567 591001000117 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 591001000118 nudix motif; other site 591001000119 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 591001000120 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 591001000121 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001000122 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 591001000123 metal binding site [ion binding]; metal-binding site 591001000124 glutamate racemase; Provisional; Region: PRK00865 591001000125 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 591001000126 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 591001000127 ATP binding site [chemical binding]; other site 591001000128 Mg2+ binding site [ion binding]; other site 591001000129 G-X-G motif; other site 591001000130 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 591001000131 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 591001000132 active site 591001000133 phosphorylation site [posttranslational modification] 591001000134 intermolecular recognition site; other site 591001000135 dimerization interface [polypeptide binding]; other site 591001000136 LytTr DNA-binding domain; Region: LytTR; smart00850 591001000137 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 591001000138 YadA-like C-terminal region; Region: YadA; pfam03895 591001000139 S-layer homology domain; Region: SLH; pfam00395 591001000140 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 591001000141 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 591001000142 Ligand Binding Site [chemical binding]; other site 591001000143 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 591001000144 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 591001000145 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001000146 catalytic residue [active] 591001000147 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 591001000148 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 591001000149 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 591001000150 dimer interface [polypeptide binding]; other site 591001000151 ssDNA binding site [nucleotide binding]; other site 591001000152 tetramer (dimer of dimers) interface [polypeptide binding]; other site 591001000153 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 591001000154 Predicted membrane protein (DUF2232); Region: DUF2232; pfam09991 591001000155 Domain of unknown function (DUF4133); Region: DUF4133; pfam13571 591001000156 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 591001000157 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 591001000158 DHH family; Region: DHH; pfam01368 591001000159 DHHA1 domain; Region: DHHA1; pfam02272 591001000160 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 591001000161 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 591001000162 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 591001000163 replicative DNA helicase; Region: DnaB; TIGR00665 591001000164 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 591001000165 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 591001000166 Walker A motif; other site 591001000167 ATP binding site [chemical binding]; other site 591001000168 Walker B motif; other site 591001000169 DNA binding loops [nucleotide binding] 591001000170 adenylosuccinate lyase; Provisional; Region: PRK07492 591001000171 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 591001000172 tetramer interface [polypeptide binding]; other site 591001000173 active site 591001000174 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 591001000175 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 591001000176 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 591001000177 GDP-binding site [chemical binding]; other site 591001000178 ACT binding site; other site 591001000179 IMP binding site; other site 591001000180 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 591001000181 Predicted permease [General function prediction only]; Region: COG2985 591001000182 Predicted Permease Membrane Region; Region: Asp-Al_Ex; pfam06826 591001000183 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 591001000184 glutaminase A; Region: Gln_ase; TIGR03814 591001000185 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 591001000186 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 591001000187 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000188 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000189 LysR substrate binding domain; Region: LysR_substrate; pfam03466 591001000190 dimerization interface [polypeptide binding]; other site 591001000191 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 591001000192 Iron-containing alcohol dehydrogenases-like; Region: Fe-ADH1; cd08185 591001000193 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 591001000194 putative active site [active] 591001000195 metal binding site [ion binding]; metal-binding site 591001000196 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 591001000197 EamA-like transporter family; Region: EamA; pfam00892 591001000198 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 591001000199 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 591001000200 AAA domain; Region: AAA_26; pfam13500 591001000201 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 591001000202 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 591001000203 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 591001000204 inhibitor-cofactor binding pocket; inhibition site 591001000205 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001000206 catalytic residue [active] 591001000207 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 591001000208 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 591001000209 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 591001000210 active site 591001000211 Predicted membrane protein [Function unknown]; Region: COG1971 591001000212 Domain of unknown function DUF; Region: DUF204; pfam02659 591001000213 Domain of unknown function DUF; Region: DUF204; pfam02659 591001000214 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 591001000215 active site 591001000216 DNA polymerase IV; Validated; Region: PRK02406 591001000217 DNA binding site [nucleotide binding] 591001000218 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 591001000219 EamA-like transporter family; Region: EamA; pfam00892 591001000220 EamA-like transporter family; Region: EamA; pfam00892 591001000221 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 591001000222 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 591001000223 homodimer interface [polypeptide binding]; other site 591001000224 substrate-cofactor binding pocket; other site 591001000225 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001000226 catalytic residue [active] 591001000227 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001000228 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 591001000229 peptidase T-like protein; Region: PepT-like; TIGR01883 591001000230 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 591001000231 metal binding site [ion binding]; metal-binding site 591001000232 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 591001000233 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 591001000234 ligand binding site [chemical binding]; other site 591001000235 NAD binding site [chemical binding]; other site 591001000236 dimerization interface [polypeptide binding]; other site 591001000237 catalytic site [active] 591001000238 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 591001000239 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000240 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000241 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 591001000242 dimerization interface [polypeptide binding]; other site 591001000243 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 591001000244 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes; Region: D-glucarate_dehydratase; cd03323 591001000245 active site 591001000246 tetramer interface [polypeptide binding]; other site 591001000247 fructuronate transporter; Provisional; Region: PRK10034; cl15264 591001000248 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 591001000249 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 591001000250 ligand binding site [chemical binding]; other site 591001000251 NAD binding site [chemical binding]; other site 591001000252 dimerization interface [polypeptide binding]; other site 591001000253 catalytic site [active] 591001000254 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 591001000255 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 591001000256 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated; Region: PRK08659 591001000257 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 591001000258 PYR/PP interface [polypeptide binding]; other site 591001000259 TPP binding site [chemical binding]; other site 591001000260 dimer interface [polypeptide binding]; other site 591001000261 substrate binding site [chemical binding]; other site 591001000262 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 591001000263 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 591001000264 TPP-binding site [chemical binding]; other site 591001000265 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 591001000266 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 591001000267 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 591001000268 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 591001000269 active site 591001000270 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 591001000271 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 591001000272 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 591001000273 Domain of unknown function (DUF2088); Region: DUF2088; cl15406 591001000274 galactarate dehydratase; Region: galactar-dH20; TIGR03248 591001000275 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 591001000276 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 591001000277 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 591001000278 ferric uptake regulator; Provisional; Region: fur; PRK09462 591001000279 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 591001000280 metal binding site 2 [ion binding]; metal-binding site 591001000281 putative DNA binding helix; other site 591001000282 metal binding site 1 [ion binding]; metal-binding site 591001000283 dimer interface [polypeptide binding]; other site 591001000284 structural Zn2+ binding site [ion binding]; other site 591001000285 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 591001000286 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 591001000287 ABC-ATPase subunit interface; other site 591001000288 dimer interface [polypeptide binding]; other site 591001000289 putative PBP binding regions; other site 591001000290 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 591001000291 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001000292 Walker A/P-loop; other site 591001000293 ATP binding site [chemical binding]; other site 591001000294 Q-loop/lid; other site 591001000295 ABC transporter signature motif; other site 591001000296 Walker B; other site 591001000297 D-loop; other site 591001000298 H-loop/switch region; other site 591001000299 Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor...; Region: AdcA; cd01017 591001000300 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 591001000301 metal binding site [ion binding]; metal-binding site 591001000302 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 591001000303 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 591001000304 active site 591001000305 phosphorylation site [posttranslational modification] 591001000306 intermolecular recognition site; other site 591001000307 dimerization interface [polypeptide binding]; other site 591001000308 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 591001000309 DNA binding site [nucleotide binding] 591001000310 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 591001000311 dimerization interface [polypeptide binding]; other site 591001000312 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001000313 dimer interface [polypeptide binding]; other site 591001000314 phosphorylation site [posttranslational modification] 591001000315 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 591001000316 ATP binding site [chemical binding]; other site 591001000317 Mg2+ binding site [ion binding]; other site 591001000318 G-X-G motif; other site 591001000319 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 591001000320 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 591001000321 potential catalytic triad [active] 591001000322 conserved cys residue [active] 591001000323 Predicted transcriptional regulators [Transcription]; Region: COG1733 591001000324 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 591001000325 Flavin reductase like domain; Region: Flavin_Reduct; pfam01613 591001000326 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000327 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000328 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 591001000329 dimerization interface [polypeptide binding]; other site 591001000330 putative hydratase; Provisional; Region: PRK11413 591001000331 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 591001000332 substrate binding site [chemical binding]; other site 591001000333 ligand binding site [chemical binding]; other site 591001000334 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 591001000335 substrate binding site [chemical binding]; other site 591001000336 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 591001000337 Citrate transporter; Region: CitMHS; pfam03600 591001000338 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 591001000339 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 591001000340 active site 591001000341 phosphorylation site [posttranslational modification] 591001000342 intermolecular recognition site; other site 591001000343 dimerization interface [polypeptide binding]; other site 591001000344 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 591001000345 DNA binding site [nucleotide binding] 591001000346 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 591001000347 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 591001000348 dimerization interface [polypeptide binding]; other site 591001000349 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001000350 dimer interface [polypeptide binding]; other site 591001000351 phosphorylation site [posttranslational modification] 591001000352 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 591001000353 ATP binding site [chemical binding]; other site 591001000354 Mg2+ binding site [ion binding]; other site 591001000355 G-X-G motif; other site 591001000356 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 591001000357 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 591001000358 FeS/SAM binding site; other site 591001000359 hypothetical protein; Provisional; Region: PRK03881 591001000360 The N-terminal domain, an extradiol dioxygenase class III subunit B-like domain, of unknown proteins containing a C-terminal AMMECR1 domain; Region: ED_3B_N_AMMECR1; cd07951 591001000361 AMMECR1; Region: AMMECR1; pfam01871 591001000362 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 591001000363 Fe-S cluster binding site [ion binding]; other site 591001000364 active site 591001000365 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 591001000366 N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431 are part of DUF1312; Region: DUF1312; cd09846 591001000367 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 591001000368 ApbE family; Region: ApbE; pfam02424 591001000369 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 591001000370 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001000371 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 591001000372 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001000373 Ferredoxin [Energy production and conversion]; Region: COG1146 591001000374 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 591001000375 electron transport complex RsxE subunit; Provisional; Region: PRK12405 591001000376 FMN-binding domain; Region: FMN_bind; cl01081 591001000377 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 591001000378 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 591001000379 SLBB domain; Region: SLBB; pfam10531 591001000380 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001000381 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 591001000382 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 591001000383 FeS/SAM binding site; other site 591001000384 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 591001000385 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 591001000386 NlpC/P60 family; Region: NLPC_P60; pfam00877 591001000387 DNA-binding transcriptional regulator DhaR; Provisional; Region: PRK11388 591001000388 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001000389 Walker A motif; other site 591001000390 ATP binding site [chemical binding]; other site 591001000391 Walker B motif; other site 591001000392 arginine finger; other site 591001000393 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 591001000394 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 591001000395 S-adenosylmethionine binding site [chemical binding]; other site 591001000396 Bacterial cell division membrane protein [Cell division and chromosome partitioning]; Region: FtsW; COG0772 591001000397 stage V sporulation protein D; Region: spoVD_pbp; TIGR02214 591001000398 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 591001000399 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 591001000400 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 591001000401 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 591001000402 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 591001000403 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 591001000404 homodimer interface [polypeptide binding]; other site 591001000405 NADP binding site [chemical binding]; other site 591001000406 substrate binding site [chemical binding]; other site 591001000407 Predicted thioesterase [General function prediction only]; Region: COG5496 591001000408 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 591001000409 S-ribosylhomocysteinase; Provisional; Region: PRK02260 591001000410 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 591001000411 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001000412 dimer interface [polypeptide binding]; other site 591001000413 phosphorylation site [posttranslational modification] 591001000414 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 591001000415 ATP binding site [chemical binding]; other site 591001000416 Mg2+ binding site [ion binding]; other site 591001000417 G-X-G motif; other site 591001000418 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 591001000419 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 591001000420 active site 591001000421 phosphorylation site [posttranslational modification] 591001000422 intermolecular recognition site; other site 591001000423 dimerization interface [polypeptide binding]; other site 591001000424 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 591001000425 DNA binding site [nucleotide binding] 591001000426 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 591001000427 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 591001000428 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 591001000429 Carbon starvation protein CstA; Region: CstA; pfam02554 591001000430 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 591001000431 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 591001000432 FAD binding domain; Region: FAD_binding_4; pfam01565 591001000433 NAD-dependent deacetylase; Provisional; Region: PRK00481 591001000434 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 591001000435 NAD+ binding site [chemical binding]; other site 591001000436 substrate binding site [chemical binding]; other site 591001000437 Zn binding site [ion binding]; other site 591001000438 seryl-tRNA synthetase; Provisional; Region: PRK05431 591001000439 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 591001000440 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 591001000441 dimer interface [polypeptide binding]; other site 591001000442 active site 591001000443 motif 1; other site 591001000444 motif 2; other site 591001000445 motif 3; other site 591001000446 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 591001000447 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 591001000448 dimer interface [polypeptide binding]; other site 591001000449 active site 591001000450 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 591001000451 catalytic residues [active] 591001000452 substrate binding site [chemical binding]; other site 591001000453 N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]; Region: NagA; COG1820 591001000454 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 591001000455 active site 591001000456 dimer interface [polypeptide binding]; other site 591001000457 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 591001000458 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 591001000459 putative active site [active] 591001000460 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cl00164 591001000461 active site turn [active] 591001000462 phosphorylation site [posttranslational modification] 591001000463 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; COG1263 591001000464 Bacterial protein of unknown function (DUF871); Region: DUF871; pfam05913 591001000465 Uncharacterized conserved protein [Function unknown]; Region: COG3589 591001000466 GTP-binding protein YchF; Reviewed; Region: PRK09601 591001000467 YchF GTPase; Region: YchF; cd01900 591001000468 G1 box; other site 591001000469 GTP/Mg2+ binding site [chemical binding]; other site 591001000470 Switch I region; other site 591001000471 G2 box; other site 591001000472 Switch II region; other site 591001000473 G3 box; other site 591001000474 G4 box; other site 591001000475 G5 box; other site 591001000476 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 591001000477 histidinol-phosphatase; Provisional; Region: PRK05588 591001000478 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 591001000479 active site 591001000480 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 591001000481 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 591001000482 active site 591001000483 (T/H)XGH motif; other site 591001000484 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001000485 Zn2+ binding site [ion binding]; other site 591001000486 Mg2+ binding site [ion binding]; other site 591001000487 Transcriptional regulator [Transcription]; Region: LytR; COG1316 591001000488 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 591001000489 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 591001000490 S1 domain; Region: S1_2; pfam13509 591001000491 S1 domain; Region: S1_2; pfam13509 591001000492 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 591001000493 putative transposase OrfB; Reviewed; Region: PHA02517 591001000494 HTH-like domain; Region: HTH_21; pfam13276 591001000495 Integrase core domain; Region: rve; pfam00665 591001000496 Integrase core domain; Region: rve_2; pfam13333 591001000497 Putative ammonia monooxygenase [General function prediction only]; Region: AbrB; COG3180 591001000498 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 591001000499 membrane protein AbrB duplication; Region: Gneg_AbrB_dup; TIGR03082 591001000500 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000501 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000502 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 591001000503 dimerization interface [polypeptide binding]; other site 591001000504 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 591001000505 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 591001000506 substrate binding site [chemical binding]; other site 591001000507 ligand binding site [chemical binding]; other site 591001000508 3-isopropylmalate dehydratase small subunit; Reviewed; Region: leuD; PRK00439 591001000509 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 591001000510 substrate binding site [chemical binding]; other site 591001000511 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 591001000512 tartrate dehydrogenase; Region: TTC; TIGR02089 591001000513 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 591001000514 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 591001000515 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 591001000516 putative valine binding site [chemical binding]; other site 591001000517 dimer interface [polypeptide binding]; other site 591001000518 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 591001000519 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 591001000520 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 591001000521 PYR/PP interface [polypeptide binding]; other site 591001000522 dimer interface [polypeptide binding]; other site 591001000523 TPP binding site [chemical binding]; other site 591001000524 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 591001000525 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 591001000526 TPP-binding site [chemical binding]; other site 591001000527 dimer interface [polypeptide binding]; other site 591001000528 ketol-acid reductoisomerase; Provisional; Region: PRK05479 591001000529 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 591001000530 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 591001000531 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 591001000532 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 591001000533 active site 591001000534 phosphorylation site [posttranslational modification] 591001000535 intermolecular recognition site; other site 591001000536 dimerization interface [polypeptide binding]; other site 591001000537 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 591001000538 DNA binding site [nucleotide binding] 591001000539 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 591001000540 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 591001000541 dimerization interface [polypeptide binding]; other site 591001000542 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001000543 dimer interface [polypeptide binding]; other site 591001000544 phosphorylation site [posttranslational modification] 591001000545 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 591001000546 ATP binding site [chemical binding]; other site 591001000547 Mg2+ binding site [ion binding]; other site 591001000548 G-X-G motif; other site 591001000549 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 591001000550 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 591001000551 PYR/PP interface [polypeptide binding]; other site 591001000552 dimer interface [polypeptide binding]; other site 591001000553 TPP binding site [chemical binding]; other site 591001000554 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 591001000555 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 591001000556 TPP-binding site [chemical binding]; other site 591001000557 dimer interface [polypeptide binding]; other site 591001000558 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 591001000559 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 591001000560 putative valine binding site [chemical binding]; other site 591001000561 dimer interface [polypeptide binding]; other site 591001000562 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 591001000563 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 591001000564 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 591001000565 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 591001000566 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 591001000567 DNA binding site [nucleotide binding] 591001000568 active site 591001000569 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 591001000570 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 591001000571 Haemagglutinin; Region: HIM; pfam05662 591001000572 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 591001000573 substrate binding site [chemical binding]; other site 591001000574 THF binding site; other site 591001000575 zinc-binding site [ion binding]; other site 591001000576 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 591001000577 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 591001000578 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 591001000579 CoA enzyme activase uncharacterized domain (DUF2229); Region: DUF2229; cl17855 591001000580 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 591001000581 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 591001000582 stage V sporulation protein B; Region: spore_V_B; TIGR02900 591001000583 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 591001000584 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 591001000585 homotrimer interaction site [polypeptide binding]; other site 591001000586 putative active site [active] 591001000587 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 591001000588 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 591001000589 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001000590 catalytic residue [active] 591001000591 aspartate aminotransferase; Provisional; Region: PRK06207 591001000592 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 591001000593 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001000594 homodimer interface [polypeptide binding]; other site 591001000595 catalytic residue [active] 591001000596 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000597 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000598 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 591001000599 dimerization interface [polypeptide binding]; other site 591001000600 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 591001000601 Peptidase family M23; Region: Peptidase_M23; pfam01551 591001000602 Predicted transcriptional regulators [Transcription]; Region: COG1695 591001000603 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 591001000604 Virulence activator alpha C-term; Region: Vir_act_alpha_C; pfam10400 591001000605 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 591001000606 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 591001000607 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 591001000608 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 591001000609 putative active site [active] 591001000610 metal binding site [ion binding]; metal-binding site 591001000611 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 591001000612 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 591001000613 NAD(P) binding site [chemical binding]; other site 591001000614 catalytic residues [active] 591001000615 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 591001000616 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 591001000617 V-type ATP synthase subunit I; Validated; Region: PRK05771 591001000618 V-type ATP synthase subunit K; Validated; Region: PRK06558 591001000619 ATP synthase subunit C; Region: ATP-synt_C; pfam00137 591001000620 V-type ATP synthase subunit E; Provisional; Region: PRK02292 591001000621 Archaeal/vacuolar-type H+-ATPase subunit C [Energy production and conversion]; Region: NtpC; COG1527 591001000622 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 591001000623 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; cl00632 591001000624 V-type ATP synthase subunit A; Provisional; Region: PRK04192 591001000625 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 591001000626 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 591001000627 Walker A motif/ATP binding site; other site 591001000628 Walker B motif; other site 591001000629 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 591001000630 V-type ATP synthase subunit B; Provisional; Region: PRK04196 591001000631 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 591001000632 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 591001000633 Walker A motif homologous position; other site 591001000634 Walker B motif; other site 591001000635 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 591001000636 V-type ATP synthase subunit D; Reviewed; Region: PRK00373 591001000637 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 591001000638 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001000639 DNA-binding site [nucleotide binding]; DNA binding site 591001000640 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 591001000641 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001000642 homodimer interface [polypeptide binding]; other site 591001000643 catalytic residue [active] 591001000644 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 591001000645 FMN binding site [chemical binding]; other site 591001000646 dimer interface [polypeptide binding]; other site 591001000647 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 591001000648 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 591001000649 active site 591001000650 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 591001000651 GIY-YIG motif/motif A; other site 591001000652 putative active site [active] 591001000653 putative metal binding site [ion binding]; other site 591001000654 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 591001000655 DNA-binding site [nucleotide binding]; DNA binding site 591001000656 RNA-binding motif; other site 591001000657 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 591001000658 classical (c) SDRs; Region: SDR_c; cd05233 591001000659 NAD(P) binding site [chemical binding]; other site 591001000660 active site 591001000661 Branched-chain amino acid transport protein; Region: Branch_AA_trans; pfam05525 591001000662 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 591001000663 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 591001000664 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 591001000665 Surface antigen; Region: Bac_surface_Ag; pfam01103 591001000666 haemagglutination activity domain; Region: Haemagg_act; cl05436 591001000667 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 591001000668 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 591001000669 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 591001000670 glutamate carboxypeptidase; Reviewed; Region: PRK06133 591001000671 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 591001000672 metal binding site [ion binding]; metal-binding site 591001000673 dimer interface [polypeptide binding]; other site 591001000674 Predicted membrane protein [Function unknown]; Region: COG1288 591001000675 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 591001000676 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 591001000677 Sodium Bile acid symporter family; Region: SBF; pfam01758 591001000678 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 591001000679 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 591001000680 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 591001000681 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 591001000682 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 591001000683 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001000684 dimer interface [polypeptide binding]; other site 591001000685 conserved gate region; other site 591001000686 putative PBP binding loops; other site 591001000687 ABC-ATPase subunit interface; other site 591001000688 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001000689 dimer interface [polypeptide binding]; other site 591001000690 conserved gate region; other site 591001000691 putative PBP binding loops; other site 591001000692 ABC-ATPase subunit interface; other site 591001000693 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 591001000694 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001000695 Walker A/P-loop; other site 591001000696 ATP binding site [chemical binding]; other site 591001000697 Q-loop/lid; other site 591001000698 ABC transporter signature motif; other site 591001000699 Walker B; other site 591001000700 D-loop; other site 591001000701 H-loop/switch region; other site 591001000702 TOBE domain; Region: TOBE_2; pfam08402 591001000703 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 591001000704 homotrimer interaction site [polypeptide binding]; other site 591001000705 putative active site [active] 591001000706 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 591001000707 Transcriptional regulator [Transcription]; Region: IclR; COG1414 591001000708 Bacterial transcriptional regulator; Region: IclR; pfam01614 591001000709 agmatinase; Region: agmatinase; TIGR01230 591001000710 Agmatinase and related proteins; Region: Agmatinase_like_1; cd11589 591001000711 oligomer interface [polypeptide binding]; other site 591001000712 active site 591001000713 Mn binding site [ion binding]; other site 591001000714 hypothetical protein; Provisional; Region: PRK09609 591001000715 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 591001000716 AzlC protein; Region: AzlC; pfam03591 591001000717 Uncharacterized conserved protein [Function unknown]; Region: COG4198 591001000718 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 591001000719 3-phosphoserine/phosphohydroxythreonine aminotransferase; Provisional; Region: PRK05355 591001000720 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001000721 catalytic residue [active] 591001000722 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 591001000723 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 591001000724 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 591001000725 Repair protein; Region: Repair_PSII; pfam04536 591001000726 RNA polymerase Rpb5, C-terminal domain; Region: RNA_pol_Rpb5_C; cl00883 591001000727 [FeFe] hydrogenase H-cluster radical SAM maturase HydG; Region: rSAM_HydG; TIGR03955 591001000728 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 591001000729 FeS/SAM binding site; other site 591001000730 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 591001000731 GTPase CgtA; Reviewed; Region: obgE; PRK12297 591001000732 GTP1/OBG; Region: GTP1_OBG; pfam01018 591001000733 Obg GTPase; Region: Obg; cd01898 591001000734 G1 box; other site 591001000735 GTP/Mg2+ binding site [chemical binding]; other site 591001000736 Switch I region; other site 591001000737 G2 box; other site 591001000738 G3 box; other site 591001000739 Switch II region; other site 591001000740 G4 box; other site 591001000741 G5 box; other site 591001000742 Domain of unknown function (DUF1967); Region: DUF1967; pfam09269 591001000743 gamma-glutamyl kinase; Provisional; Region: PRK05429 591001000744 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 591001000745 nucleotide binding site [chemical binding]; other site 591001000746 homotetrameric interface [polypeptide binding]; other site 591001000747 putative phosphate binding site [ion binding]; other site 591001000748 putative allosteric binding site; other site 591001000749 PUA domain; Region: PUA; pfam01472 591001000750 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 591001000751 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 591001000752 putative catalytic cysteine [active] 591001000753 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 591001000754 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 591001000755 HlyD family secretion protein; Region: HlyD_3; pfam13437 591001000756 putative membrane fusion protein; Region: TIGR02828 591001000757 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 591001000758 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 591001000759 Walker A/P-loop; other site 591001000760 ATP binding site [chemical binding]; other site 591001000761 Q-loop/lid; other site 591001000762 ABC transporter signature motif; other site 591001000763 Walker B; other site 591001000764 D-loop; other site 591001000765 H-loop/switch region; other site 591001000766 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 591001000767 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 591001000768 FtsX-like permease family; Region: FtsX; pfam02687 591001000769 HutD; Region: HutD; cl01532 591001000770 glutamate formiminotransferase; Region: FtcD; TIGR02024 591001000771 Formiminotransferase domain, N-terminal subdomain; Region: FTCD_N; pfam07837 591001000772 Formiminotransferase domain; Region: FTCD; pfam02971 591001000773 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 591001000774 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 591001000775 Potassium binding sites [ion binding]; other site 591001000776 Cesium cation binding sites [ion binding]; other site 591001000777 Formiminotransferase-cyclodeaminase; Region: FTCD_C; pfam04961 591001000778 Transposase domain (DUF772); Region: DUF772; pfam05598 591001000779 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 591001000780 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 591001000781 active sites [active] 591001000782 tetramer interface [polypeptide binding]; other site 591001000783 Predicted permease [General function prediction only]; Region: COG2056 591001000784 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 591001000785 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 591001000786 active sites [active] 591001000787 tetramer interface [polypeptide binding]; other site 591001000788 FAD binding domain; Region: FAD_binding_4; pfam01565 591001000789 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 591001000790 FG-GAP repeat; Region: FG-GAP; pfam01839 591001000791 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 591001000792 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 591001000793 HlyD family secretion protein; Region: HlyD_3; pfam13437 591001000794 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 591001000795 Protein export membrane protein; Region: SecD_SecF; cl14618 591001000796 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 591001000797 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 591001000798 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 591001000799 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 591001000800 amino acid carrier protein; Region: agcS; TIGR00835 591001000801 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 591001000802 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 591001000803 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001000804 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 591001000805 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 591001000806 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 591001000807 RNA polymerase factor sigma-70; Validated; Region: PRK08295 591001000808 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 591001000809 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 591001000810 AAA domain; Region: AAA_22; pfam13401 591001000811 AAA domain; Region: AAA_17; pfam13207 591001000812 6-phosphofructokinase; Provisional; Region: PRK03202 591001000813 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 591001000814 active site 591001000815 ADP/pyrophosphate binding site [chemical binding]; other site 591001000816 dimerization interface [polypeptide binding]; other site 591001000817 allosteric effector site; other site 591001000818 fructose-1,6-bisphosphate binding site; other site 591001000819 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 591001000820 elongation factor Tu; Reviewed; Region: PRK00049 591001000821 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 591001000822 G1 box; other site 591001000823 GEF interaction site [polypeptide binding]; other site 591001000824 GTP/Mg2+ binding site [chemical binding]; other site 591001000825 Switch I region; other site 591001000826 G2 box; other site 591001000827 G3 box; other site 591001000828 Switch II region; other site 591001000829 G4 box; other site 591001000830 G5 box; other site 591001000831 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 591001000832 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 591001000833 Antibiotic Binding Site [chemical binding]; other site 591001000834 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 591001000835 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 591001000836 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 591001000837 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 591001000838 putative homodimer interface [polypeptide binding]; other site 591001000839 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 591001000840 heterodimer interface [polypeptide binding]; other site 591001000841 homodimer interface [polypeptide binding]; other site 591001000842 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 591001000843 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 591001000844 23S rRNA interface [nucleotide binding]; other site 591001000845 L7/L12 interface [polypeptide binding]; other site 591001000846 putative thiostrepton binding site; other site 591001000847 L25 interface [polypeptide binding]; other site 591001000848 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 591001000849 mRNA/rRNA interface [nucleotide binding]; other site 591001000850 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 591001000851 23S rRNA interface [nucleotide binding]; other site 591001000852 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 591001000853 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 591001000854 core dimer interface [polypeptide binding]; other site 591001000855 peripheral dimer interface [polypeptide binding]; other site 591001000856 L10 interface [polypeptide binding]; other site 591001000857 L11 interface [polypeptide binding]; other site 591001000858 putative EF-Tu interaction site [polypeptide binding]; other site 591001000859 putative EF-G interaction site [polypeptide binding]; other site 591001000860 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 591001000861 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 591001000862 Walker A/P-loop; other site 591001000863 ATP binding site [chemical binding]; other site 591001000864 Q-loop/lid; other site 591001000865 ABC transporter signature motif; other site 591001000866 Walker B; other site 591001000867 D-loop; other site 591001000868 H-loop/switch region; other site 591001000869 NIL domain; Region: NIL; pfam09383 591001000870 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001000871 conserved gate region; other site 591001000872 ABC-ATPase subunit interface; other site 591001000873 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 591001000874 NLPA lipoprotein; Region: Lipoprotein_9; cl17547 591001000875 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001000876 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 591001000877 metal binding site [ion binding]; metal-binding site 591001000878 dimer interface [polypeptide binding]; other site 591001000879 Protein of unknown function (DUF441); Region: DUF441; pfam04284 591001000880 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001000881 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 591001000882 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 591001000883 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 591001000884 COG (conserved oligomeric Golgi) complex component, COG2; Region: COG2; pfam06148 591001000885 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 591001000886 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 591001000887 HlyD family secretion protein; Region: HlyD_3; pfam13437 591001000888 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 591001000889 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001000890 Walker A/P-loop; other site 591001000891 ATP binding site [chemical binding]; other site 591001000892 Q-loop/lid; other site 591001000893 ABC transporter signature motif; other site 591001000894 Walker B; other site 591001000895 D-loop; other site 591001000896 H-loop/switch region; other site 591001000897 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 591001000898 Walker A/P-loop; other site 591001000899 ATP binding site [chemical binding]; other site 591001000900 Q-loop/lid; other site 591001000901 ABC transporter signature motif; other site 591001000902 Walker B; other site 591001000903 D-loop; other site 591001000904 H-loop/switch region; other site 591001000905 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 591001000906 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 591001000907 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 591001000908 ABC-2 type transporter; Region: ABC2_membrane; cl17235 591001000909 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 591001000910 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 591001000911 putative metal binding site [ion binding]; other site 591001000912 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 591001000913 Double zinc ribbon; Region: DZR; pfam12773 591001000914 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 591001000915 tRNA_anti-like; Region: tRNA_anti-like; pfam12869 591001000916 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 591001000917 Bacterial SH3 domain; Region: SH3_3; pfam08239 591001000918 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 591001000919 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 591001000920 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 591001000921 Coenzyme A binding pocket [chemical binding]; other site 591001000922 anthranilate synthase component I, non-proteobacterial lineages; Region: trpE_most; TIGR00564 591001000923 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 591001000924 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 591001000925 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 591001000926 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 591001000927 glutamine binding [chemical binding]; other site 591001000928 catalytic triad [active] 591001000929 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 591001000930 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 591001000931 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 591001000932 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 591001000933 active site 591001000934 ribulose/triose binding site [chemical binding]; other site 591001000935 phosphate binding site [ion binding]; other site 591001000936 substrate (anthranilate) binding pocket [chemical binding]; other site 591001000937 product (indole) binding pocket [chemical binding]; other site 591001000938 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 591001000939 active site 591001000940 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 591001000941 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 591001000942 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001000943 catalytic residue [active] 591001000944 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 591001000945 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 591001000946 substrate binding site [chemical binding]; other site 591001000947 active site 591001000948 catalytic residues [active] 591001000949 heterodimer interface [polypeptide binding]; other site 591001000950 Transcriptional regulator [Transcription]; Region: LytR; COG1316 591001000951 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 591001000952 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 591001000953 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 591001000954 shikimate binding site; other site 591001000955 NAD(P) binding site [chemical binding]; other site 591001000956 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 591001000957 DctM-like transporters; Region: DctM; pfam06808 591001000958 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 591001000959 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 591001000960 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 591001000961 3-dehydroquinate dehydratase [Amino acid transport and metabolism]; Region: AroD; COG0710 591001000962 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 591001000963 active site 591001000964 catalytic residue [active] 591001000965 dimer interface [polypeptide binding]; other site 591001000966 Predicted membrane protein [Function unknown]; Region: COG1288; cl17886 591001000967 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 591001000968 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 591001000969 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 591001000970 metal binding site [ion binding]; metal-binding site 591001000971 dimer interface [polypeptide binding]; other site 591001000972 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 591001000973 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 591001000974 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001000975 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001000976 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 591001000977 dimerization interface [polypeptide binding]; other site 591001000978 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 591001000979 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 591001000980 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; cl17708 591001000981 domain interfaces; other site 591001000982 active site 591001000983 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 591001000984 active site 591001000985 SAM binding site [chemical binding]; other site 591001000986 homodimer interface [polypeptide binding]; other site 591001000987 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 591001000988 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 591001000989 active site 591001000990 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 591001000991 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 591001000992 Rubredoxin [Energy production and conversion]; Region: COG1773 591001000993 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cd00350 591001000994 iron binding site [ion binding]; other site 591001000995 Rubrerythrin [Energy production and conversion]; Region: COG1592 591001000996 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 591001000997 diiron binding motif [ion binding]; other site 591001000998 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 591001000999 Citrate lyase synthetase [Energy production and conversion]; Region: CitC; COG3053 591001001000 Citrate lyase ligase; Region: Citrate_lyase_ligase; cd02169 591001001001 putative active site [active] 591001001002 (T/H)XGH motif; other site 591001001003 S-adenosylmethionine synthetase; Validated; Region: PRK05250 591001001004 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 591001001005 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 591001001006 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 591001001007 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 591001001008 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 591001001009 ATP binding site [chemical binding]; other site 591001001010 putative Mg++ binding site [ion binding]; other site 591001001011 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 591001001012 ATP-binding site [chemical binding]; other site 591001001013 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 591001001014 active site 591001001015 catalytic residues [active] 591001001016 metal binding site [ion binding]; metal-binding site 591001001017 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 591001001018 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 591001001019 putative active site [active] 591001001020 substrate binding site [chemical binding]; other site 591001001021 putative cosubstrate binding site; other site 591001001022 catalytic site [active] 591001001023 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 591001001024 substrate binding site [chemical binding]; other site 591001001025 Protein of unknown function DUF116; Region: DUF116; pfam01976 591001001026 16S rRNA methyltransferase B; Provisional; Region: PRK14902 591001001027 NusB family; Region: NusB; pfam01029 591001001028 putative RNA binding site [nucleotide binding]; other site 591001001029 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 591001001030 S-adenosylmethionine binding site [chemical binding]; other site 591001001031 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 591001001032 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 591001001033 FeS/SAM binding site; other site 591001001034 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 591001001035 active site 591001001036 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 591001001037 Catalytic domain of Protein Kinases; Region: PKc; cd00180 591001001038 active site 591001001039 ATP binding site [chemical binding]; other site 591001001040 substrate binding site [chemical binding]; other site 591001001041 activation loop (A-loop); other site 591001001042 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 591001001043 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 591001001044 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 591001001045 GTPase RsgA; Reviewed; Region: PRK00098 591001001046 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 591001001047 RNA binding site [nucleotide binding]; other site 591001001048 homodimer interface [polypeptide binding]; other site 591001001049 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 591001001050 GTPase/Zn-binding domain interface [polypeptide binding]; other site 591001001051 GTP/Mg2+ binding site [chemical binding]; other site 591001001052 G4 box; other site 591001001053 G5 box; other site 591001001054 G1 box; other site 591001001055 Switch I region; other site 591001001056 G2 box; other site 591001001057 G3 box; other site 591001001058 Switch II region; other site 591001001059 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 591001001060 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 591001001061 substrate binding site [chemical binding]; other site 591001001062 hexamer interface [polypeptide binding]; other site 591001001063 metal binding site [ion binding]; metal-binding site 591001001064 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 591001001065 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 591001001066 intersubunit interface [polypeptide binding]; other site 591001001067 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 591001001068 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 591001001069 Walker A/P-loop; other site 591001001070 ATP binding site [chemical binding]; other site 591001001071 Q-loop/lid; other site 591001001072 ABC transporter signature motif; other site 591001001073 Walker B; other site 591001001074 D-loop; other site 591001001075 H-loop/switch region; other site 591001001076 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 591001001077 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 591001001078 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 591001001079 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 591001001080 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 591001001081 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 591001001082 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 591001001083 Peptidase family M48; Region: Peptidase_M48; cl12018 591001001084 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 591001001085 arsenical-resistance protein; Region: acr3; TIGR00832 591001001086 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 591001001087 dimerization interface [polypeptide binding]; other site 591001001088 putative DNA binding site [nucleotide binding]; other site 591001001089 putative Zn2+ binding site [ion binding]; other site 591001001090 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 591001001091 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 591001001092 active site 591001001093 metal binding site [ion binding]; metal-binding site 591001001094 Predicted transcriptional regulators [Transcription]; Region: COG1733 591001001095 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 591001001096 dimerization interface [polypeptide binding]; other site 591001001097 putative DNA binding site [nucleotide binding]; other site 591001001098 putative Zn2+ binding site [ion binding]; other site 591001001099 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 591001001100 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 591001001101 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 591001001102 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 591001001103 L,L-diaminopimelate aminotransferase; Validated; Region: PRK07590 591001001104 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 591001001105 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001001106 homodimer interface [polypeptide binding]; other site 591001001107 catalytic residue [active] 591001001108 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 591001001109 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 591001001110 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 591001001111 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001001112 dimer interface [polypeptide binding]; other site 591001001113 conserved gate region; other site 591001001114 putative PBP binding loops; other site 591001001115 ABC-ATPase subunit interface; other site 591001001116 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001001117 dimer interface [polypeptide binding]; other site 591001001118 conserved gate region; other site 591001001119 putative PBP binding loops; other site 591001001120 ABC-ATPase subunit interface; other site 591001001121 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 591001001122 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 591001001123 Walker A/P-loop; other site 591001001124 ATP binding site [chemical binding]; other site 591001001125 Q-loop/lid; other site 591001001126 ABC transporter signature motif; other site 591001001127 Walker B; other site 591001001128 D-loop; other site 591001001129 H-loop/switch region; other site 591001001130 TOBE domain; Region: TOBE_2; pfam08402 591001001131 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 591001001132 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 591001001133 Protein of unknown function (DUF464); Region: DUF464; pfam04327 591001001134 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 591001001135 DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; Region: RpoB; COG0085 591001001136 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 591001001137 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 591001001138 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 591001001139 RPB1 interaction site [polypeptide binding]; other site 591001001140 RPB10 interaction site [polypeptide binding]; other site 591001001141 RPB11 interaction site [polypeptide binding]; other site 591001001142 RPB3 interaction site [polypeptide binding]; other site 591001001143 RPB12 interaction site [polypeptide binding]; other site 591001001144 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 591001001145 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 591001001146 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 591001001147 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 591001001148 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 591001001149 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 591001001150 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 591001001151 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 591001001152 G-loop; other site 591001001153 DNA binding site [nucleotide binding] 591001001154 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 591001001155 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 591001001156 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 591001001157 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 591001001158 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13633 591001001159 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 591001001160 Walker A/P-loop; other site 591001001161 ATP binding site [chemical binding]; other site 591001001162 Q-loop/lid; other site 591001001163 ABC transporter signature motif; other site 591001001164 Walker B; other site 591001001165 D-loop; other site 591001001166 H-loop/switch region; other site 591001001167 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13637 591001001168 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 591001001169 Walker A/P-loop; other site 591001001170 ATP binding site [chemical binding]; other site 591001001171 Q-loop/lid; other site 591001001172 ABC transporter signature motif; other site 591001001173 Walker B; other site 591001001174 D-loop; other site 591001001175 H-loop/switch region; other site 591001001176 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 591001001177 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 591001001178 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 591001001179 dimerization interface 3.5A [polypeptide binding]; other site 591001001180 active site 591001001181 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 591001001182 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 591001001183 N-terminal plug; other site 591001001184 ligand-binding site [chemical binding]; other site 591001001185 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 591001001186 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 591001001187 catalytic motif [active] 591001001188 Zn binding site [ion binding]; other site 591001001189 RibD C-terminal domain; Region: RibD_C; cl17279 591001001190 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 591001001191 Lumazine binding domain; Region: Lum_binding; pfam00677 591001001192 Lumazine binding domain; Region: Lum_binding; pfam00677 591001001193 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 591001001194 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 591001001195 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 591001001196 dimerization interface [polypeptide binding]; other site 591001001197 active site 591001001198 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 591001001199 homopentamer interface [polypeptide binding]; other site 591001001200 active site 591001001201 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 591001001202 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 591001001203 dimerization interface [polypeptide binding]; other site 591001001204 domain crossover interface; other site 591001001205 redox-dependent activation switch; other site 591001001206 recombinase A; Provisional; Region: recA; PRK09354 591001001207 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 591001001208 hexamer interface [polypeptide binding]; other site 591001001209 Walker A motif; other site 591001001210 ATP binding site [chemical binding]; other site 591001001211 Walker B motif; other site 591001001212 recombination regulator RecX; Reviewed; Region: recX; PRK00117 591001001213 phosphodiesterase; Provisional; Region: PRK12704 591001001214 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001001215 Zn2+ binding site [ion binding]; other site 591001001216 Mg2+ binding site [ion binding]; other site 591001001217 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl17272 591001001218 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 591001001219 uridine phosphorylase; Provisional; Region: PRK11178 591001001220 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 591001001221 phosphopentomutase; Provisional; Region: PRK05362 591001001222 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 591001001223 ZIP Zinc transporter; Region: Zip; pfam02535 591001001224 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 591001001225 hybrid cluster protein; Provisional; Region: PRK05290 591001001226 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001001227 ACS interaction site; other site 591001001228 CODH interaction site; other site 591001001229 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 591001001230 hybrid metal cluster; other site 591001001231 Uncharacterized conserved protein [Function unknown]; Region: COG3189 591001001232 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 591001001233 Protein of unknown function (DUF2974); Region: DUF2974; pfam11187 591001001234 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 591001001235 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 591001001236 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 591001001237 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 591001001238 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001001239 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001001240 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 591001001241 dimerization interface [polypeptide binding]; other site 591001001242 BioY family; Region: BioY; pfam02632 591001001243 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 591001001244 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 591001001245 dimer interface [polypeptide binding]; other site 591001001246 active site 591001001247 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 591001001248 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 591001001249 acyl-activating enzyme (AAE) consensus motif; other site 591001001250 AMP binding site [chemical binding]; other site 591001001251 active site 591001001252 CoA binding site [chemical binding]; other site 591001001253 AIDA autotransporter-like protein ShdA; Provisional; Region: PRK15319 591001001254 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cl01109 591001001255 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 591001001256 homodimer interaction site [polypeptide binding]; other site 591001001257 cofactor binding site; other site 591001001258 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 591001001259 trimer interface [polypeptide binding]; other site 591001001260 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 591001001261 trimer interface [polypeptide binding]; other site 591001001262 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 591001001263 trimer interface [polypeptide binding]; other site 591001001264 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 591001001265 trimer interface [polypeptide binding]; other site 591001001266 YadA-like C-terminal region; Region: YadA; pfam03895 591001001267 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation," the...; Region: Lipase_3; cd00519 591001001268 active site flap/lid [active] 591001001269 nucleophilic elbow; other site 591001001270 catalytic triad [active] 591001001271 active site 591001001272 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG2159 591001001273 Domain of unknown function (DUF386); Region: DUF386; cl01047 591001001274 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 591001001275 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 591001001276 N-terminal plug; other site 591001001277 ligand-binding site [chemical binding]; other site 591001001278 putative heme utilization radical SAM enzyme HutW; Region: rSAM_HutW; TIGR04107 591001001279 Predicted permeases [General function prediction only]; Region: COG0701 591001001280 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 591001001281 putative DNA binding site [nucleotide binding]; other site 591001001282 dimerization interface [polypeptide binding]; other site 591001001283 putative Zn2+ binding site [ion binding]; other site 591001001284 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 591001001285 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 591001001286 HTH domain; Region: HTH_11; pfam08279 591001001287 3H domain; Region: 3H; pfam02829 591001001288 Protein of unknown function (DUF805); Region: DUF805; pfam05656 591001001289 MoxR-like ATPases [General function prediction only]; Region: COG0714 591001001290 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 591001001291 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 591001001292 metal ion-dependent adhesion site (MIDAS); other site 591001001293 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 591001001294 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 591001001295 active site 591001001296 HIGH motif; other site 591001001297 nucleotide binding site [chemical binding]; other site 591001001298 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 591001001299 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 591001001300 active site 591001001301 KMSKS motif; other site 591001001302 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 591001001303 tRNA binding surface [nucleotide binding]; other site 591001001304 anticodon binding site; other site 591001001305 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 591001001306 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 591001001307 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 591001001308 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 591001001309 O-Antigen ligase; Region: Wzy_C; cl04850 591001001310 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 591001001311 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 591001001312 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 591001001313 ligand binding site; other site 591001001314 oligomer interface; other site 591001001315 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 591001001316 dimer interface [polypeptide binding]; other site 591001001317 N-terminal domain interface [polypeptide binding]; other site 591001001318 sulfate 1 binding site; other site 591001001319 glucose-1-phosphate adenylyltransferase, GlgD subunit; Region: glgD; TIGR02092 591001001320 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 591001001321 active site 591001001322 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 591001001323 dimer interface [polypeptide binding]; other site 591001001324 N-terminal domain interface [polypeptide binding]; other site 591001001325 sulfate 1 binding site; other site 591001001326 This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of...; Region: GT1_Glycogen_Phosphorylase; cd04300 591001001327 homodimer interface [polypeptide binding]; other site 591001001328 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 591001001329 active site pocket [active] 591001001330 glycogen branching enzyme; Provisional; Region: PRK12313 591001001331 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 591001001332 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 591001001333 active site 591001001334 catalytic site [active] 591001001335 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 591001001336 glycogen synthase; Provisional; Region: glgA; PRK00654 591001001337 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 591001001338 ADP-binding pocket [chemical binding]; other site 591001001339 homodimer interface [polypeptide binding]; other site 591001001340 putative bifunctional 4-alpha-glucanotransferase/glycogen debranching enzyme; Provisional; Region: PRK14510 591001001341 N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes; Region: E_set_CDase_PDE_N; cd02857 591001001342 homodimer interface [polypeptide binding]; other site 591001001343 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 591001001344 active site 591001001345 homodimer interface [polypeptide binding]; other site 591001001346 catalytic site [active] 591001001347 4-alpha-glucanotransferase; Provisional; Region: PRK14508 591001001348 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 591001001349 Citrate transporter; Region: CitMHS; pfam03600 591001001350 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 591001001351 Citrate transporter; Region: CitMHS; pfam03600 591001001352 Citrate lyase, alpha subunit [Energy production and conversion]; Region: CitF; COG3051 591001001353 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 591001001354 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 591001001355 citrate lyase subunit gamma; Provisional; Region: PRK13253 591001001356 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001001357 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001001358 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 591001001359 dimerization interface [polypeptide binding]; other site 591001001360 Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; Region: CitX; pfam03802 591001001361 ATP:dephospho-CoA triphosphoribosyl transferase; Region: CitG; cl00768 591001001362 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 591001001363 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 591001001364 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 591001001365 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 591001001366 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 591001001367 C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; Region: ACT_LSD; cd04903 591001001368 putative L-serine binding site [chemical binding]; other site 591001001369 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 591001001370 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 591001001371 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001001372 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001001373 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 591001001374 dimerization interface [polypeptide binding]; other site 591001001375 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 591001001376 Protein of unknown function (DUF1385); Region: DUF1385; pfam07136 591001001377 peptide chain release factor 1; Validated; Region: prfA; PRK00591 591001001378 This domain is found in peptide chain release factors; Region: PCRF; smart00937 591001001379 RF-1 domain; Region: RF-1; pfam00472 591001001380 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 591001001381 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 591001001382 S-adenosylmethionine binding site [chemical binding]; other site 591001001383 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 591001001384 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 591001001385 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 591001001386 hypothetical protein; Provisional; Region: PRK13690 591001001387 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 591001001388 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 591001001389 dimer interface [polypeptide binding]; other site 591001001390 active site 591001001391 glycine-pyridoxal phosphate binding site [chemical binding]; other site 591001001392 folate binding site [chemical binding]; other site 591001001393 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001001394 active site 591001001395 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 591001001396 catalytic motif [active] 591001001397 Zn binding site [ion binding]; other site 591001001398 4Fe-4S single cluster domain; Region: Fer4_14; pfam13394 591001001399 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 591001001400 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; cl17221 591001001401 transmembrane helices; other site 591001001402 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001001403 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 591001001404 Double zinc ribbon; Region: DZR; pfam12773 591001001405 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 591001001406 Ligand Binding Site [chemical binding]; other site 591001001407 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 591001001408 Ligand Binding Site [chemical binding]; other site 591001001409 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 591001001410 Ligand Binding Site [chemical binding]; other site 591001001411 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 591001001412 Ligand Binding Site [chemical binding]; other site 591001001413 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 591001001414 Ligand Binding Site [chemical binding]; other site 591001001415 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 591001001416 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 591001001417 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 591001001418 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 591001001419 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 591001001420 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001001421 homodimer interface [polypeptide binding]; other site 591001001422 catalytic residue [active] 591001001423 DNA polymerase I; Provisional; Region: PRK05755 591001001424 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 591001001425 active site 591001001426 metal binding site 1 [ion binding]; metal-binding site 591001001427 putative 5' ssDNA interaction site; other site 591001001428 metal binding site 3; metal-binding site 591001001429 metal binding site 2 [ion binding]; metal-binding site 591001001430 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 591001001431 putative DNA binding site [nucleotide binding]; other site 591001001432 putative metal binding site [ion binding]; other site 591001001433 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 591001001434 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 591001001435 active site 591001001436 DNA binding site [nucleotide binding] 591001001437 catalytic site [active] 591001001438 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 591001001439 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 591001001440 DNA binding site [nucleotide binding] 591001001441 catalytic residue [active] 591001001442 H2TH interface [polypeptide binding]; other site 591001001443 putative catalytic residues [active] 591001001444 turnover-facilitating residue; other site 591001001445 intercalation triad [nucleotide binding]; other site 591001001446 8OG recognition residue [nucleotide binding]; other site 591001001447 putative reading head residues; other site 591001001448 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 591001001449 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 591001001450 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 591001001451 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 591001001452 CoA-binding site [chemical binding]; other site 591001001453 ATP-binding [chemical binding]; other site 591001001454 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 591001001455 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 591001001456 N-acetyl-D-glucosamine binding site [chemical binding]; other site 591001001457 catalytic residue [active] 591001001458 Predicted transcriptional regulator [Transcription]; Region: COG2378 591001001459 WYL domain; Region: WYL; pfam13280 591001001460 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 591001001461 fructuronate transporter; Provisional; Region: PRK10034; cl15264 591001001462 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 591001001463 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 591001001464 Walker A/P-loop; other site 591001001465 ATP binding site [chemical binding]; other site 591001001466 Q-loop/lid; other site 591001001467 ABC transporter signature motif; other site 591001001468 Walker B; other site 591001001469 D-loop; other site 591001001470 H-loop/switch region; other site 591001001471 FeS assembly protein SufB; Region: sufB; TIGR01980 591001001472 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 591001001473 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 591001001474 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 591001001475 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 591001001476 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 591001001477 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001001478 catalytic residue [active] 591001001479 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 591001001480 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 591001001481 trimerization site [polypeptide binding]; other site 591001001482 active site 591001001483 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 591001001484 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 591001001485 RNase E interface [polypeptide binding]; other site 591001001486 trimer interface [polypeptide binding]; other site 591001001487 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 591001001488 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 591001001489 RNase E interface [polypeptide binding]; other site 591001001490 trimer interface [polypeptide binding]; other site 591001001491 active site 591001001492 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 591001001493 putative nucleic acid binding region [nucleotide binding]; other site 591001001494 G-X-X-G motif; other site 591001001495 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 591001001496 RNA binding site [nucleotide binding]; other site 591001001497 domain interface; other site 591001001498 Phosphotransferase system IIA components [Carbohydrate transport and metabolism]; Region: NagE; COG2190 591001001499 HPr interaction site; other site 591001001500 glycerol kinase (GK) interaction site [polypeptide binding]; other site 591001001501 active site 591001001502 phosphorylation site [posttranslational modification] 591001001503 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 591001001504 ribosomal protein L28; Region: L28; TIGR00009 591001001505 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 591001001506 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 591001001507 ssDNA binding site; other site 591001001508 generic binding surface II; other site 591001001509 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 591001001510 ATP binding site [chemical binding]; other site 591001001511 putative Mg++ binding site [ion binding]; other site 591001001512 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 591001001513 nucleotide binding region [chemical binding]; other site 591001001514 ATP-binding site [chemical binding]; other site 591001001515 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 591001001516 elongation factor G; Reviewed; Region: PRK12740 591001001517 G1 box; other site 591001001518 putative GEF interaction site [polypeptide binding]; other site 591001001519 GTP/Mg2+ binding site [chemical binding]; other site 591001001520 Switch I region; other site 591001001521 G2 box; other site 591001001522 G3 box; other site 591001001523 Switch II region; other site 591001001524 G4 box; other site 591001001525 G5 box; other site 591001001526 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 591001001527 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 591001001528 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 591001001529 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 591001001530 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 591001001531 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 591001001532 TPP-binding site [chemical binding]; other site 591001001533 dimer interface [polypeptide binding]; other site 591001001534 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 591001001535 PYR/PP interface [polypeptide binding]; other site 591001001536 dimer interface [polypeptide binding]; other site 591001001537 TPP binding site [chemical binding]; other site 591001001538 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 591001001539 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 591001001540 dimer interface [polypeptide binding]; other site 591001001541 substrate binding site [chemical binding]; other site 591001001542 ATP binding site [chemical binding]; other site 591001001543 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 591001001544 thiamine phosphate binding site [chemical binding]; other site 591001001545 active site 591001001546 pyrophosphate binding site [ion binding]; other site 591001001547 putative DNA-binding protein; Validated; Region: PRK00118 591001001548 signal recognition particle protein; Provisional; Region: PRK10867 591001001549 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 591001001550 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 591001001551 P loop; other site 591001001552 GTP binding site [chemical binding]; other site 591001001553 Signal peptide binding domain; Region: SRP_SPB; pfam02978 591001001554 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 591001001555 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 591001001556 hypothetical protein; Provisional; Region: PRK00468 591001001557 G-X-X-G motif; other site 591001001558 Protein of unknown function (DUF2869); Region: DUF2869; pfam11068 591001001559 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 591001001560 RimM N-terminal domain; Region: RimM; pfam01782 591001001561 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 591001001562 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 591001001563 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 591001001564 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 591001001565 Catalytic site [active] 591001001566 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 591001001567 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 591001001568 GTP/Mg2+ binding site [chemical binding]; other site 591001001569 G4 box; other site 591001001570 G5 box; other site 591001001571 G1 box; other site 591001001572 Switch I region; other site 591001001573 G2 box; other site 591001001574 G3 box; other site 591001001575 Switch II region; other site 591001001576 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 591001001577 RNA/DNA hybrid binding site [nucleotide binding]; other site 591001001578 active site 591001001579 hypothetical protein; Reviewed; Region: PRK12497 591001001580 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 591001001581 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 591001001582 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001001583 Walker A motif; other site 591001001584 ATP binding site [chemical binding]; other site 591001001585 Walker B motif; other site 591001001586 arginine finger; other site 591001001587 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 591001001588 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 591001001589 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 591001001590 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 591001001591 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 591001001592 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 591001001593 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 591001001594 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 591001001595 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001001596 homodimer interface [polypeptide binding]; other site 591001001597 catalytic residue [active] 591001001598 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 591001001599 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 591001001600 active site 591001001601 aspartate aminotransferase; Provisional; Region: PRK07568 591001001602 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 591001001603 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001001604 homodimer interface [polypeptide binding]; other site 591001001605 catalytic residue [active] 591001001606 helicase 45; Provisional; Region: PTZ00424 591001001607 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 591001001608 ATP binding site [chemical binding]; other site 591001001609 Mg++ binding site [ion binding]; other site 591001001610 motif III; other site 591001001611 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 591001001612 nucleotide binding region [chemical binding]; other site 591001001613 ATP-binding site [chemical binding]; other site 591001001614 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 591001001615 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 591001001616 active site 591001001617 HIGH motif; other site 591001001618 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 591001001619 active site 591001001620 KMSKS motif; other site 591001001621 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 591001001622 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 591001001623 nucleotide binding site [chemical binding]; other site 591001001624 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 591001001625 23S rRNA interface [nucleotide binding]; other site 591001001626 L3 interface [polypeptide binding]; other site 591001001627 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 591001001628 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 591001001629 thiamine biosynthesis protein ThiC; Provisional; Region: PRK13352 591001001630 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 591001001631 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 591001001632 dimer interface [polypeptide binding]; other site 591001001633 PYR/PP interface [polypeptide binding]; other site 591001001634 TPP binding site [chemical binding]; other site 591001001635 substrate binding site [chemical binding]; other site 591001001636 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 591001001637 Domain of unknown function; Region: EKR; pfam10371 591001001638 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001001639 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 591001001640 TPP-binding site [chemical binding]; other site 591001001641 dimer interface [polypeptide binding]; other site 591001001642 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 591001001643 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 591001001644 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 591001001645 PhoU domain; Region: PhoU; pfam01895 591001001646 PhoU domain; Region: PhoU; pfam01895 591001001647 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 591001001648 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 591001001649 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 591001001650 putative metal binding site; other site 591001001651 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 591001001652 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 591001001653 Ligand binding site; other site 591001001654 metal-binding site 591001001655 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 591001001656 O-Antigen ligase; Region: Wzy_C; pfam04932 591001001657 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 591001001658 active site 591001001659 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 591001001660 active site 591001001661 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 591001001662 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 591001001663 Divergent AAA domain; Region: AAA_4; pfam04326 591001001664 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 591001001665 Sulfatase; Region: Sulfatase; cl17466 591001001666 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 591001001667 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 591001001668 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 591001001669 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 591001001670 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 591001001671 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 591001001672 putative NAD(P) binding site [chemical binding]; other site 591001001673 active site 591001001674 putative substrate binding site [chemical binding]; other site 591001001675 Predicted amidohydrolase [General function prediction only]; Region: COG0388 591001001676 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 591001001677 putative active site [active] 591001001678 catalytic triad [active] 591001001679 dimer interface [polypeptide binding]; other site 591001001680 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 591001001681 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 591001001682 trigger factor; Provisional; Region: tig; PRK01490 591001001683 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 591001001684 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 591001001685 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 591001001686 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 591001001687 oligomer interface [polypeptide binding]; other site 591001001688 active site residues [active] 591001001689 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 591001001690 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 591001001691 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001001692 Walker A motif; other site 591001001693 ATP binding site [chemical binding]; other site 591001001694 Walker B motif; other site 591001001695 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 591001001696 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 591001001697 Found in ATP-dependent protease La (LON); Region: LON; smart00464 591001001698 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001001699 Walker A motif; other site 591001001700 ATP binding site [chemical binding]; other site 591001001701 Walker B motif; other site 591001001702 arginine finger; other site 591001001703 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 591001001704 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 591001001705 G1 box; other site 591001001706 GTP/Mg2+ binding site [chemical binding]; other site 591001001707 Switch I region; other site 591001001708 G2 box; other site 591001001709 G3 box; other site 591001001710 Switch II region; other site 591001001711 G4 box; other site 591001001712 G5 box; other site 591001001713 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 591001001714 putative active site [active] 591001001715 putative CoA binding site [chemical binding]; other site 591001001716 nudix motif; other site 591001001717 metal binding site [ion binding]; metal-binding site 591001001718 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 591001001719 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 591001001720 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 591001001721 Type II/IV secretion system protein; Region: T2SE; pfam00437 591001001722 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 591001001723 Walker A motif; other site 591001001724 ATP binding site [chemical binding]; other site 591001001725 Walker B motif; other site 591001001726 Predicted membrane protein [Function unknown]; Region: COG2860 591001001727 UPF0126 domain; Region: UPF0126; pfam03458 591001001728 UPF0126 domain; Region: UPF0126; pfam03458 591001001729 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 591001001730 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 591001001731 Protein of unknown function (DUF4127); Region: DUF4127; pfam13552 591001001732 excinuclease ABC subunit B; Provisional; Region: PRK05298 591001001733 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 591001001734 ATP binding site [chemical binding]; other site 591001001735 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 591001001736 nucleotide binding region [chemical binding]; other site 591001001737 ATP-binding site [chemical binding]; other site 591001001738 Ultra-violet resistance protein B; Region: UvrB; pfam12344 591001001739 UvrB/uvrC motif; Region: UVR; pfam02151 591001001740 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 591001001741 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 591001001742 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 591001001743 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 591001001744 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 591001001745 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 591001001746 GIY-YIG motif/motif A; other site 591001001747 active site 591001001748 catalytic site [active] 591001001749 putative DNA binding site [nucleotide binding]; other site 591001001750 metal binding site [ion binding]; metal-binding site 591001001751 UvrB/uvrC motif; Region: UVR; pfam02151 591001001752 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 591001001753 Rubredoxin; Region: Rubredoxin; pfam00301 591001001754 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 591001001755 iron binding site [ion binding]; other site 591001001756 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001001757 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001001758 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 591001001759 dimerization interface [polypeptide binding]; other site 591001001760 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 591001001761 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 591001001762 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 591001001763 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 591001001764 dimer interface [polypeptide binding]; other site 591001001765 active site 591001001766 metal binding site [ion binding]; metal-binding site 591001001767 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 591001001768 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 591001001769 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001001770 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001001771 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 591001001772 dimerization interface [polypeptide binding]; other site 591001001773 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 591001001774 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 591001001775 active site 591001001776 catalytic tetrad [active] 591001001777 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 591001001778 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 591001001779 active site 591001001780 catalytic tetrad [active] 591001001781 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 591001001782 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001001783 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001001784 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 591001001785 twin arginine translocase protein A; Provisional; Region: tatA; PRK14859 591001001786 Sec-independent protein translocase protein (TatC); Region: TatC; pfam00902 591001001787 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 591001001788 active site 591001001789 catalytic triad [active] 591001001790 oxyanion hole [active] 591001001791 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001001792 Uncharacterized Fe-S center protein [General function prediction only]; Region: COG2768 591001001793 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 591001001794 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001001795 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001001796 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 591001001797 dimerization interface [polypeptide binding]; other site 591001001798 [FeFe] hydrogenase H-cluster radical SAM maturase HydE; Region: rSAM_HydE; TIGR03956 591001001799 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 591001001800 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 591001001801 active site 591001001802 motif I; other site 591001001803 motif II; other site 591001001804 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 591001001805 active site 591001001806 motif I; other site 591001001807 motif II; other site 591001001808 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 591001001809 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 591001001810 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 591001001811 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 591001001812 phosphate binding site [ion binding]; other site 591001001813 putative substrate binding pocket [chemical binding]; other site 591001001814 dimer interface [polypeptide binding]; other site 591001001815 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 591001001816 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 591001001817 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 591001001818 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 591001001819 putative active site [active] 591001001820 putative metal binding site [ion binding]; other site 591001001821 Protein of unknown function (DUF4001); Region: DUF4001; pfam13165 591001001822 SCIFF radical SAM maturase; Region: rSAM_six_Cys; TIGR03974 591001001823 PqqD family protein, HPr-rel-A system; Region: PqqD_rel_X; TIGR04353 591001001824 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; cl15377 591001001825 FeS/SAM binding site; other site 591001001826 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 591001001827 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 591001001828 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 591001001829 substrate binding site [chemical binding]; other site 591001001830 oxyanion hole (OAH) forming residues; other site 591001001831 trimer interface [polypeptide binding]; other site 591001001832 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 591001001833 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 591001001834 Beta-Casp domain; Region: Beta-Casp; smart01027 591001001835 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 591001001836 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 591001001837 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 591001001838 G1 box; other site 591001001839 putative GEF interaction site [polypeptide binding]; other site 591001001840 GTP/Mg2+ binding site [chemical binding]; other site 591001001841 Switch I region; other site 591001001842 G2 box; other site 591001001843 G3 box; other site 591001001844 Switch II region; other site 591001001845 G4 box; other site 591001001846 G5 box; other site 591001001847 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 591001001848 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 591001001849 Protein of unknown function (DUF552); Region: DUF552; pfam04472 591001001850 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06826 591001001851 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 591001001852 active site 591001001853 PHP Thumb interface [polypeptide binding]; other site 591001001854 metal binding site [ion binding]; metal-binding site 591001001855 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 591001001856 generic binding surface I; other site 591001001857 generic binding surface II; other site 591001001858 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 591001001859 Ligand binding site [chemical binding]; other site 591001001860 Electron transfer flavoprotein domain; Region: ETF; pfam01012 591001001861 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 591001001862 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 591001001863 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 591001001864 pyruvate kinase; Provisional; Region: PRK06354 591001001865 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 591001001866 domain interfaces; other site 591001001867 active site 591001001868 Phosphohistidine swiveling domain [Signal transduction mechanisms]; Region: COG3848 591001001869 Predicted O-acyltransferase [General function prediction only]; Region: COG3274 591001001870 Acyltransferase family; Region: Acyl_transf_3; pfam01757 591001001871 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 591001001872 TrkA-N domain; Region: TrkA_N; pfam02254 591001001873 TrkA-C domain; Region: TrkA_C; pfam02080 591001001874 TrkA-N domain; Region: TrkA_N; pfam02254 591001001875 TrkA-C domain; Region: TrkA_C; pfam02080 591001001876 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 591001001877 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 591001001878 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 591001001879 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 591001001880 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 591001001881 SLBB domain; Region: SLBB; pfam10531 591001001882 Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]; Region: GumC; COG3206 591001001883 Chain length determinant protein; Region: Wzz; pfam02706 591001001884 G-rich domain on putative tyrosine kinase; Region: GNVR; pfam13807 591001001885 Chain length determinant protein; Region: Wzz; cl15801 591001001886 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 591001001887 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 591001001888 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 591001001889 Bacterial sugar transferase; Region: Bac_transf; pfam02397 591001001890 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 591001001891 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 591001001892 active site 591001001893 TupA-like ATPgrasp; Region: ATPgrasp_TupA; pfam14305 591001001894 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 591001001895 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 591001001896 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 591001001897 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 591001001898 This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1); Region: GT1_CapH_like; cd03812 591001001899 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 591001001900 putative ADP-binding pocket [chemical binding]; other site 591001001901 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 591001001902 active site 591001001903 substrate binding site [chemical binding]; other site 591001001904 trimer interface [polypeptide binding]; other site 591001001905 CoA binding site [chemical binding]; other site 591001001906 Glycosyltransferase like family; Region: Glyco_tranf_2_5; pfam13712 591001001907 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 591001001908 Probable Catalytic site; other site 591001001909 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 591001001910 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001001911 AAA domain; Region: AAA_13; pfam13166 591001001912 Walker A/P-loop; other site 591001001913 ATP binding site [chemical binding]; other site 591001001914 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 591001001915 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 591001001916 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 591001001917 substrate binding site; other site 591001001918 tetramer interface; other site 591001001919 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 591001001920 four helix bundle protein; Region: TIGR02436 591001001921 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 591001001922 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 591001001923 NAD binding site [chemical binding]; other site 591001001924 substrate binding site [chemical binding]; other site 591001001925 homodimer interface [polypeptide binding]; other site 591001001926 active site 591001001927 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 591001001928 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 591001001929 NADP binding site [chemical binding]; other site 591001001930 active site 591001001931 putative substrate binding site [chemical binding]; other site 591001001932 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 591001001933 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 591001001934 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001001935 Walker A motif; other site 591001001936 ATP binding site [chemical binding]; other site 591001001937 Walker B motif; other site 591001001938 arginine finger; other site 591001001939 Helix-turn-helix domain; Region: HTH_38; pfam13936 591001001940 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like_2; cd04847 591001001941 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 591001001942 active site 591001001943 catalytic triad [active] 591001001944 Protein of unknown function (DUF3644); Region: DUF3644; pfam12358 591001001945 AAA domain; Region: AAA_21; pfam13304 591001001946 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001001947 Walker B; other site 591001001948 D-loop; other site 591001001949 H-loop/switch region; other site 591001001950 Domain of unknown function DUF1828; Region: DUF1828; pfam08861 591001001951 Domain of unknown function DUF1829; Region: DUF1829; pfam08862 591001001952 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 591001001953 trimer interface [polypeptide binding]; other site 591001001954 active site 591001001955 Capsule assembly protein Wzi; Region: Caps_assemb_Wzi; pfam14052 591001001956 glucose-6-phosphate isomerase; Provisional; Region: PRK00973 591001001957 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 591001001958 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 591001001959 dimer interface [polypeptide binding]; other site 591001001960 active site 591001001961 Transglycosylase; Region: Transgly; pfam00912 591001001962 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 591001001963 feedback inhibition sensing region; other site 591001001964 homohexameric interface [polypeptide binding]; other site 591001001965 nucleotide binding site [chemical binding]; other site 591001001966 N-acetyl-L-glutamate binding site [chemical binding]; other site 591001001967 acetylornithine aminotransferase; Provisional; Region: PRK02627 591001001968 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 591001001969 inhibitor-cofactor binding pocket; inhibition site 591001001970 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001001971 catalytic residue [active] 591001001972 ornithine carbamoyltransferase; Provisional; Region: PRK00779 591001001973 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 591001001974 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 591001001975 argininosuccinate synthase; Provisional; Region: PRK13820 591001001976 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 591001001977 ANP binding site [chemical binding]; other site 591001001978 Substrate Binding Site II [chemical binding]; other site 591001001979 Substrate Binding Site I [chemical binding]; other site 591001001980 argininosuccinate lyase; Provisional; Region: PRK00855 591001001981 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 591001001982 active sites [active] 591001001983 tetramer interface [polypeptide binding]; other site 591001001984 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001001985 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 591001001986 metal binding site [ion binding]; metal-binding site 591001001987 Uncharacterized conserved protein [Function unknown]; Region: COG1624 591001001988 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 591001001989 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 591001001990 YbbR-like protein; Region: YbbR; pfam07949 591001001991 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 591001001992 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 591001001993 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 591001001994 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 591001001995 DHHA2 domain; Region: DHHA2; pfam02833 591001001996 isocitrate dehydrogenase; Validated; Region: PRK08299 591001001997 Histidine Utilizing Protein, the hut operon positive regulatory protein; Region: HutP; cl07944 591001001998 hexamer interface [polypeptide binding]; other site 591001001999 RNA binding site [nucleotide binding]; other site 591001002000 Histidine-zinc binding site [chemical binding]; other site 591001002001 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]; Region: COG4545 591001002002 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 591001002003 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 591001002004 Coenzyme A binding pocket [chemical binding]; other site 591001002005 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 591001002006 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 591001002007 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 591001002008 Part of AAA domain; Region: AAA_19; pfam13245 591001002009 Family description; Region: UvrD_C_2; pfam13538 591001002010 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 591001002011 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 591001002012 nucleotide binding pocket [chemical binding]; other site 591001002013 K-X-D-G motif; other site 591001002014 catalytic site [active] 591001002015 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 591001002016 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 591001002017 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 591001002018 Dimer interface [polypeptide binding]; other site 591001002019 Carbon starvation protein, predicted membrane protein [Signal transduction mechanisms]; Region: CstA; COG1966 591001002020 Carbon starvation protein CstA; Region: CstA; pfam02554 591001002021 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 591001002022 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 591001002023 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 591001002024 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 591001002025 PhoH-like protein; Region: PhoH; pfam02562 591001002026 metal-binding heat shock protein; Provisional; Region: PRK00016 591001002027 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 591001002028 active site 591001002029 catalytic motif [active] 591001002030 Zn binding site [ion binding]; other site 591001002031 GTPase Era; Reviewed; Region: era; PRK00089 591001002032 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 591001002033 G1 box; other site 591001002034 GTP/Mg2+ binding site [chemical binding]; other site 591001002035 Switch I region; other site 591001002036 G2 box; other site 591001002037 Switch II region; other site 591001002038 G3 box; other site 591001002039 G4 box; other site 591001002040 G5 box; other site 591001002041 KH domain; Region: KH_2; pfam07650 591001002042 Domain of unknown function DUF21; Region: DUF21; pfam01595 591001002043 FOG: CBS domain [General function prediction only]; Region: COG0517 591001002044 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 591001002045 Transporter associated domain; Region: CorC_HlyC; smart01091 591001002046 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 591001002047 Recombination protein O N terminal; Region: RecO_N; pfam11967 591001002048 Recombination protein O C terminal; Region: RecO_C; pfam02565 591001002049 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 591001002050 active site 591001002051 putative catalytic site [active] 591001002052 DNA binding site [nucleotide binding] 591001002053 putative phosphate binding site [ion binding]; other site 591001002054 metal binding site A [ion binding]; metal-binding site 591001002055 AP binding site [nucleotide binding]; other site 591001002056 metal binding site B [ion binding]; metal-binding site 591001002057 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 591001002058 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001002059 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001002060 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 591001002061 dimerization interface [polypeptide binding]; other site 591001002062 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 591001002063 Dicarboxylate carrier protein MatC N-terminus; Region: MatC_N; pfam07158 591001002064 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001002065 putative hydratase; Provisional; Region: PRK11413 591001002066 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 591001002067 substrate binding site [chemical binding]; other site 591001002068 ligand binding site [chemical binding]; other site 591001002069 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 591001002070 substrate binding site [chemical binding]; other site 591001002071 Prolipoprotein diacylglyceryl transferase; Region: LGT; pfam01790 591001002072 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 591001002073 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 591001002074 active site 591001002075 metal binding site [ion binding]; metal-binding site 591001002076 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 591001002077 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 591001002078 HIGH motif; other site 591001002079 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 591001002080 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 591001002081 active site 591001002082 KMSKS motif; other site 591001002083 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 591001002084 tRNA binding surface [nucleotide binding]; other site 591001002085 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 591001002086 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 591001002087 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001002088 catalytic residue [active] 591001002089 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 591001002090 thymidylate kinase; Validated; Region: tmk; PRK00698 591001002091 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 591001002092 TMP-binding site; other site 591001002093 ATP-binding site [chemical binding]; other site 591001002094 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001002095 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 591001002096 Walker A motif; other site 591001002097 ATP binding site [chemical binding]; other site 591001002098 Walker B motif; other site 591001002099 arginine finger; other site 591001002100 Uncharacterized homolog of PSP1 [Function unknown]; Region: COG1774 591001002101 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 591001002102 S-adenosylmethionine binding site [chemical binding]; other site 591001002103 Predicted methyltransferases [General function prediction only]; Region: COG0313 591001002104 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 591001002105 putative SAM binding site [chemical binding]; other site 591001002106 putative homodimer interface [polypeptide binding]; other site 591001002107 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001002108 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001002109 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 591001002110 dimerization interface [polypeptide binding]; other site 591001002111 Predicted membrane protein [Function unknown]; Region: COG2855 591001002112 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001002113 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 591001002114 HD domain; Region: HD_3; pfam13023 591001002115 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 591001002116 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 591001002117 catalytic triad [active] 591001002118 hypothetical protein; Validated; Region: PRK02101 591001002119 Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in bacterial endospore germination. CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells. SleB translocates across the...; Region: GH18_CFLE_spore_hydrolase; cd02874 591001002120 active site 591001002121 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 591001002122 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 591001002123 substrate binding pocket [chemical binding]; other site 591001002124 membrane-bound complex binding site; other site 591001002125 hinge residues; other site 591001002126 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 591001002127 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 591001002128 substrate binding pocket [chemical binding]; other site 591001002129 membrane-bound complex binding site; other site 591001002130 hinge residues; other site 591001002131 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 591001002132 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001002133 dimer interface [polypeptide binding]; other site 591001002134 conserved gate region; other site 591001002135 putative PBP binding loops; other site 591001002136 ABC-ATPase subunit interface; other site 591001002137 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 591001002138 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 591001002139 Walker A/P-loop; other site 591001002140 ATP binding site [chemical binding]; other site 591001002141 Q-loop/lid; other site 591001002142 ABC transporter signature motif; other site 591001002143 Walker B; other site 591001002144 D-loop; other site 591001002145 H-loop/switch region; other site 591001002146 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 591001002147 30S subunit binding site; other site 591001002148 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 591001002149 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 591001002150 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 591001002151 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 591001002152 nucleotide binding region [chemical binding]; other site 591001002153 ATP-binding site [chemical binding]; other site 591001002154 peptide chain release factor 2; Validated; Region: prfB; PRK00578 591001002155 PCRF domain; Region: PCRF; pfam03462 591001002156 RF-1 domain; Region: RF-1; pfam00472 591001002157 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; COG2327 591001002158 polysaccharide pyruvyl transferase CsaB; Region: S_layer_CsaB; TIGR03609 591001002159 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 591001002160 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001002161 Walker A/P-loop; other site 591001002162 ATP binding site [chemical binding]; other site 591001002163 Q-loop/lid; other site 591001002164 ABC transporter signature motif; other site 591001002165 Walker B; other site 591001002166 D-loop; other site 591001002167 H-loop/switch region; other site 591001002168 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 591001002169 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 591001002170 FtsX-like permease family; Region: FtsX; pfam02687 591001002171 AmiB activator; Provisional; Region: PRK11637 591001002172 Peptidase family M23; Region: Peptidase_M23; pfam01551 591001002173 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 591001002174 C-terminal peptidase (prc); Region: prc; TIGR00225 591001002175 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 591001002176 protein binding site [polypeptide binding]; other site 591001002177 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 591001002178 Catalytic dyad [active] 591001002179 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 591001002180 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001002181 dimer interface [polypeptide binding]; other site 591001002182 phosphorylation site [posttranslational modification] 591001002183 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 591001002184 ATP binding site [chemical binding]; other site 591001002185 G-X-G motif; other site 591001002186 endonuclease IV; Provisional; Region: PRK01060 591001002187 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 591001002188 AP (apurinic/apyrimidinic) site pocket; other site 591001002189 DNA interaction; other site 591001002190 Metal-binding active site; metal-binding site 591001002191 Thiamine transporter protein (Thia_YuaJ); Region: Thia_YuaJ; pfam09515 591001002192 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 591001002193 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 591001002194 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 591001002195 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 591001002196 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 591001002197 23S rRNA binding site [nucleotide binding]; other site 591001002198 L21 binding site [polypeptide binding]; other site 591001002199 L13 binding site [polypeptide binding]; other site 591001002200 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 591001002201 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 591001002202 HicB family; Region: HicB; pfam05534 591001002203 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 591001002204 16S/18S rRNA binding site [nucleotide binding]; other site 591001002205 S13e-L30e interaction site [polypeptide binding]; other site 591001002206 25S rRNA binding site [nucleotide binding]; other site 591001002207 uracil transporter; Provisional; Region: PRK10720 591001002208 GMP synthase; Reviewed; Region: guaA; PRK00074 591001002209 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 591001002210 AMP/PPi binding site [chemical binding]; other site 591001002211 candidate oxyanion hole; other site 591001002212 catalytic triad [active] 591001002213 potential glutamine specificity residues [chemical binding]; other site 591001002214 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 591001002215 ATP Binding subdomain [chemical binding]; other site 591001002216 Ligand Binding sites [chemical binding]; other site 591001002217 Dimerization subdomain; other site 591001002218 Domain of unknown function (DUF4160); Region: DUF4160; pfam13711 591001002219 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 591001002220 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 591001002221 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001002222 catalytic residue [active] 591001002223 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 591001002224 dimerization interface [polypeptide binding]; other site 591001002225 putative DNA binding site [nucleotide binding]; other site 591001002226 putative Zn2+ binding site [ion binding]; other site 591001002227 Chromate transporter; Region: Chromate_transp; pfam02417 591001002228 Chromate transporter; Region: Chromate_transp; pfam02417 591001002229 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001002230 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 591001002231 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001002232 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 591001002233 metal binding site [ion binding]; metal-binding site 591001002234 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 591001002235 RibD C-terminal domain; Region: RibD_C; cl17279 591001002236 spermidine synthase; Provisional; Region: PRK03612 591001002237 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 591001002238 S-adenosylmethionine binding site [chemical binding]; other site 591001002239 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001002240 Walker A/P-loop; other site 591001002241 ATP binding site [chemical binding]; other site 591001002242 Q-loop/lid; other site 591001002243 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 591001002244 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001002245 ABC transporter signature motif; other site 591001002246 Walker B; other site 591001002247 D-loop; other site 591001002248 H-loop/switch region; other site 591001002249 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001002250 Walker A/P-loop; other site 591001002251 ATP binding site [chemical binding]; other site 591001002252 Q-loop/lid; other site 591001002253 ABC transporter signature motif; other site 591001002254 Walker B; other site 591001002255 D-loop; other site 591001002256 H-loop/switch region; other site 591001002257 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 591001002258 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 591001002259 Hemerythrin-like domain; Region: Hr-like; cd12108 591001002260 Fe binding site [ion binding]; other site 591001002261 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 591001002262 PAS domain; Region: PAS_9; pfam13426 591001002263 putative active site [active] 591001002264 heme pocket [chemical binding]; other site 591001002265 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 591001002266 PAS fold; Region: PAS_3; pfam08447 591001002267 putative active site [active] 591001002268 heme pocket [chemical binding]; other site 591001002269 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001002270 metal binding site [ion binding]; metal-binding site 591001002271 active site 591001002272 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 591001002273 Predicted transcriptional regulator [Transcription]; Region: COG1959 591001002274 Transcriptional regulator; Region: Rrf2; pfam02082 591001002275 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 591001002276 active site 591001002277 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; pfam01996 591001002278 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 591001002279 active site 591001002280 dimerization interface [polypeptide binding]; other site 591001002281 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 591001002282 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 591001002283 active site 591001002284 metal binding site [ion binding]; metal-binding site 591001002285 homotetramer interface [polypeptide binding]; other site 591001002286 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 591001002287 Malic enzyme, N-terminal domain; Region: malic; pfam00390 591001002288 Malic enzyme, NAD binding domain; Region: Malic_M; smart00919 591001002289 NAD(P) binding pocket [chemical binding]; other site 591001002290 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 591001002291 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 591001002292 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 591001002293 non-specific DNA binding site [nucleotide binding]; other site 591001002294 salt bridge; other site 591001002295 sequence-specific DNA binding site [nucleotide binding]; other site 591001002296 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001002297 Zn2+ binding site [ion binding]; other site 591001002298 Mg2+ binding site [ion binding]; other site 591001002299 nicotinate (nicotinamide) nucleotide adenylyltransferase; Region: TIGR00482 591001002300 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 591001002301 active site 591001002302 nucleotide binding site [chemical binding]; other site 591001002303 HIGH motif; other site 591001002304 KMSKS motif; other site 591001002305 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 591001002306 NAD(P) binding site [chemical binding]; other site 591001002307 LDH/MDH dimer interface [polypeptide binding]; other site 591001002308 substrate binding site [chemical binding]; other site 591001002309 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 591001002310 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 591001002311 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001002312 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; cd00625 591001002313 transmembrane helices; other site 591001002314 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 591001002315 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 591001002316 active site 591001002317 coproporphyrinogen III oxidase; Provisional; Region: PRK08599 591001002318 HemN C-terminal domain; Region: HemN_C; pfam06969 591001002319 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 591001002320 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 591001002321 GrpE; Region: GrpE; pfam01025 591001002322 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 591001002323 dimer interface [polypeptide binding]; other site 591001002324 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 591001002325 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 591001002326 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 591001002327 nucleotide binding site [chemical binding]; other site 591001002328 NEF interaction site [polypeptide binding]; other site 591001002329 SBD interface [polypeptide binding]; other site 591001002330 chaperone protein DnaJ; Provisional; Region: PRK10767 591001002331 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 591001002332 HSP70 interaction site [polypeptide binding]; other site 591001002333 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 591001002334 substrate binding site [polypeptide binding]; other site 591001002335 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 591001002336 Zn binding sites [ion binding]; other site 591001002337 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 591001002338 dimer interface [polypeptide binding]; other site 591001002339 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 591001002340 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 591001002341 Surface antigen; Region: Bac_surface_Ag; pfam01103 591001002342 haemagglutination activity domain; Region: Haemagg_act; pfam05860 591001002343 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 591001002344 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 591001002345 S-adenosylmethionine binding site [chemical binding]; other site 591001002346 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 591001002347 RNA methyltransferase, RsmE family; Region: TIGR00046 591001002348 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 591001002349 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 591001002350 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 591001002351 nucleotide binding site/active site [active] 591001002352 HIT family signature motif; other site 591001002353 catalytic residue [active] 591001002354 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 591001002355 Yqey-like protein; Region: YqeY; pfam09424 591001002356 aspartate aminotransferase; Provisional; Region: PRK06836 591001002357 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 591001002358 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001002359 homodimer interface [polypeptide binding]; other site 591001002360 catalytic residue [active] 591001002361 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 591001002362 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 591001002363 Integral membrane protein (PIN domain superfamily) [General function prediction only]; Region: COG4956 591001002364 PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; Region: PIN_YacL; cd09877 591001002365 putative active site [active] 591001002366 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 591001002367 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 591001002368 substrate binding site; other site 591001002369 dimer interface; other site 591001002370 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 591001002371 homotrimer interaction site [polypeptide binding]; other site 591001002372 zinc binding site [ion binding]; other site 591001002373 CDP-binding sites; other site 591001002374 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 591001002375 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 591001002376 active site 591001002377 HIGH motif; other site 591001002378 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 591001002379 active site 591001002380 KMSKS motif; other site 591001002381 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 591001002382 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 591001002383 active site 591001002384 HIGH motif; other site 591001002385 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 591001002386 KMSKS motif; other site 591001002387 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 591001002388 tRNA binding surface [nucleotide binding]; other site 591001002389 anticodon binding site; other site 591001002390 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 591001002391 active site 591001002392 metal binding site [ion binding]; metal-binding site 591001002393 dimerization interface [polypeptide binding]; other site 591001002394 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 591001002395 PAP2 superfamily; Region: PAP2; pfam01569 591001002396 Undecaprenyl-phosphate galactose phosphotransferase, WbaP; Region: WbaP_sugtrans; TIGR03022 591001002397 Bacterial sugar transferase; Region: Bac_transf; pfam02397 591001002398 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 591001002399 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 591001002400 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 591001002401 UDP-galactopyranose mutase; Region: GLF; pfam03275 591001002402 S23 ribosomal protein; Region: Ribosomal_S23p; pfam05635 591001002403 four helix bundle protein; Region: TIGR02436 591001002404 Domain of unknown function (DUF4422); Region: DUF4422; pfam14393 591001002405 HTH-like domain; Region: HTH_21; pfam13276 591001002406 AAA domain; Region: AAA_21; pfam13304 591001002407 RloB-like protein; Region: RloB; pfam13707 591001002408 HAD superfamily (subfamily IA) hydrolase, TIGR02254; Region: YjjG/YfnB 591001002409 lytic murein endotransglycosylase E; Provisional; Region: emtA; PRK15470 591001002410 putative transposase OrfB; Reviewed; Region: PHA02517 591001002411 HTH-like domain; Region: HTH_21; pfam13276 591001002412 Integrase core domain; Region: rve; pfam00665 591001002413 Integrase core domain; Region: rve_2; pfam13333 591001002414 LicD family; Region: LicD; cl01378 591001002415 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 591001002416 substrate binding site; other site 591001002417 dimer interface; other site 591001002418 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 591001002419 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 591001002420 NAD(P) binding site [chemical binding]; other site 591001002421 active site 591001002422 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 591001002423 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 591001002424 active site 591001002425 colanic acid biosynthesis glycosyl transferase WcaA; Region: WcaA; TIGR04017 591001002426 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 591001002427 active site 591001002428 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 591001002429 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 591001002430 active site 591001002431 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 591001002432 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 591001002433 AAA domain; Region: AAA_21; pfam13304 591001002434 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 591001002435 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 591001002436 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 591001002437 non-specific DNA binding site [nucleotide binding]; other site 591001002438 salt bridge; other site 591001002439 sequence-specific DNA binding site [nucleotide binding]; other site 591001002440 Domain of unknown function (DUF955); Region: DUF955; pfam06114 591001002441 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 591001002442 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 591001002443 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 591001002444 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-C; cd09752 591001002445 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 591001002446 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cd09757 591001002447 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 591001002448 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]; Region: COG1468 591001002449 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-C; cd09721 591001002450 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 591001002451 glutamate carboxypeptidase; Reviewed; Region: PRK06133 591001002452 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 591001002453 metal binding site [ion binding]; metal-binding site 591001002454 dimer interface [polypeptide binding]; other site 591001002455 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 591001002456 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 591001002457 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 591001002458 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 591001002459 G1 box; other site 591001002460 putative GEF interaction site [polypeptide binding]; other site 591001002461 GTP/Mg2+ binding site [chemical binding]; other site 591001002462 Switch I region; other site 591001002463 G2 box; other site 591001002464 G3 box; other site 591001002465 Switch II region; other site 591001002466 G4 box; other site 591001002467 G5 box; other site 591001002468 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 591001002469 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 591001002470 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 591001002471 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 591001002472 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 591001002473 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 591001002474 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 591001002475 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 591001002476 DXD motif; other site 591001002477 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 591001002478 magnesium-transporting ATPase; Provisional; Region: PRK15122 591001002479 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 591001002480 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 591001002481 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 591001002482 motif II; other site 591001002483 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 591001002484 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 591001002485 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 591001002486 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 591001002487 Sodium Bile acid symporter family; Region: SBF; pfam01758 591001002488 pantoate--beta-alanine ligase; Region: panC; TIGR00018 591001002489 Pantoate-beta-alanine ligase; Region: PanC; cd00560 591001002490 active site 591001002491 ATP-binding site [chemical binding]; other site 591001002492 pantoate-binding site; other site 591001002493 HXXH motif; other site 591001002494 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 591001002495 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 591001002496 Walker A/P-loop; other site 591001002497 ATP binding site [chemical binding]; other site 591001002498 Q-loop/lid; other site 591001002499 ABC transporter signature motif; other site 591001002500 Walker B; other site 591001002501 D-loop; other site 591001002502 H-loop/switch region; other site 591001002503 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed; Region: PRK11917 591001002504 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 591001002505 substrate binding pocket [chemical binding]; other site 591001002506 membrane-bound complex binding site; other site 591001002507 hinge residues; other site 591001002508 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001002509 dimer interface [polypeptide binding]; other site 591001002510 conserved gate region; other site 591001002511 putative PBP binding loops; other site 591001002512 ABC-ATPase subunit interface; other site 591001002513 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001002514 dimer interface [polypeptide binding]; other site 591001002515 conserved gate region; other site 591001002516 putative PBP binding loops; other site 591001002517 ABC-ATPase subunit interface; other site 591001002518 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001002519 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 591001002520 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 591001002521 FMN binding site [chemical binding]; other site 591001002522 dimer interface [polypeptide binding]; other site 591001002523 Asp23 family; Region: Asp23; cl00574 591001002524 DNA polymerase IV; Reviewed; Region: PRK03103 591001002525 Y-family of DNA polymerases; Region: PolY; cl12025 591001002526 active site 591001002527 DNA binding site [nucleotide binding] 591001002528 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 591001002529 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 591001002530 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 591001002531 nudix motif; other site 591001002532 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK06130 591001002533 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 591001002534 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 591001002535 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 591001002536 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 591001002537 ligand binding site [chemical binding]; other site 591001002538 flexible hinge region; other site 591001002539 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 591001002540 putative switch regulator; other site 591001002541 non-specific DNA interactions [nucleotide binding]; other site 591001002542 DNA binding site [nucleotide binding] 591001002543 sequence specific DNA binding site [nucleotide binding]; other site 591001002544 putative cAMP binding site [chemical binding]; other site 591001002545 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 591001002546 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 591001002547 FeS/SAM binding site; other site 591001002548 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 591001002549 Pyruvate formate lyase 1; Region: PFL1; cd01678 591001002550 coenzyme A binding site [chemical binding]; other site 591001002551 active site 591001002552 catalytic residues [active] 591001002553 glycine loop; other site 591001002554 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 591001002555 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 591001002556 hypothetical protein; Provisional; Region: PRK08262 591001002557 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 591001002558 metal binding site [ion binding]; metal-binding site 591001002559 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 591001002560 S4 RNA-binding domain; Region: S4; smart00363 591001002561 RNA binding surface [nucleotide binding]; other site 591001002562 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 591001002563 active site 591001002564 pyridoxamine kinase; Validated; Region: PRK05756 591001002565 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 591001002566 dimer interface [polypeptide binding]; other site 591001002567 pyridoxal binding site [chemical binding]; other site 591001002568 ATP binding site [chemical binding]; other site 591001002569 P-loop Domain of unknown function (DUF2791); Region: DUF2791; pfam10923 591001002570 AAA ATPase domain; Region: AAA_16; pfam13191 591001002571 DEAD-like helicases superfamily; Region: DEXDc; smart00487 591001002572 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 591001002573 ATP binding site [chemical binding]; other site 591001002574 putative Mg++ binding site [ion binding]; other site 591001002575 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 591001002576 nucleotide binding region [chemical binding]; other site 591001002577 ATP-binding site [chemical binding]; other site 591001002578 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001002579 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 591001002580 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 591001002581 PAS domain; Region: PAS_9; pfam13426 591001002582 putative active site [active] 591001002583 heme pocket [chemical binding]; other site 591001002584 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001002585 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001002586 metal binding site [ion binding]; metal-binding site 591001002587 active site 591001002588 I-site; other site 591001002589 Domain of unknown function (DUF1848); Region: DUF1848; pfam08902 591001002590 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 591001002591 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 591001002592 Coenzyme A binding pocket [chemical binding]; other site 591001002593 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001002594 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001002595 metal binding site [ion binding]; metal-binding site 591001002596 active site 591001002597 I-site; other site 591001002598 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 591001002599 PAS domain; Region: PAS_9; pfam13426 591001002600 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001002601 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 591001002602 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001002603 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001002604 metal binding site [ion binding]; metal-binding site 591001002605 active site 591001002606 I-site; other site 591001002607 Thiamine-precursor transporter protein (ThiW); Region: ThiW; pfam09512 591001002608 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 591001002609 substrate binding site [chemical binding]; other site 591001002610 multimerization interface [polypeptide binding]; other site 591001002611 ATP binding site [chemical binding]; other site 591001002612 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 591001002613 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 591001002614 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 591001002615 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 591001002616 active site 591001002617 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 591001002618 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_family; cd02803 591001002619 active site 591001002620 FMN binding site [chemical binding]; other site 591001002621 substrate binding site [chemical binding]; other site 591001002622 putative catalytic residue [active] 591001002623 Peptidase family C69; Region: Peptidase_C69; pfam03577 591001002624 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 591001002625 dimerization interface [polypeptide binding]; other site 591001002626 putative DNA binding site [nucleotide binding]; other site 591001002627 putative Zn2+ binding site [ion binding]; other site 591001002628 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 591001002629 dimerization domain swap beta strand [polypeptide binding]; other site 591001002630 regulatory protein interface [polypeptide binding]; other site 591001002631 active site 591001002632 regulatory phosphorylation site [posttranslational modification]; other site 591001002633 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 591001002634 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 591001002635 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 591001002636 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 591001002637 bifunctional UGMP family protein/serine/threonine protein kinase; Validated; Region: PRK09605 591001002638 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 591001002639 Family of unknown function (DUF633); Region: DUF633; pfam04816 591001002640 Uncharacterized conserved protein [Function unknown]; Region: COG0327 591001002641 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 591001002642 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 591001002643 generic binding surface II; other site 591001002644 generic binding surface I; other site 591001002645 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001002646 Zn2+ binding site [ion binding]; other site 591001002647 Mg2+ binding site [ion binding]; other site 591001002648 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 591001002649 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 591001002650 catalytic residues [active] 591001002651 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 591001002652 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 591001002653 Ligand binding site; other site 591001002654 Putative Catalytic site; other site 591001002655 DXD motif; other site 591001002656 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 591001002657 NlpC/P60 family; Region: NLPC_P60; pfam00877 591001002658 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 591001002659 Helix-turn-helix diphteria tox regulatory element; Region: HTH_DTXR; smart00529 591001002660 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 591001002661 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 591001002662 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 591001002663 active site 591001002664 phosphorylation site [posttranslational modification] 591001002665 intermolecular recognition site; other site 591001002666 dimerization interface [polypeptide binding]; other site 591001002667 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 591001002668 DNA binding site [nucleotide binding] 591001002669 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 591001002670 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 591001002671 dimerization interface [polypeptide binding]; other site 591001002672 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001002673 dimer interface [polypeptide binding]; other site 591001002674 phosphorylation site [posttranslational modification] 591001002675 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 591001002676 ATP binding site [chemical binding]; other site 591001002677 Mg2+ binding site [ion binding]; other site 591001002678 G-X-G motif; other site 591001002679 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 591001002680 Protein of unknown function (DUF964); Region: DUF964; pfam06133 591001002681 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 591001002682 FAD binding domain; Region: FAD_binding_4; pfam01565 591001002683 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 591001002684 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 591001002685 EamA-like transporter family; Region: EamA; pfam00892 591001002686 EamA-like transporter family; Region: EamA; pfam00892 591001002687 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 591001002688 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 591001002689 dimer interface [polypeptide binding]; other site 591001002690 active site 591001002691 metal binding site [ion binding]; metal-binding site 591001002692 glutathione binding site [chemical binding]; other site 591001002693 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 591001002694 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 591001002695 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 591001002696 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 591001002697 active site 591001002698 HIGH motif; other site 591001002699 dimer interface [polypeptide binding]; other site 591001002700 KMSKS motif; other site 591001002701 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 591001002702 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 591001002703 acyl-activating enzyme (AAE) consensus motif; other site 591001002704 AMP binding site [chemical binding]; other site 591001002705 active site 591001002706 CoA binding site [chemical binding]; other site 591001002707 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 591001002708 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 591001002709 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 591001002710 active site 591001002711 phosphorylation site [posttranslational modification] 591001002712 intermolecular recognition site; other site 591001002713 dimerization interface [polypeptide binding]; other site 591001002714 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 591001002715 DNA binding residues [nucleotide binding] 591001002716 dimerization interface [polypeptide binding]; other site 591001002717 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 591001002718 active site 591001002719 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 591001002720 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 591001002721 active site 591001002722 metal binding site [ion binding]; metal-binding site 591001002723 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 591001002724 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 591001002725 DNA directed RNA polymerase, 7 kDa subunit; Region: DNA_RNApol_7kD; cl00874 591001002726 Repair protein; Region: Repair_PSII; pfam04536 591001002727 Asp23 family; Region: Asp23; pfam03780 591001002728 Asp23 family; Region: Asp23; cl00574 591001002729 Small integral membrane protein (DUF2273); Region: DUF2273; cl11575 591001002730 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 591001002731 putative RNA binding site [nucleotide binding]; other site 591001002732 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: QRI7; COG0533 591001002733 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 591001002734 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 591001002735 generic binding surface I; other site 591001002736 generic binding surface II; other site 591001002737 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 591001002738 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 591001002739 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 591001002740 substrate binding pocket [chemical binding]; other site 591001002741 chain length determination region; other site 591001002742 substrate-Mg2+ binding site; other site 591001002743 catalytic residues [active] 591001002744 aspartate-rich region 1; other site 591001002745 active site lid residues [active] 591001002746 aspartate-rich region 2; other site 591001002747 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 591001002748 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 591001002749 TPP-binding site; other site 591001002750 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 591001002751 PYR/PP interface [polypeptide binding]; other site 591001002752 dimer interface [polypeptide binding]; other site 591001002753 TPP binding site [chemical binding]; other site 591001002754 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 591001002755 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 591001002756 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 591001002757 RNA binding surface [nucleotide binding]; other site 591001002758 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 591001002759 S-adenosylmethionine binding site [chemical binding]; other site 591001002760 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 591001002761 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK03708 591001002762 arginine repressor; Provisional; Region: PRK04280 591001002763 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 591001002764 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 591001002765 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 591001002766 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 591001002767 Walker A/P-loop; other site 591001002768 ATP binding site [chemical binding]; other site 591001002769 Q-loop/lid; other site 591001002770 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 591001002771 ABC transporter signature motif; other site 591001002772 Walker B; other site 591001002773 D-loop; other site 591001002774 H-loop/switch region; other site 591001002775 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 591001002776 dimer interface [polypeptide binding]; other site 591001002777 ADP-ribose binding site [chemical binding]; other site 591001002778 active site 591001002779 nudix motif; other site 591001002780 metal binding site [ion binding]; metal-binding site 591001002781 Stage V sporulation protein S (SpoVS); Region: SpoVS; pfam04232 591001002782 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 591001002783 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 591001002784 membrane-bound complex binding site; other site 591001002785 hinge residues; other site 591001002786 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 591001002787 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 591001002788 Walker A/P-loop; other site 591001002789 ATP binding site [chemical binding]; other site 591001002790 Q-loop/lid; other site 591001002791 ABC transporter signature motif; other site 591001002792 Walker B; other site 591001002793 D-loop; other site 591001002794 H-loop/switch region; other site 591001002795 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 591001002796 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001002797 dimer interface [polypeptide binding]; other site 591001002798 ABC-ATPase subunit interface; other site 591001002799 putative PBP binding loops; other site 591001002800 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 591001002801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 591001002802 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 591001002803 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 591001002804 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 591001002805 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 591001002806 dimer interface [polypeptide binding]; other site 591001002807 active site 591001002808 metal binding site [ion binding]; metal-binding site 591001002809 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 591001002810 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001002811 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 591001002812 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 591001002813 PAS fold; Region: PAS_4; pfam08448 591001002814 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001002815 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001002816 metal binding site [ion binding]; metal-binding site 591001002817 I-site; other site 591001002818 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional; Region: PRK11921 591001002819 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 591001002820 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001002821 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 591001002822 active site 591001002823 NTP binding site [chemical binding]; other site 591001002824 metal binding triad [ion binding]; metal-binding site 591001002825 antibiotic binding site [chemical binding]; other site 591001002826 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 591001002827 FeoA domain; Region: FeoA; pfam04023 591001002828 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 591001002829 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 591001002830 G1 box; other site 591001002831 GTP/Mg2+ binding site [chemical binding]; other site 591001002832 Switch I region; other site 591001002833 G2 box; other site 591001002834 G3 box; other site 591001002835 Switch II region; other site 591001002836 G4 box; other site 591001002837 G5 box; other site 591001002838 CobD/Cbib protein; Region: CobD_Cbib; cl00561 591001002839 Nucleoside recognition; Region: Gate; pfam07670 591001002840 Nucleoside recognition; Region: Gate; pfam07670 591001002841 Heavy-metal-associated domain; Region: HMA; pfam00403 591001002842 metal-binding site [ion binding] 591001002843 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 591001002844 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 591001002845 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 591001002846 motif I; other site 591001002847 motif II; other site 591001002848 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 591001002849 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 591001002850 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 591001002851 amidase catalytic site [active] 591001002852 Zn binding residues [ion binding]; other site 591001002853 substrate binding site [chemical binding]; other site 591001002854 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 591001002855 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 591001002856 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 591001002857 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001002858 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 591001002859 Walker A/P-loop; other site 591001002860 ATP binding site [chemical binding]; other site 591001002861 Q-loop/lid; other site 591001002862 ABC transporter signature motif; other site 591001002863 Walker B; other site 591001002864 D-loop; other site 591001002865 H-loop/switch region; other site 591001002866 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 591001002867 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001002868 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001002869 Walker A/P-loop; other site 591001002870 ATP binding site [chemical binding]; other site 591001002871 Q-loop/lid; other site 591001002872 ABC transporter signature motif; other site 591001002873 Walker B; other site 591001002874 D-loop; other site 591001002875 H-loop/switch region; other site 591001002876 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 591001002877 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 591001002878 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 591001002879 dimer interface [polypeptide binding]; other site 591001002880 motif 1; other site 591001002881 active site 591001002882 motif 2; other site 591001002883 motif 3; other site 591001002884 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 591001002885 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 591001002886 putative tRNA-binding site [nucleotide binding]; other site 591001002887 B3/4 domain; Region: B3_4; pfam03483 591001002888 tRNA synthetase B5 domain; Region: B5; pfam03484 591001002889 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 591001002890 dimer interface [polypeptide binding]; other site 591001002891 motif 1; other site 591001002892 motif 3; other site 591001002893 motif 2; other site 591001002894 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 591001002895 HIRAN domain; Region: HIRAN; cl07418 591001002896 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 591001002897 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 591001002898 tetramer interface [polypeptide binding]; other site 591001002899 catalytic Zn binding site [ion binding]; other site 591001002900 NADP binding site [chemical binding]; other site 591001002901 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 591001002902 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 591001002903 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 591001002904 Firmicute transcriptional repressor of class III stress genes (CtsR); Region: CtsR; cl01850 591001002905 DNA repair protein RadA; Provisional; Region: PRK11823 591001002906 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 591001002907 Walker A motif/ATP binding site; other site 591001002908 ATP binding site [chemical binding]; other site 591001002909 Walker B motif; other site 591001002910 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 591001002911 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 591001002912 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 591001002913 motif 1; other site 591001002914 active site 591001002915 motif 2; other site 591001002916 motif 3; other site 591001002917 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 591001002918 DHHA1 domain; Region: DHHA1; pfam02272 591001002919 probable dihydroxyacetone kinase regulator; Region: DHAK_reg; TIGR02366 591001002920 hypothetical protein; Provisional; Region: PRK05473 591001002921 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 591001002922 Protein of unknown function (DUF1292); Region: DUF1292; cl01608 591001002923 YceG-like family; Region: YceG; pfam02618 591001002924 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 591001002925 dimerization interface [polypeptide binding]; other site 591001002926 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 591001002927 Peptidase family U32; Region: Peptidase_U32; pfam01136 591001002928 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 591001002929 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 591001002930 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 591001002931 active site 591001002932 elongation factor P; Validated; Region: PRK00529 591001002933 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 591001002934 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 591001002935 RNA binding site [nucleotide binding]; other site 591001002936 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 591001002937 RNA binding site [nucleotide binding]; other site 591001002938 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 591001002939 catalytic core [active] 591001002940 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 591001002941 Acetyltransferase (GNAT) domain; Region: Acetyltransf_9; pfam13527 591001002942 Sterol carrier protein domain; Region: SCP2_2; pfam13530 591001002943 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 591001002944 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 591001002945 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 591001002946 dimerization interface [polypeptide binding]; other site 591001002947 ATP binding site [chemical binding]; other site 591001002948 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 591001002949 dimerization interface [polypeptide binding]; other site 591001002950 ATP binding site [chemical binding]; other site 591001002951 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 591001002952 putative active site [active] 591001002953 catalytic triad [active] 591001002954 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]; Region: COG1026 591001002955 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 591001002956 Peptidase M16C associated; Region: M16C_assoc; pfam08367 591001002957 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 591001002958 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 591001002959 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 591001002960 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains; Region: ACT_Bt0572_1; cd04908 591001002961 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 591001002962 HD domain; Region: HD_4; pfam13328 591001002963 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001002964 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001002965 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 591001002966 dimerization interface [polypeptide binding]; other site 591001002967 mycofactocin system FadH/OYE family oxidoreductase 2; Region: mycofact_OYE_2; TIGR03997 591001002968 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_family; cd02803 591001002969 active site 591001002970 FMN binding site [chemical binding]; other site 591001002971 substrate binding site [chemical binding]; other site 591001002972 putative catalytic residue [active] 591001002973 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 591001002974 Trp repressor protein; Region: Trp_repressor; cl17266 591001002975 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 591001002976 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 591001002977 dimer interface [polypeptide binding]; other site 591001002978 motif 1; other site 591001002979 active site 591001002980 motif 2; other site 591001002981 motif 3; other site 591001002982 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 591001002983 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 591001002984 histidinol dehydrogenase; Region: hisD; TIGR00069 591001002985 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 591001002986 NAD binding site [chemical binding]; other site 591001002987 dimerization interface [polypeptide binding]; other site 591001002988 product binding site; other site 591001002989 substrate binding site [chemical binding]; other site 591001002990 zinc binding site [ion binding]; other site 591001002991 catalytic residues [active] 591001002992 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 591001002993 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 591001002994 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001002995 homodimer interface [polypeptide binding]; other site 591001002996 catalytic residue [active] 591001002997 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 591001002998 putative active site pocket [active] 591001002999 4-fold oligomerization interface [polypeptide binding]; other site 591001003000 metal binding residues [ion binding]; metal-binding site 591001003001 3-fold/trimer interface [polypeptide binding]; other site 591001003002 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 591001003003 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 591001003004 putative active site [active] 591001003005 oxyanion strand; other site 591001003006 catalytic triad [active] 591001003007 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 591001003008 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 591001003009 catalytic residues [active] 591001003010 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 591001003011 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 591001003012 substrate binding site [chemical binding]; other site 591001003013 glutamase interaction surface [polypeptide binding]; other site 591001003014 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 591001003015 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 591001003016 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 591001003017 metal binding site [ion binding]; metal-binding site 591001003018 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 591001003019 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 591001003020 active site 591001003021 substrate binding site [chemical binding]; other site 591001003022 metal binding site [ion binding]; metal-binding site 591001003023 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 591001003024 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 591001003025 glutaminase active site [active] 591001003026 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 591001003027 dimer interface [polypeptide binding]; other site 591001003028 active site 591001003029 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 591001003030 dimer interface [polypeptide binding]; other site 591001003031 active site 591001003032 Quinolinate synthetase A protein; Region: NadA; pfam02445 591001003033 L-aspartate oxidase; Provisional; Region: PRK06175 591001003034 Aspartate oxidase [Coenzyme metabolism]; Region: NadB; COG0029 591001003035 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 591001003036 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 591001003037 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 591001003038 dimerization interface [polypeptide binding]; other site 591001003039 active site 591001003040 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 591001003041 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 591001003042 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 591001003043 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK07729 591001003044 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 591001003045 bifunctional phosphoglycerate kinase/triosephosphate isomerase; Provisional; Region: PRK13962 591001003046 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 591001003047 substrate binding site [chemical binding]; other site 591001003048 hinge regions; other site 591001003049 ADP binding site [chemical binding]; other site 591001003050 catalytic site [active] 591001003051 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 591001003052 substrate binding site [chemical binding]; other site 591001003053 dimer interface [polypeptide binding]; other site 591001003054 catalytic triad [active] 591001003055 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 591001003056 phosphoglyceromutase; Provisional; Region: PRK05434 591001003057 enolase; Provisional; Region: eno; PRK00077 591001003058 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 591001003059 dimer interface [polypeptide binding]; other site 591001003060 metal binding site [ion binding]; metal-binding site 591001003061 substrate binding pocket [chemical binding]; other site 591001003062 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001003063 Zn2+ binding site [ion binding]; other site 591001003064 Mg2+ binding site [ion binding]; other site 591001003065 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 591001003066 synthetase active site [active] 591001003067 NTP binding site [chemical binding]; other site 591001003068 metal binding site [ion binding]; metal-binding site 591001003069 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 591001003070 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 591001003071 active site 591001003072 phosphorylation site [posttranslational modification] 591001003073 intermolecular recognition site; other site 591001003074 dimerization interface [polypeptide binding]; other site 591001003075 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 591001003076 DNA binding site [nucleotide binding] 591001003077 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 591001003078 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 591001003079 dimer interface [polypeptide binding]; other site 591001003080 phosphorylation site [posttranslational modification] 591001003081 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 591001003082 ATP binding site [chemical binding]; other site 591001003083 Mg2+ binding site [ion binding]; other site 591001003084 G-X-G motif; other site 591001003085 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 591001003086 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 591001003087 addiction module antitoxin, RelB/DinJ family; Region: RelB_DinJ; TIGR02384 591001003088 YjcQ protein; Region: YjcQ; pfam09639 591001003089 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 591001003090 Uncharacterized conserved protein [Function unknown]; Region: COG4925 591001003091 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 591001003092 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 591001003093 putative substrate translocation pore; other site 591001003094 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 591001003095 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 591001003096 Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases); Region: nitrilases_CHs; cd07564 591001003097 Predicted amidohydrolase [General function prediction only]; Region: COG0388 591001003098 putative active site [active] 591001003099 catalytic triad [active] 591001003100 putative dimer interface [polypeptide binding]; other site 591001003101 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001003102 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001003103 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 591001003104 dimerization interface [polypeptide binding]; other site 591001003105 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 591001003106 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 591001003107 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 591001003108 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 591001003109 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 591001003110 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 591001003111 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 591001003112 active site 591001003113 catalytic residues [active] 591001003114 metal binding site [ion binding]; metal-binding site 591001003115 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 591001003116 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 591001003117 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 591001003118 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 591001003119 catalytic residues [active] 591001003120 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 591001003121 Protein of unknown function (DUF1097); Region: DUF1097; pfam06496 591001003122 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001003123 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001003124 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 591001003125 dimerization interface [polypeptide binding]; other site 591001003126 substrate binding pocket [chemical binding]; other site 591001003127 Esterase/lipase [General function prediction only]; Region: COG1647 591001003128 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; cd03440 591001003129 active site 2 [active] 591001003130 active site 1 [active] 591001003131 ribonuclease R; Region: RNase_R; TIGR02063 591001003132 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 591001003133 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 591001003134 RNB domain; Region: RNB; pfam00773 591001003135 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 591001003136 RNA binding site [nucleotide binding]; other site 591001003137 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 591001003138 SmpB-tmRNA interface; other site 591001003139 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 591001003140 (R)-2-Hydroxyglutarate Dehydrogenase and related dehydrogenases, NAD-binding and catalytic domains; Region: HGDH_like; cd12184 591001003141 putative homodimer interface [polypeptide binding]; other site 591001003142 putative ligand binding site [chemical binding]; other site 591001003143 putative NAD binding site [chemical binding]; other site 591001003144 catalytic site [active] 591001003145 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 591001003146 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 591001003147 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 591001003148 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 591001003149 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 591001003150 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 591001003151 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 591001003152 catalytic residue [active] 591001003153 Protein of unknown function (DUF552); Region: DUF552; pfam04472 591001003154 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 591001003155 pyrroline-5-carboxylate reductase; Region: PLN02688 591001003156 Uncharacterized conserved protein, contains S4-like domain [Function unknown]; Region: COG2302 591001003157 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 591001003158 RNA binding surface [nucleotide binding]; other site 591001003159 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 591001003160 catalytic core [active] 591001003161 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 591001003162 Ligand binding site [chemical binding]; other site 591001003163 Electron transfer flavoprotein domain; Region: ETF; pfam01012 591001003164 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 591001003165 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 591001003166 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 591001003167 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 591001003168 active site 591001003169 catalytic site [active] 591001003170 substrate binding site [chemical binding]; other site 591001003171 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 591001003172 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 591001003173 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 591001003174 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 591001003175 active site 591001003176 dimer interface [polypeptide binding]; other site 591001003177 motif 1; other site 591001003178 motif 2; other site 591001003179 motif 3; other site 591001003180 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 591001003181 anticodon binding site; other site 591001003182 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 591001003183 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 591001003184 active site 591001003185 catalytic triad [active] 591001003186 oxyanion hole [active] 591001003187 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 591001003188 Sulfatase; Region: Sulfatase; cl17466 591001003189 Rubredoxin [Energy production and conversion]; Region: COG1773 591001003190 Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either...; Region: rubredoxin_like; cd00350 591001003191 iron binding site [ion binding]; other site 591001003192 Rubrerythrin [Energy production and conversion]; Region: COG1592 591001003193 rubrerythrin-like, diiron-binding domain; Region: Rubrerythrin_like; cd01046 591001003194 diiron binding motif [ion binding]; other site 591001003195 AAA ATPase domain; Region: AAA_15; pfam13175 591001003196 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001003197 Walker A/P-loop; other site 591001003198 ATP binding site [chemical binding]; other site 591001003199 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 591001003200 putative active site [active] 591001003201 putative metal-binding site [ion binding]; other site 591001003202 Predicted permeases [General function prediction only]; Region: COG0679 591001003203 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 591001003204 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 591001003205 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 591001003206 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 591001003207 intersubunit interface [polypeptide binding]; other site 591001003208 active site 591001003209 zinc binding site [ion binding]; other site 591001003210 Na+ binding site [ion binding]; other site 591001003211 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 591001003212 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 591001003213 active site 591001003214 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 591001003215 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]; Region: COG1606 591001003216 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_I; cd01990 591001003217 Ligand Binding Site [chemical binding]; other site 591001003218 NCAIR mutase (PurE)-related proteins [General function prediction only]; Region: COG1691 591001003219 AIR carboxylase; Region: AIRC; smart01001 591001003220 Protein of unknown function DUF111; Region: DUF111; pfam01969 591001003221 ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism]; Region: CbiM; COG0310 591001003222 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 591001003223 PDGLE domain; Region: PDGLE; pfam13190 591001003224 Cobalt transport protein; Region: CbiQ; cl00463 591001003225 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 591001003226 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 591001003227 Walker A/P-loop; other site 591001003228 ATP binding site [chemical binding]; other site 591001003229 Q-loop/lid; other site 591001003230 ABC transporter signature motif; other site 591001003231 Walker B; other site 591001003232 D-loop; other site 591001003233 H-loop/switch region; other site 591001003234 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 591001003235 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 591001003236 catalytic residues [active] 591001003237 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 591001003238 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 591001003239 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 591001003240 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 591001003241 LexA repressor; Validated; Region: PRK00215 591001003242 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 591001003243 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 591001003244 Catalytic site [active] 591001003245 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 591001003246 Aluminium resistance protein; Region: Alum_res; pfam06838 591001003247 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 591001003248 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 591001003249 HflX GTPase family; Region: HflX; cd01878 591001003250 G1 box; other site 591001003251 GTP/Mg2+ binding site [chemical binding]; other site 591001003252 Switch I region; other site 591001003253 G2 box; other site 591001003254 G3 box; other site 591001003255 Switch II region; other site 591001003256 G4 box; other site 591001003257 G5 box; other site 591001003258 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 591001003259 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 591001003260 ATP binding site [chemical binding]; other site 591001003261 Mg++ binding site [ion binding]; other site 591001003262 motif III; other site 591001003263 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 591001003264 nucleotide binding region [chemical binding]; other site 591001003265 ATP-binding site [chemical binding]; other site 591001003266 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 591001003267 RNA binding site [nucleotide binding]; other site 591001003268 competence damage-inducible protein A; Provisional; Region: PRK00549 591001003269 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 591001003270 putative MPT binding site; other site 591001003271 Competence-damaged protein; Region: CinA; pfam02464 591001003272 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 591001003273 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 591001003274 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 591001003275 FeS/SAM binding site; other site 591001003276 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 591001003277 non-specific DNA binding site [nucleotide binding]; other site 591001003278 salt bridge; other site 591001003279 sequence-specific DNA binding site [nucleotide binding]; other site 591001003280 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 591001003281 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 591001003282 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 591001003283 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 591001003284 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 591001003285 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 591001003286 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 591001003287 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 591001003288 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 591001003289 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 591001003290 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 591001003291 NAD(P) binding site [chemical binding]; other site 591001003292 active site 591001003293 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 591001003294 bacterial Ribonuclease HIII-like; Region: RNase_HII_bacteria_HIII_like; cd06590 591001003295 RNA/DNA hybrid binding site [nucleotide binding]; other site 591001003296 active site 591001003297 Asp23 family; Region: Asp23; pfam03780 591001003298 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 591001003299 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 591001003300 active site 591001003301 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 591001003302 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 591001003303 Major Facilitator Superfamily; Region: MFS_1; pfam07690 591001003304 putative substrate translocation pore; other site 591001003305 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001003306 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001003307 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 591001003308 dimerization interface [polypeptide binding]; other site 591001003309 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 591001003310 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 591001003311 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 591001003312 active site 591001003313 phosphorylation site [posttranslational modification] 591001003314 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 591001003315 active site 591001003316 P-loop; other site 591001003317 phosphorylation site [posttranslational modification] 591001003318 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; COG1299 591001003319 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 591001003320 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 591001003321 putative substrate binding site [chemical binding]; other site 591001003322 putative ATP binding site [chemical binding]; other site 591001003323 Escherichia coli YdjC-like family of proteins; Region: YdjC; cd10808 591001003324 putative active site [active] 591001003325 YdjC motif; other site 591001003326 Mg binding site [ion binding]; other site 591001003327 putative homodimer interface [polypeptide binding]; other site 591001003328 Predicted membrane protein [Function unknown]; Region: COG3601 591001003329 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 591001003330 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl17195 591001003331 L-lactate dehydrogenase; Region: L-LDH-NAD; TIGR01771 591001003332 LDH/MDH dimer interface [polypeptide binding]; other site 591001003333 NAD(P) binding site [chemical binding]; other site 591001003334 substrate binding site [chemical binding]; other site 591001003335 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 591001003336 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 591001003337 active site 591001003338 metal binding site [ion binding]; metal-binding site 591001003339 Amino acid permease; Region: AA_permease_2; pfam13520 591001003340 Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is...; Region: Peptidase_C1B; cd00585 591001003341 trimer interface [polypeptide binding]; other site 591001003342 active site 591001003343 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 591001003344 EamA-like transporter family; Region: EamA; pfam00892 591001003345 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 591001003346 Uncharacterized protein conserved in bacteria (DUF2128); Region: DUF2128; pfam09901 591001003347 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 591001003348 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001003349 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 591001003350 Walker A/P-loop; other site 591001003351 ATP binding site [chemical binding]; other site 591001003352 Q-loop/lid; other site 591001003353 ABC transporter signature motif; other site 591001003354 Walker B; other site 591001003355 D-loop; other site 591001003356 H-loop/switch region; other site 591001003357 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 591001003358 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001003359 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001003360 Walker A/P-loop; other site 591001003361 ATP binding site [chemical binding]; other site 591001003362 Q-loop/lid; other site 591001003363 ABC transporter signature motif; other site 591001003364 Walker B; other site 591001003365 D-loop; other site 591001003366 H-loop/switch region; other site 591001003367 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001003368 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001003369 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 591001003370 dimerization interface [polypeptide binding]; other site 591001003371 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 591001003372 Low molecular weight phosphatase family; Region: LMWPc; cd00115 591001003373 active site 591001003374 putative transposase OrfB; Reviewed; Region: PHA02517 591001003375 HTH-like domain; Region: HTH_21; pfam13276 591001003376 Integrase core domain; Region: rve; pfam00665 591001003377 Integrase core domain; Region: rve_2; pfam13333 591001003378 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 591001003379 Sel1-like repeats; Region: SEL1; smart00671 591001003380 Sel1-like repeats; Region: SEL1; smart00671 591001003381 Sel1-like repeats; Region: SEL1; smart00671 591001003382 Sel1-like repeats; Region: SEL1; smart00671 591001003383 Transposase; Region: HTH_Tnp_1; cl17663 591001003384 DNA binding domain of tn916 integrase; Region: Integrase_DNA; pfam02920 591001003385 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 591001003386 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 591001003387 active site 591001003388 DNA binding site [nucleotide binding] 591001003389 Int/Topo IB signature motif; other site 591001003390 Excisionase from transposon Tn916; Region: Tn916-Xis; pfam09035 591001003391 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 591001003392 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 591001003393 HSP70 interaction site [polypeptide binding]; other site 591001003394 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001003395 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; cl17221 591001003396 transmembrane helices; other site 591001003397 FAD dependent oxidoreductase; Region: FAD_oxidored; pfam12831 591001003398 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001003399 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001003400 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 591001003401 dimerization interface [polypeptide binding]; other site 591001003402 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 591001003403 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 591001003404 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 591001003405 Citrate transporter; Region: CitMHS; pfam03600 591001003406 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 591001003407 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001003408 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001003409 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 591001003410 dimerization interface [polypeptide binding]; other site 591001003411 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 591001003412 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 591001003413 non-specific DNA binding site [nucleotide binding]; other site 591001003414 salt bridge; other site 591001003415 sequence-specific DNA binding site [nucleotide binding]; other site 591001003416 Putative amidoligase enzyme; Region: Amidoligase_2; pfam12224 591001003417 Domain of unknown function (DUF4314); Region: DUF4314; pfam14192 591001003418 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 591001003419 ParB-like nuclease domain; Region: ParBc; pfam02195 591001003420 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 591001003421 DNA methylase; Region: N6_N4_Mtase; pfam01555 591001003422 Phage terminase, small subunit; Region: Terminase_4; cl01525 591001003423 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 591001003424 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 591001003425 active site 591001003426 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 591001003427 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 591001003428 ATP binding site [chemical binding]; other site 591001003429 putative Mg++ binding site [ion binding]; other site 591001003430 VRR-NUC domain; Region: VRR_NUC; pfam08774 591001003431 potential frameshift: common BLAST hit: gi|76786816|ref|YP_329358.1| prophage LambdaSa04, DNA primase 591001003432 D5 N terminal like; Region: D5_N; pfam08706 591001003433 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 591001003434 Virulence-associated protein E; Region: VirE; pfam05272 591001003435 Primase C terminal 1 (PriCT-1); Region: PriCT_1; smart00942 591001003436 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 591001003437 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 591001003438 active site 591001003439 DNA binding site [nucleotide binding] 591001003440 catalytic site [active] 591001003441 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 591001003442 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 591001003443 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 591001003444 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 591001003445 Predicted amidohydrolase [General function prediction only]; Region: COG0388 591001003446 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 591001003447 active site 591001003448 catalytic triad [active] 591001003449 dimer interface [polypeptide binding]; other site 591001003450 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 591001003451 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 591001003452 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 591001003453 Transcriptional regulators [Transcription]; Region: FadR; COG2186 591001003454 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001003455 DNA-binding site [nucleotide binding]; DNA binding site 591001003456 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 591001003457 Family description; Region: ACT_7; pfam13840 591001003458 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 591001003459 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 591001003460 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 591001003461 DNA methylase; Region: N6_N4_Mtase; pfam01555 591001003462 DNA methylase; Region: N6_N4_Mtase; pfam01555 591001003463 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 591001003464 active site 591001003465 8-oxo-dGMP binding site [chemical binding]; other site 591001003466 nudix motif; other site 591001003467 metal binding site [ion binding]; metal-binding site 591001003468 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 591001003469 Domain of unknown function (DUF4343); Region: DUF4343; pfam14243 591001003470 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 591001003471 Prophage maintenance system killer protein [General function prediction only]; Region: Doc; COG3654 591001003472 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 591001003473 non-specific DNA binding site [nucleotide binding]; other site 591001003474 salt bridge; other site 591001003475 sequence-specific DNA binding site [nucleotide binding]; other site 591001003476 Cysteine-rich CPCC; Region: Cys_rich_CPCC; pfam14206 591001003477 Domain of unknown function (DUF4343); Region: DUF4343; pfam14243 591001003478 DNA binding domain of tn916 integrase; Region: Integrase_DNA; pfam02920 591001003479 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 591001003480 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 591001003481 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 591001003482 Int/Topo IB signature motif; other site 591001003483 Excisionase from transposon Tn916; Region: Tn916-Xis; pfam09035 591001003484 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 591001003485 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 591001003486 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 591001003487 active site 591001003488 metal binding site [ion binding]; metal-binding site 591001003489 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_A; cd08642 591001003490 active site 591001003491 DNA binding site [nucleotide binding] 591001003492 catalytic site [active] 591001003493 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 591001003494 Protein of unknown function (DUF2800); Region: DUF2800; pfam10926 591001003495 Protein of unknown function (DUF1266); Region: DUF1266; cl14673 591001003496 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-terminal...; Region: MIP; cd00333 591001003497 amphipathic channel; other site 591001003498 Asn-Pro-Ala signature motifs; other site 591001003499 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 591001003500 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 591001003501 trimer interface [polypeptide binding]; other site 591001003502 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 591001003503 trimer interface [polypeptide binding]; other site 591001003504 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 591001003505 trimer interface [polypeptide binding]; other site 591001003506 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 591001003507 trimer interface [polypeptide binding]; other site 591001003508 Haemagglutinin; Region: HIM; pfam05662 591001003509 Haemagglutinin; Region: HIM; pfam05662 591001003510 YadA-like C-terminal region; Region: YadA; pfam03895 591001003511 S-layer homology domain; Region: SLH; pfam00395 591001003512 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 591001003513 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 591001003514 catalytic residues [active] 591001003515 catalytic nucleophile [active] 591001003516 Recombinase; Region: Recombinase; pfam07508 591001003517 putative transposase OrfB; Reviewed; Region: PHA02517 591001003518 HTH-like domain; Region: HTH_21; pfam13276 591001003519 Integrase core domain; Region: rve; pfam00665 591001003520 Integrase core domain; Region: rve_2; pfam13333 591001003521 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 591001003522 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 591001003523 salt bridge; other site 591001003524 non-specific DNA binding site [nucleotide binding]; other site 591001003525 sequence-specific DNA binding site [nucleotide binding]; other site 591001003526 Fic family protein [Function unknown]; Region: COG3177 591001003527 Fic/DOC family; Region: Fic; pfam02661 591001003528 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 591001003529 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 591001003530 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 591001003531 FeS/SAM binding site; other site 591001003532 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 591001003533 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 591001003534 Probable transposase; Region: OrfB_IS605; pfam01385 591001003535 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 591001003536 Transposase IS200 like; Region: Y1_Tnp; pfam01797 591001003537 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 591001003538 dimerization interface [polypeptide binding]; other site 591001003539 putative DNA binding site [nucleotide binding]; other site 591001003540 putative Zn2+ binding site [ion binding]; other site 591001003541 Methyltransferase domain; Region: Methyltransf_31; pfam13847 591001003542 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 591001003543 S-adenosylmethionine binding site [chemical binding]; other site 591001003544 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 591001003545 Int/Topo IB signature motif; other site 591001003546 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 591001003547 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 591001003548 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 591001003549 ATP binding site [chemical binding]; other site 591001003550 putative Mg++ binding site [ion binding]; other site 591001003551 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 591001003552 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 591001003553 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 591001003554 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 591001003555 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 591001003556 HsdM N-terminal domain; Region: HsdM_N; pfam12161 591001003557 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 591001003558 Methyltransferase domain; Region: Methyltransf_26; pfam13659 591001003559 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 591001003560 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 591001003561 putative DNA binding site [nucleotide binding]; other site 591001003562 putative Zn2+ binding site [ion binding]; other site 591001003563 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 591001003564 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 591001003565 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 591001003566 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 591001003567 Walker A/P-loop; other site 591001003568 ATP binding site [chemical binding]; other site 591001003569 Q-loop/lid; other site 591001003570 ABC transporter signature motif; other site 591001003571 Walker B; other site 591001003572 D-loop; other site 591001003573 H-loop/switch region; other site 591001003574 NIL domain; Region: NIL; pfam09383 591001003575 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001003576 dimer interface [polypeptide binding]; other site 591001003577 conserved gate region; other site 591001003578 ABC-ATPase subunit interface; other site 591001003579 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 591001003580 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 591001003581 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 591001003582 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 591001003583 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 591001003584 ATP binding site [chemical binding]; other site 591001003585 Walker A motif; other site 591001003586 hexamer interface [polypeptide binding]; other site 591001003587 Walker B motif; other site 591001003588 TadE-like protein; Region: TadE; pfam07811 591001003589 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 591001003590 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 591001003591 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 591001003592 Response regulator receiver domain; Region: Response_reg; pfam00072 591001003593 active site 591001003594 phosphorylation site [posttranslational modification] 591001003595 intermolecular recognition site; other site 591001003596 dimerization interface [polypeptide binding]; other site 591001003597 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 591001003598 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 591001003599 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 591001003600 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 591001003601 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 591001003602 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 591001003603 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 591001003604 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 591001003605 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 591001003606 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 591001003607 hypothetical protein; Provisional; Region: PRK07208 591001003608 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 591001003609 UDP-galactopyranose mutase; Region: GLF; pfam03275 591001003610 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 591001003611 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 591001003612 dimer interface [polypeptide binding]; other site 591001003613 active site 591001003614 catalytic residue [active] 591001003615 aspartate kinase I; Reviewed; Region: PRK08210 591001003616 AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli; Region: AAK_AK-DapG-like; cd04246 591001003617 putative catalytic residues [active] 591001003618 putative nucleotide binding site [chemical binding]; other site 591001003619 putative aspartate binding site [chemical binding]; other site 591001003620 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 591001003621 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 591001003622 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 591001003623 dihydrodipicolinate reductase; Provisional; Region: PRK00048 591001003624 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 591001003625 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 591001003626 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 591001003627 trimer interface [polypeptide binding]; other site 591001003628 active site 591001003629 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 591001003630 thiamine phosphate binding site [chemical binding]; other site 591001003631 active site 591001003632 pyrophosphate binding site [ion binding]; other site 591001003633 desulfoferrodoxin; Region: dfx_rbo; TIGR00320 591001003634 Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small; Region: DSRD; cl00018 591001003635 non-heme iron binding site [ion binding]; other site 591001003636 dimer interface [polypeptide binding]; other site 591001003637 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 591001003638 non-heme iron binding site [ion binding]; other site 591001003639 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 591001003640 ATP cone domain; Region: ATP-cone; pfam03477 591001003641 Class III ribonucleotide reductase; Region: RNR_III; cd01675 591001003642 effector binding site; other site 591001003643 active site 591001003644 Zn binding site [ion binding]; other site 591001003645 glycine loop; other site 591001003646 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 591001003647 catalytic residues [active] 591001003648 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 591001003649 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 591001003650 FeS/SAM binding site; other site 591001003651 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 591001003652 M48 family peptidase; Provisional; Region: PRK03001 591001003653 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 591001003654 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 591001003655 active site 591001003656 Int/Topo IB signature motif; other site 591001003657 bacterial Hfq-like; Region: Hfq; cd01716 591001003658 hexamer interface [polypeptide binding]; other site 591001003659 Sm1 motif; other site 591001003660 RNA binding site [nucleotide binding]; other site 591001003661 Sm2 motif; other site 591001003662 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 591001003663 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 591001003664 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 591001003665 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 591001003666 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 591001003667 ATP binding site [chemical binding]; other site 591001003668 Mg2+ binding site [ion binding]; other site 591001003669 G-X-G motif; other site 591001003670 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 591001003671 ATP binding site [chemical binding]; other site 591001003672 MutL C terminal dimerisation domain; Region: MutL_C; smart00853 591001003673 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 591001003674 MutS domain I; Region: MutS_I; pfam01624 591001003675 MutS domain II; Region: MutS_II; pfam05188 591001003676 MutS domain III; Region: MutS_III; pfam05192 591001003677 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 591001003678 Walker A/P-loop; other site 591001003679 ATP binding site [chemical binding]; other site 591001003680 Q-loop/lid; other site 591001003681 ABC transporter signature motif; other site 591001003682 Walker B; other site 591001003683 D-loop; other site 591001003684 H-loop/switch region; other site 591001003685 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14328 591001003686 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 591001003687 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 591001003688 FeS/SAM binding site; other site 591001003689 TRAM domain; Region: TRAM; pfam01938 591001003690 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 591001003691 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 591001003692 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 591001003693 DNA methylase; Region: N6_N4_Mtase; cl17433 591001003694 DNA methylase; Region: N6_N4_Mtase; pfam01555 591001003695 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 591001003696 DNA methylase; Region: N6_N4_Mtase; pfam01555 591001003697 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 591001003698 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 591001003699 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001003700 Walker A motif; other site 591001003701 ATP binding site [chemical binding]; other site 591001003702 Walker B motif; other site 591001003703 arginine finger; other site 591001003704 Protein of unknown function (DUF1659); Region: DUF1659; pfam07872 591001003705 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 591001003706 YvrJ protein family; Region: YvrJ; pfam12841 591001003707 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 591001003708 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 591001003709 DXD motif; other site 591001003710 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 591001003711 catalytic center binding site [active] 591001003712 ATP binding site [chemical binding]; other site 591001003713 dihydropteroate synthase; Region: DHPS; TIGR01496 591001003714 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 591001003715 substrate binding pocket [chemical binding]; other site 591001003716 dimer interface [polypeptide binding]; other site 591001003717 inhibitor binding site; inhibition site 591001003718 putative GTP cyclohydrolase; Provisional; Region: PRK13674 591001003719 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 591001003720 active site 591001003721 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 591001003722 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 591001003723 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 591001003724 Na binding site [ion binding]; other site 591001003725 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 591001003726 metal-dependent hydrolase; Provisional; Region: PRK00685 591001003727 homoserine kinase; Provisional; Region: PRK01212 591001003728 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 591001003729 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 591001003730 homoserine dehydrogenase; Provisional; Region: PRK06349 591001003731 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 591001003732 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 591001003733 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 591001003734 hypothetical protein; Provisional; Region: PRK04435 591001003735 C-terminal ACT domain of a small (; 147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains; Region: ACT_PheB-BS; cd04888 591001003736 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 591001003737 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 591001003738 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 591001003739 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 591001003740 GTP-binding protein Der; Reviewed; Region: PRK00093 591001003741 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 591001003742 G1 box; other site 591001003743 GTP/Mg2+ binding site [chemical binding]; other site 591001003744 Switch I region; other site 591001003745 G2 box; other site 591001003746 Switch II region; other site 591001003747 G3 box; other site 591001003748 G4 box; other site 591001003749 G5 box; other site 591001003750 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 591001003751 G1 box; other site 591001003752 GTP/Mg2+ binding site [chemical binding]; other site 591001003753 Switch I region; other site 591001003754 G2 box; other site 591001003755 G3 box; other site 591001003756 Switch II region; other site 591001003757 G4 box; other site 591001003758 G5 box; other site 591001003759 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 591001003760 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 591001003761 homotetramer interface [polypeptide binding]; other site 591001003762 FMN binding site [chemical binding]; other site 591001003763 homodimer contacts [polypeptide binding]; other site 591001003764 putative active site [active] 591001003765 putative substrate binding site [chemical binding]; other site 591001003766 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed; Region: PRK00087 591001003767 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 591001003768 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 591001003769 RNA binding site [nucleotide binding]; other site 591001003770 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 591001003771 RNA binding site [nucleotide binding]; other site 591001003772 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 591001003773 RNA binding site [nucleotide binding]; other site 591001003774 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 591001003775 RNA binding site [nucleotide binding]; other site 591001003776 domain interface; other site 591001003777 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 591001003778 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 591001003779 putative acyl-acceptor binding pocket; other site 591001003780 cytidylate kinase; Provisional; Region: cmk; PRK00023 591001003781 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 591001003782 CMP-binding site; other site 591001003783 The sites determining sugar specificity; other site 591001003784 flavoprotein, HI0933 family; Region: TIGR00275 591001003785 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 591001003786 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 591001003787 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 591001003788 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 591001003789 RNA binding surface [nucleotide binding]; other site 591001003790 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 591001003791 active site 591001003792 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 591001003793 ScpA/B protein; Region: ScpA_ScpB; cl00598 591001003794 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 591001003795 Peptidase family M50; Region: Peptidase_M50; pfam02163 591001003796 active site 591001003797 putative substrate binding region [chemical binding]; other site 591001003798 transcriptional repressor CodY; Validated; Region: PRK04158 591001003799 CodY GAF-like domain; Region: CodY; pfam06018 591001003800 CodY helix-turn-helix domain; Region: HTH_CodY; pfam08222 591001003801 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 591001003802 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 591001003803 active site 591001003804 DNA binding site [nucleotide binding] 591001003805 Int/Topo IB signature motif; other site 591001003806 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 591001003807 Glucose inhibited division protein A; Region: GIDA; pfam01134 591001003808 DNA topoisomerase I; Validated; Region: PRK05582 591001003809 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 591001003810 active site 591001003811 interdomain interaction site; other site 591001003812 putative metal-binding site [ion binding]; other site 591001003813 nucleotide binding site [chemical binding]; other site 591001003814 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 591001003815 domain I; other site 591001003816 DNA binding groove [nucleotide binding] 591001003817 phosphate binding site [ion binding]; other site 591001003818 domain II; other site 591001003819 domain III; other site 591001003820 nucleotide binding site [chemical binding]; other site 591001003821 catalytic site [active] 591001003822 domain IV; other site 591001003823 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 591001003824 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 591001003825 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 591001003826 DNA protecting protein DprA; Region: dprA; TIGR00732 591001003827 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 591001003828 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 591001003829 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 591001003830 G1 box; other site 591001003831 GTP/Mg2+ binding site [chemical binding]; other site 591001003832 Switch I region; other site 591001003833 G2 box; other site 591001003834 Switch II region; other site 591001003835 G3 box; other site 591001003836 G4 box; other site 591001003837 G5 box; other site 591001003838 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 591001003839 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 591001003840 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 591001003841 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 591001003842 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 591001003843 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 591001003844 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 591001003845 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 591001003846 ATP binding site [chemical binding]; other site 591001003847 putative Mg++ binding site [ion binding]; other site 591001003848 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 591001003849 nucleotide binding region [chemical binding]; other site 591001003850 ATP-binding site [chemical binding]; other site 591001003851 flagellar motor protein MotB; Validated; Region: motB; PRK06667 591001003852 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 591001003853 ligand binding site [chemical binding]; other site 591001003854 Protein of unknown function (DUF805); Region: DUF805; pfam05656 591001003855 EamA-like transporter family; Region: EamA; pfam00892 591001003856 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 591001003857 EamA-like transporter family; Region: EamA; pfam00892 591001003858 Predicted periplasmic protein (DUF2271); Region: DUF2271; cl17856 591001003859 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001003860 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 591001003861 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 591001003862 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 591001003863 active site 591001003864 HIGH motif; other site 591001003865 dimer interface [polypeptide binding]; other site 591001003866 KMSKS motif; other site 591001003867 serine/threonine transporter SstT; Provisional; Region: PRK13628 591001003868 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 591001003869 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 591001003870 Sodium Bile acid symporter family; Region: SBF; pfam01758 591001003871 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 591001003872 MgtE intracellular N domain; Region: MgtE_N; pfam03448 591001003873 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 591001003874 Divalent cation transporter; Region: MgtE; pfam01769 591001003875 PUA domain; Region: PUA; cl00607 591001003876 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 591001003877 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 591001003878 putative RNA binding site [nucleotide binding]; other site 591001003879 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 591001003880 S-adenosylmethionine binding site [chemical binding]; other site 591001003881 inosine 5-monophosphate dehydrogenase; Validated; Region: PRK07107 591001003882 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 591001003883 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH_2; cd04602 591001003884 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 591001003885 active site 591001003886 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 591001003887 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 591001003888 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 591001003889 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 591001003890 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 591001003891 purine monophosphate binding site [chemical binding]; other site 591001003892 dimer interface [polypeptide binding]; other site 591001003893 putative catalytic residues [active] 591001003894 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 591001003895 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 591001003896 active site 591001003897 substrate binding site [chemical binding]; other site 591001003898 cosubstrate binding site; other site 591001003899 catalytic site [active] 591001003900 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 591001003901 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 591001003902 dimerization interface [polypeptide binding]; other site 591001003903 putative ATP binding site [chemical binding]; other site 591001003904 Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]; Region: PurF; COG0034 591001003905 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 591001003906 active site 591001003907 tetramer interface [polypeptide binding]; other site 591001003908 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001003909 active site 591001003910 AIR carboxylase; Region: AIRC; pfam00731 591001003911 Curli production assembly/transport component CsgG; Region: CsgG; cl17434 591001003912 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 591001003913 MutS domain III; Region: MutS_III; pfam05192 591001003914 ATP-binding cassette domain of MutS2; Region: ABC_MutS2; cd03280 591001003915 Walker A/P-loop; other site 591001003916 ATP binding site [chemical binding]; other site 591001003917 Q-loop/lid; other site 591001003918 ABC transporter signature motif; other site 591001003919 Walker B; other site 591001003920 D-loop; other site 591001003921 H-loop/switch region; other site 591001003922 Smr domain; Region: Smr; pfam01713 591001003923 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 591001003924 Peptidase family U32; Region: Peptidase_U32; pfam01136 591001003925 PAAR motif; Region: PAAR_motif; pfam05488 591001003926 Collagenase; Region: DUF3656; pfam12392 591001003927 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 591001003928 Peptidase family U32; Region: Peptidase_U32; pfam01136 591001003929 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 591001003930 PAS fold; Region: PAS_3; pfam08447 591001003931 Chagasin family peptidase inhibitor I42; Region: Inhibitor_I42; pfam09394 591001003932 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 591001003933 YcfA-like protein; Region: YcfA; pfam07927 591001003934 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 591001003935 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 591001003936 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 591001003937 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 591001003938 ATP cone domain; Region: ATP-cone; pfam03477 591001003939 cell division protein FtsZ; Validated; Region: PRK09330 591001003940 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 591001003941 nucleotide binding site [chemical binding]; other site 591001003942 SulA interaction site; other site 591001003943 Protein of unknown function (DUF1290); Region: DUF1290; pfam06947 591001003944 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 591001003945 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 591001003946 Cell division protein FtsQ; Region: FtsQ; pfam03799 591001003947 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 591001003948 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 591001003949 ATP-grasp domain; Region: ATP-grasp_4; cl17255 591001003950 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 591001003951 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 591001003952 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 591001003953 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 591001003954 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 591001003955 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 591001003956 active site 591001003957 homodimer interface [polypeptide binding]; other site 591001003958 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK14106 591001003959 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 591001003960 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 591001003961 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 591001003962 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 591001003963 Mg++ binding site [ion binding]; other site 591001003964 putative catalytic motif [active] 591001003965 putative substrate binding site [chemical binding]; other site 591001003966 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 591001003967 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 591001003968 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 591001003969 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 591001003970 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 591001003971 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 591001003972 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 591001003973 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 591001003974 Septum formation initiator; Region: DivIC; cl17659 591001003975 MraW methylase family; Region: Methyltransf_5; pfam01795 591001003976 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 591001003977 cell division protein MraZ; Reviewed; Region: PRK00326 591001003978 MraZ protein; Region: MraZ; pfam02381 591001003979 MraZ protein; Region: MraZ; pfam02381 591001003980 hybrid cluster protein-associated redox disulfide domain; Region: prismane_assoc; TIGR03980 591001003981 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001003982 active site 591001003983 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 591001003984 active site 591001003985 dimer interface [polypeptide binding]; other site 591001003986 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 591001003987 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine...; Region: DHOD_1B_like; cd04740 591001003988 heterodimer interface [polypeptide binding]; other site 591001003989 active site 591001003990 FMN binding site [chemical binding]; other site 591001003991 homodimer interface [polypeptide binding]; other site 591001003992 substrate binding site [chemical binding]; other site 591001003993 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 591001003994 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 591001003995 FAD binding pocket [chemical binding]; other site 591001003996 FAD binding motif [chemical binding]; other site 591001003997 phosphate binding motif [ion binding]; other site 591001003998 beta-alpha-beta structure motif; other site 591001003999 NAD binding pocket [chemical binding]; other site 591001004000 Iron coordination center [ion binding]; other site 591001004001 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 591001004002 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 591001004003 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 591001004004 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 591001004005 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 591001004006 ATP-grasp domain; Region: ATP-grasp_4; cl17255 591001004007 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 591001004008 IMP binding site; other site 591001004009 dimer interface [polypeptide binding]; other site 591001004010 interdomain contacts; other site 591001004011 partial ornithine binding site; other site 591001004012 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 591001004013 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 591001004014 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 591001004015 catalytic site [active] 591001004016 subunit interface [polypeptide binding]; other site 591001004017 dihydroorotase; Validated; Region: pyrC; PRK09357 591001004018 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 591001004019 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 591001004020 active site 591001004021 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 591001004022 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 591001004023 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 591001004024 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 591001004025 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b1; cd09203 591001004026 PLD-like domain; Region: PLDc_2; pfam13091 591001004027 putative homodimer interface [polypeptide binding]; other site 591001004028 putative active site [active] 591001004029 catalytic site [active] 591001004030 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 591001004031 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 591001004032 ATP binding site [chemical binding]; other site 591001004033 putative Mg++ binding site [ion binding]; other site 591001004034 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 591001004035 nucleotide binding region [chemical binding]; other site 591001004036 ATP-binding site [chemical binding]; other site 591001004037 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 591001004038 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001004039 M20 Peptidases Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase from bacteria and archaea; Region: M20_Acy1_IAAspH_bact; cd05665 591001004040 putative metal binding site [ion binding]; other site 591001004041 dimer interface [polypeptide binding]; other site 591001004042 Protein of unknown function (DUF4127); Region: DUF4127; pfam13552 591001004043 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001004044 Zn2+ binding site [ion binding]; other site 591001004045 Mg2+ binding site [ion binding]; other site 591001004046 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 591001004047 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 591001004048 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 591001004049 ligand binding site [chemical binding]; other site 591001004050 putative oxidoreductase; Provisional; Region: PRK12831 591001004051 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 591001004052 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 591001004053 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 591001004054 FAD binding pocket [chemical binding]; other site 591001004055 FAD binding motif [chemical binding]; other site 591001004056 phosphate binding motif [ion binding]; other site 591001004057 beta-alpha-beta structure motif; other site 591001004058 NAD binding pocket [chemical binding]; other site 591001004059 Iron coordination center [ion binding]; other site 591001004060 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 591001004061 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 591001004062 active site 591001004063 putative substrate binding pocket [chemical binding]; other site 591001004064 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 591001004065 pyrophosphatase PpaX; Provisional; Region: PRK13288 591001004066 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 591001004067 motif II; other site 591001004068 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 591001004069 Part of AAA domain; Region: AAA_19; pfam13245 591001004070 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 591001004071 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 591001004072 Family description; Region: UvrD_C_2; pfam13538 591001004073 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 591001004074 ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]; Region: AddB; COG3857 591001004075 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 591001004076 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; cl17221 591001004077 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001004078 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 591001004079 active site residue [active] 591001004080 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 591001004081 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 591001004082 Ligand Binding Site [chemical binding]; other site 591001004083 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 591001004084 putative DNA-binding transcriptional regulator; Reviewed; Region: PRK00347 591001004085 2-isopropylmalate synthase; Validated; Region: PRK03739 591001004086 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 591001004087 active site 591001004088 catalytic residues [active] 591001004089 metal binding site [ion binding]; metal-binding site 591001004090 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 591001004091 5-aminoimidazole-4-carboxamide ribonucleotide transformylase; Provisional; Region: PRK07106 591001004092 AICAR transformylase/IMP cyclohydrolase PurH (only IMP cyclohydrolase domain in Aful) [Nucleotide transport and metabolism]; Region: PurH; COG0138 591001004093 Radical SAM superfamily; Region: Radical_SAM; pfam04055 591001004094 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 591001004095 FeS/SAM binding site; other site 591001004096 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 591001004097 EamA-like transporter family; Region: EamA; pfam00892 591001004098 EamA-like transporter family; Region: EamA; pfam00892 591001004099 L(+)-tartrate dehydratase subunit beta; Validated; Region: PRK08228 591001004100 tartrate dehydratase subunit alpha; Validated; Region: PRK08230 591001004101 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001004102 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 591001004103 transmembrane helices; other site 591001004104 Transcriptional regulators [Transcription]; Region: GntR; COG1802 591001004105 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001004106 DNA-binding site [nucleotide binding]; DNA binding site 591001004107 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001004108 DNA-binding site [nucleotide binding]; DNA binding site 591001004109 Transcriptional regulators [Transcription]; Region: FadR; COG2186 591001004110 FCD domain; Region: FCD; pfam07729 591001004111 GTP-binding protein LepA; Provisional; Region: PRK05433 591001004112 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 591001004113 G1 box; other site 591001004114 putative GEF interaction site [polypeptide binding]; other site 591001004115 GTP/Mg2+ binding site [chemical binding]; other site 591001004116 Switch I region; other site 591001004117 G2 box; other site 591001004118 G3 box; other site 591001004119 Switch II region; other site 591001004120 G4 box; other site 591001004121 G5 box; other site 591001004122 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 591001004123 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 591001004124 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 591001004125 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 591001004126 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 591001004127 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 591001004128 active site 591001004129 Riboflavin kinase; Region: Flavokinase; pfam01687 591001004130 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 591001004131 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 591001004132 RNA binding site [nucleotide binding]; other site 591001004133 active site 591001004134 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 591001004135 DHH family; Region: DHH; pfam01368 591001004136 DHHA1 domain; Region: DHHA1; pfam02272 591001004137 Ribosome-binding factor A; Region: RBFA; pfam02033 591001004138 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 591001004139 translation initiation factor IF-2; Region: IF-2; TIGR00487 591001004140 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 591001004141 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 591001004142 G1 box; other site 591001004143 putative GEF interaction site [polypeptide binding]; other site 591001004144 GTP/Mg2+ binding site [chemical binding]; other site 591001004145 Switch I region; other site 591001004146 G2 box; other site 591001004147 G3 box; other site 591001004148 Switch II region; other site 591001004149 G4 box; other site 591001004150 G5 box; other site 591001004151 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 591001004152 Translation-initiation factor 2; Region: IF-2; pfam11987 591001004153 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 591001004154 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 591001004155 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 591001004156 putative RNA binding cleft [nucleotide binding]; other site 591001004157 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 591001004158 NusA N-terminal domain; Region: NusA_N; pfam08529 591001004159 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 591001004160 RNA binding site [nucleotide binding]; other site 591001004161 homodimer interface [polypeptide binding]; other site 591001004162 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 591001004163 G-X-X-G motif; other site 591001004164 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 591001004165 G-X-X-G motif; other site 591001004166 Sm and related proteins; Region: Sm_like; cl00259 591001004167 ribosome maturation protein RimP; Reviewed; Region: PRK00092 591001004168 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 591001004169 putative oligomer interface [polypeptide binding]; other site 591001004170 putative RNA binding site [nucleotide binding]; other site 591001004171 Transglycosylase; Region: Transgly; pfam00912 591001004172 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 591001004173 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 591001004174 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]; Region: COG5016 591001004175 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 591001004176 active site 591001004177 catalytic residues [active] 591001004178 metal binding site [ion binding]; metal-binding site 591001004179 homodimer binding site [polypeptide binding]; other site 591001004180 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001004181 M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family; Region: M20_Acy1L2; cd03887 591001004182 putative metal binding site [ion binding]; other site 591001004183 HD domain; Region: HD_3; cl17350 591001004184 homocysteine methyltransferase; Provisional; Region: mmuM; PRK09485 591001004185 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 591001004186 putative transposase OrfB; Reviewed; Region: PHA02517 591001004187 HTH-like domain; Region: HTH_21; pfam13276 591001004188 Integrase core domain; Region: rve; pfam00665 591001004189 Integrase core domain; Region: rve_2; pfam13333 591001004190 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 591001004191 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 591001004192 allantoate amidohydrolase; Reviewed; Region: PRK09290 591001004193 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 591001004194 active site 591001004195 metal binding site [ion binding]; metal-binding site 591001004196 dimer interface [polypeptide binding]; other site 591001004197 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 591001004198 generic binding surface I; other site 591001004199 generic binding surface II; other site 591001004200 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; Region: PHP_PolIIIA_POLC; cd07435 591001004201 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 591001004202 active site 591001004203 putative PHP Thumb interface [polypeptide binding]; other site 591001004204 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 591001004205 Uncharacterized membrane protein [Function unknown]; Region: SapB; COG1285 591001004206 MgtC family; Region: MgtC; pfam02308 591001004207 prolyl-tRNA synthetase; Provisional; Region: PRK09194 591001004208 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 591001004209 dimer interface [polypeptide binding]; other site 591001004210 motif 1; other site 591001004211 active site 591001004212 motif 2; other site 591001004213 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 591001004214 putative deacylase active site [active] 591001004215 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 591001004216 active site 591001004217 motif 3; other site 591001004218 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 591001004219 anticodon binding site; other site 591001004220 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 591001004221 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 591001004222 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 591001004223 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 591001004224 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 591001004225 active site 591001004226 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 591001004227 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 591001004228 putative substrate binding region [chemical binding]; other site 591001004229 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 591001004230 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 591001004231 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 591001004232 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 591001004233 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 591001004234 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 591001004235 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 591001004236 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 591001004237 catalytic residue [active] 591001004238 putative FPP diphosphate binding site; other site 591001004239 putative FPP binding hydrophobic cleft; other site 591001004240 dimer interface [polypeptide binding]; other site 591001004241 putative IPP diphosphate binding site; other site 591001004242 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 591001004243 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 591001004244 ribosome recycling factor; Reviewed; Region: frr; PRK00083 591001004245 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 591001004246 hinge region; other site 591001004247 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 591001004248 putative nucleotide binding site [chemical binding]; other site 591001004249 uridine monophosphate binding site [chemical binding]; other site 591001004250 homohexameric interface [polypeptide binding]; other site 591001004251 elongation factor Ts; Provisional; Region: tsf; PRK09377 591001004252 UBA/TS-N domain; Region: UBA; pfam00627 591001004253 Elongation factor TS; Region: EF_TS; pfam00889 591001004254 Elongation factor TS; Region: EF_TS; pfam00889 591001004255 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 591001004256 rRNA interaction site [nucleotide binding]; other site 591001004257 S8 interaction site; other site 591001004258 putative laminin-1 binding site; other site 591001004259 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 591001004260 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 591001004261 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 591001004262 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 591001004263 FeS/SAM binding site; other site 591001004264 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 591001004265 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 591001004266 homodimer interface [polypeptide binding]; other site 591001004267 substrate-cofactor binding pocket; other site 591001004268 catalytic residue [active] 591001004269 Cache domain; Region: Cache_1; pfam02743 591001004270 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 591001004271 dimerization interface [polypeptide binding]; other site 591001004272 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001004273 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001004274 metal binding site [ion binding]; metal-binding site 591001004275 active site 591001004276 I-site; other site 591001004277 Cache domain; Region: Cache_1; pfam02743 591001004278 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 591001004279 dimerization interface [polypeptide binding]; other site 591001004280 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001004281 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001004282 metal binding site [ion binding]; metal-binding site 591001004283 active site 591001004284 I-site; other site 591001004285 ribonuclease III; Reviewed; Region: rnc; PRK00102 591001004286 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 591001004287 dimerization interface [polypeptide binding]; other site 591001004288 active site 591001004289 metal binding site [ion binding]; metal-binding site 591001004290 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 591001004291 dsRNA binding site [nucleotide binding]; other site 591001004292 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 591001004293 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 591001004294 dimer interface [polypeptide binding]; other site 591001004295 active site 591001004296 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 591001004297 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 591001004298 FMN binding site [chemical binding]; other site 591001004299 substrate binding site [chemical binding]; other site 591001004300 putative catalytic residue [active] 591001004301 acyl carrier protein; Provisional; Region: acpP; PRK00982 591001004302 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 591001004303 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 591001004304 NAD(P) binding site [chemical binding]; other site 591001004305 homotetramer interface [polypeptide binding]; other site 591001004306 homodimer interface [polypeptide binding]; other site 591001004307 active site 591001004308 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 591001004309 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 591001004310 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 591001004311 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 591001004312 dimer interface [polypeptide binding]; other site 591001004313 active site 591001004314 CoA binding pocket [chemical binding]; other site 591001004315 putative phosphate acyltransferase; Provisional; Region: PRK05331 591001004316 fatty acid biosynthesis transcriptional regulator; Provisional; Region: PRK04424 591001004317 HGG motif-containing thioesterase, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PaaI; COG2050 591001004318 active site 2 [active] 591001004319 active site 1 [active] 591001004320 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 591001004321 active site 591001004322 intersubunit interactions; other site 591001004323 catalytic residue [active] 591001004324 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 591001004325 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 591001004326 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 591001004327 propionate/acetate kinase; Provisional; Region: PRK12379 591001004328 hypothetical protein; Provisional; Region: PRK13670 591001004329 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 591001004330 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 591001004331 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 591001004332 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 591001004333 active site 591001004334 (T/H)XGH motif; other site 591001004335 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 591001004336 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 591001004337 S-adenosylmethionine binding site [chemical binding]; other site 591001004338 Protein of unknown function (DUF4127); Region: DUF4127; pfam13552 591001004339 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 591001004340 Double zinc ribbon; Region: DZR; pfam12773 591001004341 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 591001004342 Double zinc ribbon; Region: DZR; pfam12773 591001004343 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 591001004344 4Fe-4S single cluster domain; Region: Fer4_13; pfam13370 591001004345 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 591001004346 amidohydrolase; Region: amidohydrolases; TIGR01891 591001004347 putative metal binding site [ion binding]; other site 591001004348 Hemerythrin-like domain; Region: Hr-like; cd12108 591001004349 Fe binding site [ion binding]; other site 591001004350 hybrid cluster protein-associated redox disulfide domain; Region: prismane_assoc; TIGR03980 591001004351 [FeFe] hydrogenase H-cluster radical SAM maturase HydE; Region: rSAM_HydE; TIGR03956 591001004352 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 591001004353 FeS/SAM binding site; other site 591001004354 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 591001004355 Tubby C 2; Region: Tub_2; cl02043 591001004356 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 591001004357 Flavoprotein; Region: Flavoprotein; pfam02441 591001004358 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 591001004359 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 591001004360 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 591001004361 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 591001004362 catalytic site [active] 591001004363 G-X2-G-X-G-K; other site 591001004364 hypothetical protein; Provisional; Region: PRK04323 591001004365 hypothetical protein; Provisional; Region: PRK11820 591001004366 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 591001004367 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 591001004368 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 591001004369 Domain of unknown function (DUF814); Region: DUF814; pfam05670 591001004370 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 591001004371 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 591001004372 putative efflux protein, MATE family; Region: matE; TIGR00797 591001004373 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 591001004374 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 591001004375 dimer interface [polypeptide binding]; other site 591001004376 putative anticodon binding site; other site 591001004377 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 591001004378 motif 1; other site 591001004379 active site 591001004380 motif 2; other site 591001004381 motif 3; other site 591001004382 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 591001004383 dimer interface [polypeptide binding]; other site 591001004384 putative tRNA-binding site [nucleotide binding]; other site 591001004385 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 591001004386 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 591001004387 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 591001004388 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; cl17221 591001004389 transmembrane helices; other site 591001004390 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001004391 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 591001004392 dimer interface [polypeptide binding]; other site 591001004393 catalytic triad [active] 591001004394 peroxidatic and resolving cysteines [active] 591001004395 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 591001004396 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 591001004397 ring oligomerisation interface [polypeptide binding]; other site 591001004398 ATP/Mg binding site [chemical binding]; other site 591001004399 stacking interactions; other site 591001004400 hinge regions; other site 591001004401 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 591001004402 oligomerisation interface [polypeptide binding]; other site 591001004403 mobile loop; other site 591001004404 roof hairpin; other site 591001004405 Cysteine-rich small domain; Region: zf-like; cl00946 591001004406 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 591001004407 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 591001004408 S-adenosylmethionine binding site [chemical binding]; other site 591001004409 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 591001004410 TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low...; Region: TOPRIM_RNase_M5_like; cd01027 591001004411 putative active site [active] 591001004412 putative metal binding site [ion binding]; other site 591001004413 Domain of unknown function (DUF4093); Region: DUF4093; pfam13331 591001004414 Domain of unknown function (DUF348); Region: DUF348; pfam03990 591001004415 G5 domain; Region: G5; pfam07501 591001004416 3D domain; Region: 3D; cl01439 591001004417 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 591001004418 active site 591001004419 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 591001004420 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 591001004421 active site 591001004422 HIGH motif; other site 591001004423 KMSKS motif; other site 591001004424 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 591001004425 tRNA binding surface [nucleotide binding]; other site 591001004426 anticodon binding site; other site 591001004427 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 591001004428 dimer interface [polypeptide binding]; other site 591001004429 putative tRNA-binding site [nucleotide binding]; other site 591001004430 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 591001004431 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001004432 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001004433 metal binding site [ion binding]; metal-binding site 591001004434 active site 591001004435 I-site; other site 591001004436 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 591001004437 dimer interface [polypeptide binding]; other site 591001004438 FMN binding site [chemical binding]; other site 591001004439 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 591001004440 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 591001004441 active site 591001004442 tetramer interface; other site 591001004443 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 591001004444 putative active site [active] 591001004445 catalytic residue [active] 591001004446 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 591001004447 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 591001004448 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001004449 active site 591001004450 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 591001004451 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 591001004452 Substrate binding site; other site 591001004453 Mg++ binding site; other site 591001004454 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 591001004455 active site 591001004456 substrate binding site [chemical binding]; other site 591001004457 CoA binding site [chemical binding]; other site 591001004458 threonine dehydratase; Provisional; Region: PRK08198 591001004459 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 591001004460 tetramer interface [polypeptide binding]; other site 591001004461 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001004462 catalytic residue [active] 591001004463 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 591001004464 pur operon repressor; Provisional; Region: PRK09213 591001004465 Bacterial purine repressor, N-terminal; Region: PuR_N; pfam09182 591001004466 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001004467 active site 591001004468 Transcriptional regulators [Transcription]; Region: GntR; COG1802 591001004469 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001004470 DNA-binding site [nucleotide binding]; DNA binding site 591001004471 FCD domain; Region: FCD; pfam07729 591001004472 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00128 591001004473 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 591001004474 Uncharacterized conserved protein [Function unknown]; Region: COG1284 591001004475 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 591001004476 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 591001004477 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 591001004478 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 591001004479 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 591001004480 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 591001004481 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 591001004482 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 591001004483 Competence protein; Region: Competence; pfam03772 591001004484 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 591001004485 SLBB domain; Region: SLBB; pfam10531 591001004486 comEA protein; Region: comE; TIGR01259 591001004487 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 591001004488 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 591001004489 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 591001004490 active site 591001004491 motif I; other site 591001004492 motif II; other site 591001004493 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 591001004494 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 591001004495 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 591001004496 substrate binding pocket [chemical binding]; other site 591001004497 membrane-bound complex binding site; other site 591001004498 hinge residues; other site 591001004499 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001004500 Zn2+ binding site [ion binding]; other site 591001004501 Mg2+ binding site [ion binding]; other site 591001004502 TSCPD domain; Region: TSCPD; cl14834 591001004503 Protein of unknown function (DUF554); Region: DUF554; pfam04474 591001004504 alanine racemase; Reviewed; Region: alr; PRK00053 591001004505 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 591001004506 active site 591001004507 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 591001004508 dimer interface [polypeptide binding]; other site 591001004509 substrate binding site [chemical binding]; other site 591001004510 catalytic residues [active] 591001004511 Inosine-uridine preferring nucleoside hydrolase; Region: IU_nuc_hydro; pfam01156 591001004512 active site 591001004513 Bacterial PH domain; Region: DUF304; pfam03703 591001004514 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 591001004515 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001004516 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 591001004517 Walker A/P-loop; other site 591001004518 ATP binding site [chemical binding]; other site 591001004519 Q-loop/lid; other site 591001004520 ABC transporter signature motif; other site 591001004521 Walker B; other site 591001004522 D-loop; other site 591001004523 H-loop/switch region; other site 591001004524 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 591001004525 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001004526 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001004527 Walker A/P-loop; other site 591001004528 ATP binding site [chemical binding]; other site 591001004529 Q-loop/lid; other site 591001004530 ABC transporter signature motif; other site 591001004531 Walker B; other site 591001004532 D-loop; other site 591001004533 H-loop/switch region; other site 591001004534 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 591001004535 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001004536 active site 591001004537 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 591001004538 AAA domain; Region: AAA_30; pfam13604 591001004539 Family description; Region: UvrD_C_2; pfam13538 591001004540 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 591001004541 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 591001004542 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 591001004543 motif II; other site 591001004544 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 591001004545 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 591001004546 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 591001004547 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 591001004548 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 591001004549 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 591001004550 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 591001004551 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 591001004552 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 591001004553 oligomer interface [polypeptide binding]; other site 591001004554 putative active site [active] 591001004555 metal binding site [ion binding]; metal-binding site 591001004556 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 591001004557 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 591001004558 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 591001004559 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 591001004560 substrate binding site [chemical binding]; other site 591001004561 oxyanion hole (OAH) forming residues; other site 591001004562 trimer interface [polypeptide binding]; other site 591001004563 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 591001004564 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 591001004565 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 591001004566 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 591001004567 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 591001004568 FAD binding site [chemical binding]; other site 591001004569 homotetramer interface [polypeptide binding]; other site 591001004570 substrate binding pocket [chemical binding]; other site 591001004571 catalytic base [active] 591001004572 putative acyltransferase; Provisional; Region: PRK05790 591001004573 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 591001004574 dimer interface [polypeptide binding]; other site 591001004575 active site 591001004576 zinc-ribbon domain; Region: zf-ribbon_3; cl11198 591001004577 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 591001004578 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 591001004579 minor groove reading motif; other site 591001004580 helix-hairpin-helix signature motif; other site 591001004581 substrate binding pocket [chemical binding]; other site 591001004582 active site 591001004583 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 591001004584 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 591001004585 hypothetical protein; Validated; Region: PRK00194 591001004586 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 591001004587 ATP binding site [chemical binding]; other site 591001004588 active site 591001004589 substrate binding site [chemical binding]; other site 591001004590 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 591001004591 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 591001004592 Predicted transcriptional regulator [Transcription]; Region: COG1959 591001004593 Transcriptional regulator; Region: Rrf2; pfam02082 591001004594 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 591001004595 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 591001004596 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 591001004597 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 591001004598 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 591001004599 catalytic residues [active] 591001004600 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 591001004601 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 591001004602 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 591001004603 periplasmic chaperone; Provisional; Region: PRK10780 591001004604 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 591001004605 metal-binding site [ion binding] 591001004606 C-terminal domain of Faecalibacterium prausnitzii A2-165 FrmR , and related domains; this domain family was previously known as part of DUF156; Region: FpFrmR-Cterm-like_DUF156; cd10156 591001004607 putative homodimer interface [polypeptide binding]; other site 591001004608 putative homotetramer interface [polypeptide binding]; other site 591001004609 putative allosteric switch controlling residues; other site 591001004610 putative metal binding site [ion binding]; other site 591001004611 putative homodimer-homodimer interface [polypeptide binding]; other site 591001004612 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 591001004613 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 591001004614 HIGH motif; other site 591001004615 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 591001004616 active site 591001004617 KMSKS motif; other site 591001004618 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 591001004619 tRNA binding surface [nucleotide binding]; other site 591001004620 anticodon binding site; other site 591001004621 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 591001004622 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 591001004623 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 591001004624 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 591001004625 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 591001004626 TrkA-N domain; Region: TrkA_N; pfam02254 591001004627 TrkA-C domain; Region: TrkA_C; pfam02080 591001004628 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 591001004629 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 591001004630 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 591001004631 active site 591001004632 substrate binding site [chemical binding]; other site 591001004633 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 591001004634 FMN binding site [chemical binding]; other site 591001004635 putative catalytic residues [active] 591001004636 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 591001004637 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 591001004638 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 591001004639 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 591001004640 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 591001004641 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 591001004642 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 591001004643 GTP binding site [chemical binding]; other site 591001004644 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 591001004645 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 591001004646 Walker A/P-loop; other site 591001004647 ATP binding site [chemical binding]; other site 591001004648 Q-loop/lid; other site 591001004649 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 591001004650 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 591001004651 ABC transporter signature motif; other site 591001004652 Walker B; other site 591001004653 D-loop; other site 591001004654 H-loop/switch region; other site 591001004655 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 591001004656 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001004657 active site 591001004658 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 591001004659 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 591001004660 RNA binding surface [nucleotide binding]; other site 591001004661 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 591001004662 active site 591001004663 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 591001004664 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 591001004665 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 591001004666 motif II; other site 591001004667 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 591001004668 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 591001004669 dimer interface [polypeptide binding]; other site 591001004670 anticodon binding site; other site 591001004671 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 591001004672 homodimer interface [polypeptide binding]; other site 591001004673 motif 1; other site 591001004674 active site 591001004675 motif 2; other site 591001004676 GAD domain; Region: GAD; pfam02938 591001004677 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 591001004678 motif 3; other site 591001004679 histidyl-tRNA synthetase; Region: hisS; TIGR00442 591001004680 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 591001004681 dimer interface [polypeptide binding]; other site 591001004682 motif 1; other site 591001004683 active site 591001004684 motif 2; other site 591001004685 motif 3; other site 591001004686 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 591001004687 anticodon binding site; other site 591001004688 Domain of unknown function DUF20; Region: UPF0118; pfam01594 591001004689 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 591001004690 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 591001004691 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 591001004692 putative active site [active] 591001004693 dimerization interface [polypeptide binding]; other site 591001004694 putative tRNAtyr binding site [nucleotide binding]; other site 591001004695 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 591001004696 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001004697 Zn2+ binding site [ion binding]; other site 591001004698 Mg2+ binding site [ion binding]; other site 591001004699 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 591001004700 synthetase active site [active] 591001004701 NTP binding site [chemical binding]; other site 591001004702 metal binding site [ion binding]; metal-binding site 591001004703 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 591001004704 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 591001004705 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 591001004706 DHH family; Region: DHH; pfam01368 591001004707 DHHA1 domain; Region: DHHA1; pfam02272 591001004708 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 591001004709 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 591001004710 NAD binding site [chemical binding]; other site 591001004711 ligand binding site [chemical binding]; other site 591001004712 catalytic site [active] 591001004713 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 591001004714 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 591001004715 Protein export membrane protein; Region: SecD_SecF; pfam02355 591001004716 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 591001004717 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 591001004718 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 591001004719 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 591001004720 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 591001004721 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 591001004722 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 591001004723 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 591001004724 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 591001004725 Stage II sporulation protein; Region: SpoIID; pfam08486 591001004726 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 591001004727 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 591001004728 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001004729 Walker A motif; other site 591001004730 ATP binding site [chemical binding]; other site 591001004731 Walker B motif; other site 591001004732 arginine finger; other site 591001004733 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 591001004734 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 591001004735 RuvA N terminal domain; Region: RuvA_N; pfam01330 591001004736 Y-family of DNA polymerases; Region: PolY; cl12025 591001004737 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 591001004738 active site 591001004739 putative DNA-binding cleft [nucleotide binding]; other site 591001004740 dimer interface [polypeptide binding]; other site 591001004741 hypothetical protein; Validated; Region: PRK00110 591001004742 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 591001004743 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001004744 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 591001004745 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 591001004746 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 591001004747 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001004748 catalytic residue [active] 591001004749 NAD synthetase; Provisional; Region: PRK13981 591001004750 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 591001004751 multimer interface [polypeptide binding]; other site 591001004752 active site 591001004753 catalytic triad [active] 591001004754 protein interface 1 [polypeptide binding]; other site 591001004755 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 591001004756 Ligand Binding Site [chemical binding]; other site 591001004757 QueT transporter; Region: QueT; pfam06177 591001004758 Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of...; Region: TRX_superfamily; cd01659 591001004759 biotin synthase; Region: bioB; TIGR00433 591001004760 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 591001004761 FeS/SAM binding site; other site 591001004762 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 591001004763 Rubrerythrin [Energy production and conversion]; Region: COG1592 591001004764 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 591001004765 binuclear metal center [ion binding]; other site 591001004766 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 591001004767 iron binding site [ion binding]; other site 591001004768 Diaminopimelate epimerase [Amino acid transport and metabolism]; Region: DapF; COG0253 591001004769 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 591001004770 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 591001004771 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 591001004772 substrate binding site [chemical binding]; other site 591001004773 THF binding site; other site 591001004774 zinc-binding site [ion binding]; other site 591001004775 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001004776 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001004777 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 591001004778 dimerization interface [polypeptide binding]; other site 591001004779 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 591001004780 dimerization interface [polypeptide binding]; other site 591001004781 putative DNA binding site [nucleotide binding]; other site 591001004782 putative Zn2+ binding site [ion binding]; other site 591001004783 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 591001004784 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 591001004785 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 591001004786 P loop; other site 591001004787 Nucleotide binding site [chemical binding]; other site 591001004788 DTAP/Switch II; other site 591001004789 Switch I; other site 591001004790 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 591001004791 P loop; other site 591001004792 Nucleotide binding site [chemical binding]; other site 591001004793 DTAP/Switch II; other site 591001004794 Switch I; other site 591001004795 Low molecular weight phosphatase family; Region: LMWPc; cl00105 591001004796 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 591001004797 active site 591001004798 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 591001004799 arsenical-resistance protein; Region: acr3; TIGR00832 591001004800 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 591001004801 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 591001004802 LytTr DNA-binding domain; Region: LytTR; smart00850 591001004803 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 591001004804 Beta-lactamase enzyme family; Region: Beta-lactamase2; pfam13354 591001004805 Protein of unknown function DUF45; Region: DUF45; pfam01863 591001004806 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 591001004807 Domain of unknown function DUF21; Region: DUF21; pfam01595 591001004808 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 591001004809 Transporter associated domain; Region: CorC_HlyC; pfam03471 591001004810 Isochorismatase family; Region: Isochorismatase; pfam00857 591001004811 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 591001004812 catalytic triad [active] 591001004813 conserved cis-peptide bond; other site 591001004814 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 591001004815 FMN binding site [chemical binding]; other site 591001004816 dimer interface [polypeptide binding]; other site 591001004817 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 591001004818 active site 591001004819 Domain of unknown function (DUF368); Region: DUF368; pfam04018 591001004820 FeoA domain; Region: FeoA; pfam04023 591001004821 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 591001004822 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 591001004823 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 591001004824 G1 box; other site 591001004825 GTP/Mg2+ binding site [chemical binding]; other site 591001004826 Switch I region; other site 591001004827 G2 box; other site 591001004828 G3 box; other site 591001004829 Switch II region; other site 591001004830 G4 box; other site 591001004831 G5 box; other site 591001004832 Nucleoside recognition; Region: Gate; pfam07670 591001004833 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 591001004834 Nucleoside recognition; Region: Gate; pfam07670 591001004835 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001004836 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK12315 591001004837 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 591001004838 TPP-binding site; other site 591001004839 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 591001004840 PYR/PP interface [polypeptide binding]; other site 591001004841 dimer interface [polypeptide binding]; other site 591001004842 TPP binding site [chemical binding]; other site 591001004843 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 591001004844 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 591001004845 active site 591001004846 oxyanion hole [active] 591001004847 catalytic triad [active] 591001004848 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 591001004849 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001004850 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001004851 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 591001004852 dimerization interface [polypeptide binding]; other site 591001004853 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 591001004854 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 591001004855 FAD binding site [chemical binding]; other site 591001004856 homotetramer interface [polypeptide binding]; other site 591001004857 substrate binding pocket [chemical binding]; other site 591001004858 catalytic base [active] 591001004859 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 591001004860 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 591001004861 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 591001004862 Rubredoxin; Region: Rubredoxin; pfam00301 591001004863 iron binding site [ion binding]; other site 591001004864 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 591001004865 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 591001004866 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001004867 Transposase domain (DUF772); Region: DUF772; pfam05598 591001004868 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 591001004869 UGMP family protein; Validated; Region: PRK09604 591001004870 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 591001004871 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 591001004872 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 591001004873 Coenzyme A binding pocket [chemical binding]; other site 591001004874 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 591001004875 Glycoprotease family; Region: Peptidase_M22; pfam00814 591001004876 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 591001004877 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 591001004878 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 591001004879 active site 591001004880 substrate-binding site [chemical binding]; other site 591001004881 metal-binding site [ion binding] 591001004882 ATP binding site [chemical binding]; other site 591001004883 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 591001004884 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 591001004885 FAD binding site [chemical binding]; other site 591001004886 homotetramer interface [polypeptide binding]; other site 591001004887 substrate binding pocket [chemical binding]; other site 591001004888 catalytic base [active] 591001004889 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 591001004890 CoenzymeA binding site [chemical binding]; other site 591001004891 subunit interaction site [polypeptide binding]; other site 591001004892 PHB binding site; other site 591001004893 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 591001004894 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3584 591001004895 glutamine synthetase, type I; Region: GlnA; TIGR00653 591001004896 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 591001004897 Domain of unknown function (DUF3870); Region: DUF3870; pfam12986 591001004898 Predicted integral membrane protein [Function unknown]; Region: COG5505 591001004899 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 591001004900 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 of...; Region: L-Ala-DL-Glu_epimerase; cd03319 591001004901 active site 591001004902 dipeptidase PepV; Reviewed; Region: PRK07318 591001004903 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 591001004904 active site 591001004905 metal binding site [ion binding]; metal-binding site 591001004906 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 591001004907 Beta-lactamase; Region: Beta-lactamase; pfam00144 591001004908 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 591001004909 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 591001004910 FMN binding site [chemical binding]; other site 591001004911 active site 591001004912 catalytic residues [active] 591001004913 substrate binding site [chemical binding]; other site 591001004914 pantothenate kinase; Reviewed; Region: PRK13318 591001004915 BioY family; Region: BioY; pfam02632 591001004916 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 591001004917 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 591001004918 putative Zn2+ binding site [ion binding]; other site 591001004919 putative DNA binding site [nucleotide binding]; other site 591001004920 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 591001004921 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 591001004922 FtsH Extracellular; Region: FtsH_ext; pfam06480 591001004923 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 591001004924 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001004925 Walker A motif; other site 591001004926 ATP binding site [chemical binding]; other site 591001004927 Walker B motif; other site 591001004928 arginine finger; other site 591001004929 Peptidase family M41; Region: Peptidase_M41; pfam01434 591001004930 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 591001004931 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001004932 active site 591001004933 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 591001004934 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 591001004935 Ligand Binding Site [chemical binding]; other site 591001004936 hypothetical protein; Provisional; Region: PRK08582 591001004937 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 591001004938 RNA binding site [nucleotide binding]; other site 591001004939 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 591001004940 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 591001004941 metal-binding site [ion binding] 591001004942 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 591001004943 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 591001004944 motif II; other site 591001004945 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 591001004946 metal-binding site [ion binding] 591001004947 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 591001004948 metal-binding site [ion binding] 591001004949 Protein of unknown function (DUF3100); Region: DUF3100; pfam11299 591001004950 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001004951 M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family; Region: M20_Acy1L2_like_2; cd09849 591001004952 metal binding site [ion binding]; metal-binding site 591001004953 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 591001004954 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 591001004955 MOFRL family; Region: MOFRL; pfam05161 591001004956 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 591001004957 Mechanosensitive ion channel; Region: MS_channel; pfam00924 591001004958 shikimate kinase; Reviewed; Region: aroK; PRK00131 591001004959 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 591001004960 ADP binding site [chemical binding]; other site 591001004961 magnesium binding site [ion binding]; other site 591001004962 putative shikimate binding site; other site 591001004963 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 591001004964 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 591001004965 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 591001004966 shikimate binding site; other site 591001004967 NAD(P) binding site [chemical binding]; other site 591001004968 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 591001004969 Prephenate dehydratase; Region: PDT; pfam00800 591001004970 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 591001004971 putative L-Phe binding site [chemical binding]; other site 591001004972 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 591001004973 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 591001004974 Tetramer interface [polypeptide binding]; other site 591001004975 active site 591001004976 FMN-binding site [chemical binding]; other site 591001004977 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 591001004978 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 591001004979 hinge; other site 591001004980 active site 591001004981 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 591001004982 active site 591001004983 dimer interface [polypeptide binding]; other site 591001004984 metal binding site [ion binding]; metal-binding site 591001004985 prephenate dehydrogenase; Validated; Region: PRK08507 591001004986 Prephenate dehydrogenase; Region: PDH; pfam02153 591001004987 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 591001004988 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 591001004989 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 591001004990 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 591001004991 Septum formation initiator; Region: DivIC; pfam04977 591001004992 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 591001004993 IHF dimer interface [polypeptide binding]; other site 591001004994 IHF - DNA interface [nucleotide binding]; other site 591001004995 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 591001004996 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 591001004997 homodimer interface [polypeptide binding]; other site 591001004998 metal binding site [ion binding]; metal-binding site 591001004999 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 591001005000 homodimer interface [polypeptide binding]; other site 591001005001 active site 591001005002 putative chemical substrate binding site [chemical binding]; other site 591001005003 metal binding site [ion binding]; metal-binding site 591001005004 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 591001005005 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 591001005006 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 591001005007 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 591001005008 ATP binding site [chemical binding]; other site 591001005009 putative Mg++ binding site [ion binding]; other site 591001005010 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 591001005011 nucleotide binding region [chemical binding]; other site 591001005012 ATP-binding site [chemical binding]; other site 591001005013 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 591001005014 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 591001005015 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 591001005016 putative active site [active] 591001005017 CTP synthetase; Validated; Region: pyrG; PRK05380 591001005018 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 591001005019 Catalytic site [active] 591001005020 active site 591001005021 UTP binding site [chemical binding]; other site 591001005022 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 591001005023 active site 591001005024 putative oxyanion hole; other site 591001005025 catalytic triad [active] 591001005026 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 591001005027 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 591001005028 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 591001005029 active site 591001005030 HIGH motif; other site 591001005031 KMSK motif region; other site 591001005032 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 591001005033 tRNA binding surface [nucleotide binding]; other site 591001005034 anticodon binding site; other site 591001005035 Domain of unknown function (DUF1934); Region: DUF1934; pfam09148 591001005036 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 591001005037 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 591001005038 Na binding site [ion binding]; other site 591001005039 Sporulation and spore germination; Region: Germane; pfam10646 591001005040 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 591001005041 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 591001005042 active site 591001005043 metal binding site [ion binding]; metal-binding site 591001005044 Uncharacterized conserved protein [Function unknown]; Region: COG0062 591001005045 putative carbohydrate kinase; Provisional; Region: PRK10565 591001005046 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 591001005047 putative substrate binding site [chemical binding]; other site 591001005048 putative ATP binding site [chemical binding]; other site 591001005049 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 591001005050 recombination factor protein RarA; Reviewed; Region: PRK13342 591001005051 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001005052 Walker A motif; other site 591001005053 ATP binding site [chemical binding]; other site 591001005054 Walker B motif; other site 591001005055 arginine finger; other site 591001005056 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 591001005057 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 591001005058 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 591001005059 Cl- selectivity filter; other site 591001005060 Cl- binding residues [ion binding]; other site 591001005061 pore gating glutamate residue; other site 591001005062 dimer interface [polypeptide binding]; other site 591001005063 H+/Cl- coupling transport residue; other site 591001005064 TrkA-C domain; Region: TrkA_C; pfam02080 591001005065 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 591001005066 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 591001005067 active site 591001005068 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 591001005069 substrate binding site [chemical binding]; other site 591001005070 catalytic residues [active] 591001005071 dimer interface [polypeptide binding]; other site 591001005072 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 591001005073 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001005074 Walker A/P-loop; other site 591001005075 ATP binding site [chemical binding]; other site 591001005076 Q-loop/lid; other site 591001005077 ABC transporter signature motif; other site 591001005078 Walker B; other site 591001005079 D-loop; other site 591001005080 H-loop/switch region; other site 591001005081 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 591001005082 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 591001005083 TM-ABC transporter signature motif; other site 591001005084 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 591001005085 zinc binding site [ion binding]; other site 591001005086 putative ligand binding site [chemical binding]; other site 591001005087 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 591001005088 zinc binding site [ion binding]; other site 591001005089 putative ligand binding site [chemical binding]; other site 591001005090 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 591001005091 Peptidase family M48; Region: Peptidase_M48; pfam01435 591001005092 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 591001005093 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 591001005094 active site 591001005095 metal binding site [ion binding]; metal-binding site 591001005096 DNA binding site [nucleotide binding] 591001005097 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 591001005098 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 591001005099 AAA domain; Region: AAA_23; pfam13476 591001005100 Walker A/P-loop; other site 591001005101 ATP binding site [chemical binding]; other site 591001005102 Q-loop/lid; other site 591001005103 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 591001005104 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 591001005105 ABC transporter signature motif; other site 591001005106 Walker B; other site 591001005107 D-loop; other site 591001005108 H-loop/switch region; other site 591001005109 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Region: rSAM_QueE_Clost; TIGR03963 591001005110 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 591001005111 FeS/SAM binding site; other site 591001005112 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 591001005113 active site 591001005114 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 591001005115 Ligand Binding Site [chemical binding]; other site 591001005116 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 591001005117 Putative redox-active protein (C_GCAxxG_C_C); Region: C_GCAxxG_C_C; pfam09719 591001005118 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 591001005119 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 591001005120 hypothetical protein; Provisional; Region: PRK13665 591001005121 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 591001005122 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 591001005123 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 591001005124 putative active site [active] 591001005125 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 591001005126 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 591001005127 putative active site [active] 591001005128 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 591001005129 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 591001005130 active site 591001005131 motif I; other site 591001005132 motif II; other site 591001005133 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 591001005134 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 591001005135 NADP binding site [chemical binding]; other site 591001005136 homopentamer interface [polypeptide binding]; other site 591001005137 substrate binding site [chemical binding]; other site 591001005138 active site 591001005139 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 591001005140 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 591001005141 putative ribose interaction site [chemical binding]; other site 591001005142 putative ADP binding site [chemical binding]; other site 591001005143 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 591001005144 active site 591001005145 nucleotide binding site [chemical binding]; other site 591001005146 HIGH motif; other site 591001005147 KMSKS motif; other site 591001005148 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 591001005149 dimer interface [polypeptide binding]; other site 591001005150 active site 591001005151 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 591001005152 Protein of unknown function (DUF535); Region: DUF535; cl01128 591001005153 Bacterial SH3 domain; Region: SH3_3; pfam08239 591001005154 Bacterial SH3 domain; Region: SH3_3; pfam08239 591001005155 Bacterial SH3 domain homologues; Region: SH3b; smart00287 591001005156 Bacterial SH3 domain; Region: SH3_3; pfam08239 591001005157 Uncharacterized conserved protein [Function unknown]; Region: COG1739 591001005158 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 591001005159 putative transposase OrfB; Reviewed; Region: PHA02517 591001005160 HTH-like domain; Region: HTH_21; pfam13276 591001005161 Integrase core domain; Region: rve; pfam00665 591001005162 Integrase core domain; Region: rve_3; pfam13683 591001005163 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 591001005164 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 591001005165 NlpC/P60 family; Region: NLPC_P60; cl17555 591001005166 S-layer homology domain; Region: SLH; pfam00395 591001005167 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 591001005168 S-layer homology domain; Region: SLH; pfam00395 591001005169 S-layer homology domain; Region: SLH; pfam00395 591001005170 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 591001005171 S-layer homology domain; Region: SLH; pfam00395 591001005172 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 591001005173 Uncharacterized protein family (UPF0081); Region: UPF0081; cl17278 591001005174 Protein of unknown function (DUF3084); Region: DUF3084; pfam11283 591001005175 DNA/RNA non-specific endonuclease; Region: Endonuclea_NS_2; pfam13930 591001005176 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 591001005177 Predicted permeases [General function prediction only]; Region: COG0795 591001005178 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 591001005179 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 591001005180 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 591001005181 Walker A/P-loop; other site 591001005182 ATP binding site [chemical binding]; other site 591001005183 Q-loop/lid; other site 591001005184 ABC transporter signature motif; other site 591001005185 Walker B; other site 591001005186 D-loop; other site 591001005187 H-loop/switch region; other site 591001005188 OstA-like protein; Region: OstA; cl00844 591001005189 OstA-like protein; Region: OstA; cl00844 591001005190 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 591001005191 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 591001005192 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 591001005193 putative acyl-acceptor binding pocket; other site 591001005194 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 591001005195 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 591001005196 active site 591001005197 motif I; other site 591001005198 motif II; other site 591001005199 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 591001005200 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 591001005201 putative active site [active] 591001005202 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 591001005203 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 591001005204 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 591001005205 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 591001005206 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 591001005207 Ligand binding site; other site 591001005208 oligomer interface; other site 591001005209 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 591001005210 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 591001005211 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 591001005212 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 591001005213 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 591001005214 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 591001005215 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 591001005216 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 591001005217 Walker A/P-loop; other site 591001005218 ATP binding site [chemical binding]; other site 591001005219 Q-loop/lid; other site 591001005220 ABC transporter signature motif; other site 591001005221 Walker B; other site 591001005222 D-loop; other site 591001005223 H-loop/switch region; other site 591001005224 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 591001005225 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 591001005226 Protein of unknown function (DUF1009); Region: DUF1009; pfam06230 591001005227 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 591001005228 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 591001005229 active site 591001005230 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed; Region: PRK13188 591001005231 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 591001005232 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 591001005233 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 591001005234 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 591001005235 putative acyl-acceptor binding pocket; other site 591001005236 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 591001005237 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 591001005238 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 591001005239 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 591001005240 trimer interface [polypeptide binding]; other site 591001005241 active site 591001005242 UDP-GlcNAc binding site [chemical binding]; other site 591001005243 lipid binding site [chemical binding]; lipid-binding site 591001005244 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 591001005245 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 591001005246 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 591001005247 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 591001005248 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 591001005249 Surface antigen; Region: Bac_surface_Ag; pfam01103 591001005250 Family of unknown function (DUF490); Region: DUF490; pfam04357 591001005251 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 591001005252 Family of unknown function (DUF490); Region: DUF490; pfam04357 591001005253 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 591001005254 virulence factor Mce family protein; Region: Mtu_fam_mce; TIGR00996 591001005255 mce related protein; Region: MCE; pfam02470 591001005256 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 591001005257 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 591001005258 Walker A/P-loop; other site 591001005259 ATP binding site [chemical binding]; other site 591001005260 Q-loop/lid; other site 591001005261 ABC transporter signature motif; other site 591001005262 Walker B; other site 591001005263 D-loop; other site 591001005264 H-loop/switch region; other site 591001005265 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 591001005266 Permease; Region: Permease; pfam02405 591001005267 SpoIVB peptidase S55; Region: Peptidase_S55; pfam05580 591001005268 AMIN domain; Region: AMIN; pfam11741 591001005269 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 591001005270 Predicted periplasmic protein [Function unknown]; Region: COG3698 591001005271 rod shape-determining protein MreB; Provisional; Region: PRK13930 591001005272 MreB and similar proteins; Region: MreB_like; cd10225 591001005273 nucleotide binding site [chemical binding]; other site 591001005274 Mg binding site [ion binding]; other site 591001005275 putative protofilament interaction site [polypeptide binding]; other site 591001005276 RodZ interaction site [polypeptide binding]; other site 591001005277 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 591001005278 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 591001005279 hinge; other site 591001005280 active site 591001005281 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 591001005282 gamma subunit interface [polypeptide binding]; other site 591001005283 epsilon subunit interface [polypeptide binding]; other site 591001005284 LBP interface [polypeptide binding]; other site 591001005285 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 591001005286 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 591001005287 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 591001005288 alpha subunit interaction interface [polypeptide binding]; other site 591001005289 Walker A motif; other site 591001005290 ATP binding site [chemical binding]; other site 591001005291 Walker B motif; other site 591001005292 inhibitor binding site; inhibition site 591001005293 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 591001005294 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 591001005295 core domain interface [polypeptide binding]; other site 591001005296 delta subunit interface [polypeptide binding]; other site 591001005297 epsilon subunit interface [polypeptide binding]; other site 591001005298 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 591001005299 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 591001005300 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 591001005301 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 591001005302 beta subunit interaction interface [polypeptide binding]; other site 591001005303 Walker A motif; other site 591001005304 ATP binding site [chemical binding]; other site 591001005305 Walker B motif; other site 591001005306 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 591001005307 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 591001005308 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 591001005309 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 591001005310 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 591001005311 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 591001005312 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 591001005313 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 591001005314 active site 591001005315 homodimer interface [polypeptide binding]; other site 591001005316 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 591001005317 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 591001005318 Mg++ binding site [ion binding]; other site 591001005319 putative catalytic motif [active] 591001005320 substrate binding site [chemical binding]; other site 591001005321 Chromate transporter; Region: Chromate_transp; pfam02417 591001005322 Chromate transporter; Region: Chromate_transp; pfam02417 591001005323 multidrug efflux protein; Reviewed; Region: PRK01766 591001005324 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 591001005325 cation binding site [ion binding]; other site 591001005326 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 591001005327 Sulfatase; Region: Sulfatase; cl17466 591001005328 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 591001005329 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 591001005330 Predicted membrane protein [Function unknown]; Region: COG2246 591001005331 GtrA-like protein; Region: GtrA; pfam04138 591001005332 SigmaK-factor processing regulatory protein BofA; Region: BofA; cl06466 591001005333 recombination protein RecR; Reviewed; Region: recR; PRK00076 591001005334 RecR protein; Region: RecR; pfam02132 591001005335 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 591001005336 putative active site [active] 591001005337 putative metal-binding site [ion binding]; other site 591001005338 tetramer interface [polypeptide binding]; other site 591001005339 hypothetical protein; Validated; Region: PRK00153 591001005340 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 591001005341 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001005342 Walker A motif; other site 591001005343 ATP binding site [chemical binding]; other site 591001005344 Walker B motif; other site 591001005345 arginine finger; other site 591001005346 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 591001005347 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 591001005348 FAD binding domain; Region: FAD_binding_4; pfam01565 591001005349 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 591001005350 nucleoside/Zn binding site; other site 591001005351 dimer interface [polypeptide binding]; other site 591001005352 catalytic motif [active] 591001005353 Homoserine O-succinyltransferase; Region: HTS; pfam04204 591001005354 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 591001005355 conserved cys residue [active] 591001005356 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 591001005357 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 591001005358 ligand binding site [chemical binding]; other site 591001005359 flexible hinge region; other site 591001005360 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 591001005361 putative switch regulator; other site 591001005362 non-specific DNA interactions [nucleotide binding]; other site 591001005363 DNA binding site [nucleotide binding] 591001005364 sequence specific DNA binding site [nucleotide binding]; other site 591001005365 putative cAMP binding site [chemical binding]; other site 591001005366 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 591001005367 putative active site [active] 591001005368 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 591001005369 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 591001005370 putative active site [active] 591001005371 putative metal binding site [ion binding]; other site 591001005372 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 591001005373 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 591001005374 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 591001005375 S-adenosylmethionine binding site [chemical binding]; other site 591001005376 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 591001005377 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 591001005378 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 591001005379 Predicted permeases [General function prediction only]; Region: COG0679 591001005380 short chain dehydrogenase; Validated; Region: PRK06182 591001005381 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 591001005382 NADP binding site [chemical binding]; other site 591001005383 active site 591001005384 steroid binding site; other site 591001005385 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 591001005386 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 591001005387 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 591001005388 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 591001005389 4Fe-4S binding domain; Region: Fer4_6; pfam12837 591001005390 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 591001005391 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; cd02062 591001005392 FMN binding site [chemical binding]; other site 591001005393 dimer interface [polypeptide binding]; other site 591001005394 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 591001005395 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 591001005396 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 591001005397 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 591001005398 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001005399 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001005400 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 591001005401 dimerization interface [polypeptide binding]; other site 591001005402 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 591001005403 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 591001005404 metal binding site [ion binding]; metal-binding site 591001005405 dimer interface [polypeptide binding]; other site 591001005406 Predicted membrane protein [Function unknown]; Region: COG1288 591001005407 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 591001005408 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 591001005409 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 591001005410 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 591001005411 EamA-like transporter family; Region: EamA; pfam00892 591001005412 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 591001005413 HTH domain; Region: HTH_11; pfam08279 591001005414 3H domain; Region: 3H; pfam02829 591001005415 glutamate racemase; Provisional; Region: PRK00865 591001005416 Domain of unknown function (DUF3870); Region: DUF3870; pfam12986 591001005417 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 591001005418 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 591001005419 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 591001005420 NAD(P) binding site [chemical binding]; other site 591001005421 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 591001005422 HD domain; Region: HD_3; pfam13023 591001005423 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 591001005424 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 591001005425 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 591001005426 active site 591001005427 catalytic triad [active] 591001005428 oxyanion hole [active] 591001005429 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 591001005430 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 591001005431 GatB domain; Region: GatB_Yqey; smart00845 591001005432 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 591001005433 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 591001005434 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 591001005435 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 591001005436 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 591001005437 homodimer interface [polypeptide binding]; other site 591001005438 substrate-cofactor binding pocket; other site 591001005439 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001005440 catalytic residue [active] 591001005441 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 591001005442 tartrate dehydrogenase; Provisional; Region: PRK08194 591001005443 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001005444 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001005445 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 591001005446 dimerization interface [polypeptide binding]; other site 591001005447 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 591001005448 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 591001005449 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 591001005450 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 591001005451 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 591001005452 transposase; Provisional; Region: PRK06526 591001005453 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001005454 Walker A motif; other site 591001005455 ATP binding site [chemical binding]; other site 591001005456 Walker B motif; other site 591001005457 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 591001005458 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 591001005459 non-specific DNA binding site [nucleotide binding]; other site 591001005460 salt bridge; other site 591001005461 sequence-specific DNA binding site [nucleotide binding]; other site 591001005462 Integrase core domain; Region: rve; pfam00665 591001005463 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 591001005464 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; cl01733 591001005465 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 591001005466 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 591001005467 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 591001005468 haemagglutination activity domain; Region: Haemagg_act; pfam05860 591001005469 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 591001005470 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 591001005471 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 591001005472 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 591001005473 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 591001005474 DALR anticodon binding domain; Region: DALR_1; pfam05746 591001005475 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 591001005476 dimer interface [polypeptide binding]; other site 591001005477 motif 1; other site 591001005478 active site 591001005479 motif 2; other site 591001005480 motif 3; other site 591001005481 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 591001005482 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 591001005483 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 591001005484 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 591001005485 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 591001005486 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 591001005487 DNA binding residues [nucleotide binding] 591001005488 CHC2 zinc finger; Region: zf-CHC2; pfam01807 591001005489 DNA primase; Validated; Region: dnaG; PRK05667 591001005490 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 591001005491 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 591001005492 active site 591001005493 metal binding site [ion binding]; metal-binding site 591001005494 interdomain interaction site; other site 591001005495 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 591001005496 PEP synthetase regulatory protein; Provisional; Region: PRK05339 591001005497 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 591001005498 HTH domain; Region: HTH_11; pfam08279 591001005499 FOG: CBS domain [General function prediction only]; Region: COG0517 591001005500 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 591001005501 phosphoenolpyruvate synthase; Validated; Region: PRK06464 591001005502 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 591001005503 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 591001005504 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 591001005505 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 591001005506 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 591001005507 ABC-ATPase subunit interface; other site 591001005508 dimer interface [polypeptide binding]; other site 591001005509 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 591001005510 putative PBP binding regions; other site 591001005511 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 591001005512 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 591001005513 active site 591001005514 metal binding site [ion binding]; metal-binding site 591001005515 Protein of unknown function (DUF2397); Region: DUF2397; pfam09660 591001005516 Uncharacterized Fe-S center protein [General function prediction only]; Region: COG2768 591001005517 Uncharacterized conserved protein [Function unknown]; Region: COG2006 591001005518 4Fe-4S binding domain; Region: Fer4; pfam00037 591001005519 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 591001005520 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 591001005521 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 591001005522 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 591001005523 protein binding site [polypeptide binding]; other site 591001005524 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 591001005525 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 591001005526 metal binding site 2 [ion binding]; metal-binding site 591001005527 putative DNA binding helix; other site 591001005528 metal binding site 1 [ion binding]; metal-binding site 591001005529 dimer interface [polypeptide binding]; other site 591001005530 structural Zn2+ binding site [ion binding]; other site 591001005531 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 591001005532 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 591001005533 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 591001005534 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 591001005535 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 591001005536 trimer interface [polypeptide binding]; other site 591001005537 active site 591001005538 substrate binding site [chemical binding]; other site 591001005539 CoA binding site [chemical binding]; other site 591001005540 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 591001005541 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 591001005542 dimer interface [polypeptide binding]; other site 591001005543 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001005544 catalytic residue [active] 591001005545 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 591001005546 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cl17915 591001005547 active site 591001005548 motif I; other site 591001005549 motif II; other site 591001005550 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 591001005551 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 591001005552 Na2 binding site [ion binding]; other site 591001005553 putative substrate binding site 1 [chemical binding]; other site 591001005554 Na binding site 1 [ion binding]; other site 591001005555 putative substrate binding site 2 [chemical binding]; other site 591001005556 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 591001005557 Na2 binding site [ion binding]; other site 591001005558 putative substrate binding site 1 [chemical binding]; other site 591001005559 Na binding site 1 [ion binding]; other site 591001005560 putative substrate binding site 2 [chemical binding]; other site 591001005561 Flavodoxin domain; Region: Flavodoxin_5; cl17428 591001005562 Ferredoxin [Energy production and conversion]; Region: COG1146 591001005563 4Fe-4S binding domain; Region: Fer4; pfam00037 591001005564 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 591001005565 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 591001005566 active site 591001005567 catalytic triad [active] 591001005568 oxyanion hole [active] 591001005569 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001005570 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 591001005571 metal binding site [ion binding]; metal-binding site 591001005572 dimer interface [polypeptide binding]; other site 591001005573 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 591001005574 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 591001005575 FeS/SAM binding site; other site 591001005576 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 591001005577 ATP cone domain; Region: ATP-cone; pfam03477 591001005578 Class III ribonucleotide reductase; Region: RNR_III; cd01675 591001005579 effector binding site; other site 591001005580 active site 591001005581 Zn binding site [ion binding]; other site 591001005582 glycine loop; other site 591001005583 M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily; Region: M20_ACY1L2_like; cd05672 591001005584 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001005585 metal binding site [ion binding]; metal-binding site 591001005586 Predicted membrane protein [Function unknown]; Region: COG1288 591001005587 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 591001005588 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001005589 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001005590 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 591001005591 dimerization interface [polypeptide binding]; other site 591001005592 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 591001005593 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 591001005594 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 591001005595 Transposase domain (DUF772); Region: DUF772; pfam05598 591001005596 Transposase DDE domain; Region: DDE_Tnp_1_6; pfam13751 591001005597 Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]; Region: HgdB; COG1775 591001005598 benzoyl-CoA reductase, subunit C; Region: benz_CoA_red_C; TIGR02263 591001005599 benzoyl-CoA reductase, bcr type, subunit B; Region: benz_CoA_red_B; TIGR02260 591001005600 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 591001005601 Carboxyl transferase domain; Region: Carboxyl_trans; pfam01039 591001005602 Coenzyme A transferase; Region: CoA_trans; pfam01144 591001005603 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 591001005604 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 591001005605 active site 591001005606 NTP binding site [chemical binding]; other site 591001005607 metal binding triad [ion binding]; metal-binding site 591001005608 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 591001005609 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001005610 Zn2+ binding site [ion binding]; other site 591001005611 Mg2+ binding site [ion binding]; other site 591001005612 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 591001005613 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 591001005614 homodimer interface [polypeptide binding]; other site 591001005615 oligonucleotide binding site [chemical binding]; other site 591001005616 radical SAM-linked protein; Region: sam_1_link_chp; TIGR03936 591001005617 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; pfam10105 591001005618 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 591001005619 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 591001005620 FeS/SAM binding site; other site 591001005621 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 591001005622 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 591001005623 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 591001005624 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 591001005625 rod shape-determining protein MreC; Provisional; Region: PRK13922 591001005626 rod shape-determining protein MreC; Region: MreC; pfam04085 591001005627 rod shape-determining protein MreB; Provisional; Region: PRK13930 591001005628 MreB and similar proteins; Region: MreB_like; cd10225 591001005629 nucleotide binding site [chemical binding]; other site 591001005630 Mg binding site [ion binding]; other site 591001005631 putative protofilament interaction site [polypeptide binding]; other site 591001005632 RodZ interaction site [polypeptide binding]; other site 591001005633 hypothetical protein; Reviewed; Region: PRK00024 591001005634 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 591001005635 MPN+ (JAMM) motif; other site 591001005636 Zinc-binding site [ion binding]; other site 591001005637 Maf-like protein; Region: Maf; pfam02545 591001005638 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 591001005639 active site 591001005640 dimer interface [polypeptide binding]; other site 591001005641 Domain of unknown function (DUF4321); Region: DUF4321; pfam14209 591001005642 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 591001005643 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 591001005644 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 591001005645 carboxyltransferase (CT) interaction site; other site 591001005646 biotinylation site [posttranslational modification]; other site 591001005647 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 591001005648 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 591001005649 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 591001005650 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 591001005651 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 591001005652 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 591001005653 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 591001005654 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 591001005655 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 591001005656 Putative Fe-S cluster; Region: FeS; cl17515 591001005657 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 591001005658 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 591001005659 ATP binding site [chemical binding]; other site 591001005660 G-X-G motif; other site 591001005661 DRTGG domain; Region: DRTGG; pfam07085 591001005662 potential frameshift: common BLAST hit: gi|150391764|ref|YP_001321813.1| transcriptional activator domain-containing protein 591001005663 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 591001005664 binding surface 591001005665 TPR motif; other site 591001005666 Tetratricopeptide repeat; Region: TPR_12; pfam13424 591001005667 Tetratricopeptide repeat; Region: TPR_12; pfam13424 591001005668 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 591001005669 binding surface 591001005670 TPR motif; other site 591001005671 DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]; Region: DnrI; COG3629 591001005672 PPR repeat; Region: PPR; cl03252 591001005673 imidazolonepropionase; Validated; Region: PRK09356 591001005674 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 591001005675 active site 591001005676 urocanate hydratase; Provisional; Region: PRK05414 591001005677 biotin synthase; Provisional; Region: PRK07094 591001005678 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 591001005679 FeS/SAM binding site; other site 591001005680 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 591001005681 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 591001005682 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 591001005683 amino acid transporter; Region: 2A0306; TIGR00909 591001005684 Spore germination protein; Region: Spore_permease; cl17796 591001005685 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 591001005686 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 591001005687 catalytic triad [active] 591001005688 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 591001005689 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 591001005690 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 591001005691 substrate binding pocket [chemical binding]; other site 591001005692 dimer interface [polypeptide binding]; other site 591001005693 inhibitor binding site; inhibition site 591001005694 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 591001005695 B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or...; Region: corrinoid_protein_B12-BD; cd02070 591001005696 B12 binding site [chemical binding]; other site 591001005697 cobalt ligand [ion binding]; other site 591001005698 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 591001005699 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 591001005700 FAD binding site [chemical binding]; other site 591001005701 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 591001005702 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001005703 DNA-binding site [nucleotide binding]; DNA binding site 591001005704 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 591001005705 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001005706 homodimer interface [polypeptide binding]; other site 591001005707 catalytic residue [active] 591001005708 AzlC protein; Region: AzlC; cl00570 591001005709 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 591001005710 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001005711 active site 591001005712 polyphosphate kinase; Provisional; Region: PRK05443 591001005713 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 591001005714 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 591001005715 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 591001005716 putative domain interface [polypeptide binding]; other site 591001005717 putative active site [active] 591001005718 catalytic site [active] 591001005719 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 591001005720 putative domain interface [polypeptide binding]; other site 591001005721 putative active site [active] 591001005722 catalytic site [active] 591001005723 exopolyphosphatase; Region: exo_poly_only; TIGR03706 591001005724 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 591001005725 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 591001005726 Zn2+ binding site [ion binding]; other site 591001005727 Mg2+ binding site [ion binding]; other site 591001005728 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 591001005729 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 591001005730 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cl17503 591001005731 FtsH Extracellular; Region: FtsH_ext; pfam06480 591001005732 NADH dehydrogenase subunit 5 C-terminus; Region: NADH5_C; pfam06455 591001005733 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 591001005734 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001005735 Walker A motif; other site 591001005736 ATP binding site [chemical binding]; other site 591001005737 Walker B motif; other site 591001005738 arginine finger; other site 591001005739 Peptidase family M41; Region: Peptidase_M41; pfam01434 591001005740 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 591001005741 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 591001005742 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 591001005743 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 591001005744 minor groove reading motif; other site 591001005745 helix-hairpin-helix signature motif; other site 591001005746 substrate binding pocket [chemical binding]; other site 591001005747 active site 591001005748 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 591001005749 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 591001005750 DNA binding and oxoG recognition site [nucleotide binding] 591001005751 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the...; Region: MTH1; cd03427 591001005752 putative active site [active] 591001005753 nucleotide binding site [chemical binding]; other site 591001005754 nudix motif; other site 591001005755 putative metal binding site [ion binding]; other site 591001005756 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 591001005757 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 591001005758 metal binding site [ion binding]; metal-binding site 591001005759 dimer interface [polypeptide binding]; other site 591001005760 Allophanate hydrolase subunit 2; Region: AHS2; smart00797 591001005761 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 591001005762 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 591001005763 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 591001005764 LamB/YcsF family of lactam utilization protein; Region: LamB_YcsF_like; cd10787 591001005765 putative active site [active] 591001005766 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 591001005767 Haemagglutinin; Region: HIM; pfam05662 591001005768 YadA-like C-terminal region; Region: YadA; pfam03895 591001005769 S-layer homology domain; Region: SLH; pfam00395 591001005770 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 591001005771 HTH domain; Region: HTH_11; pfam08279 591001005772 3H domain; Region: 3H; pfam02829 591001005773 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001005774 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001005775 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 591001005776 dimerization interface [polypeptide binding]; other site 591001005777 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001005778 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001005779 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 591001005780 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 591001005781 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 591001005782 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 591001005783 Walker A/P-loop; other site 591001005784 ATP binding site [chemical binding]; other site 591001005785 Q-loop/lid; other site 591001005786 ABC transporter signature motif; other site 591001005787 Walker B; other site 591001005788 D-loop; other site 591001005789 H-loop/switch region; other site 591001005790 Alkaline phosphatase [Inorganic ion transport and metabolism]; Region: PhoA; COG1785 591001005791 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 591001005792 dimer interface [polypeptide binding]; other site 591001005793 active site 591001005794 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cl15837 591001005795 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 591001005796 PhoU domain; Region: PhoU; pfam01895 591001005797 PhoU domain; Region: PhoU; pfam01895 591001005798 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 591001005799 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 591001005800 Walker A/P-loop; other site 591001005801 ATP binding site [chemical binding]; other site 591001005802 Q-loop/lid; other site 591001005803 ABC transporter signature motif; other site 591001005804 Walker B; other site 591001005805 D-loop; other site 591001005806 H-loop/switch region; other site 591001005807 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 591001005808 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001005809 dimer interface [polypeptide binding]; other site 591001005810 conserved gate region; other site 591001005811 putative PBP binding loops; other site 591001005812 ABC-ATPase subunit interface; other site 591001005813 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 591001005814 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 591001005815 dimerization interface [polypeptide binding]; other site 591001005816 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 591001005817 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 591001005818 dimer interface [polypeptide binding]; other site 591001005819 active site 591001005820 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 591001005821 catalytic residues [active] 591001005822 substrate binding site [chemical binding]; other site 591001005823 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 591001005824 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 591001005825 NAD(P) binding pocket [chemical binding]; other site 591001005826 agmatinase; Region: agmatinase; TIGR01230 591001005827 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 591001005828 putative active site [active] 591001005829 Mn binding site [ion binding]; other site 591001005830 spermidine synthase; Provisional; Region: PRK00811 591001005831 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 591001005832 S-adenosylmethionine binding site [chemical binding]; other site 591001005833 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 591001005834 Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine...; Region: Orn_deC_like; cd00615 591001005835 homodimer interface [polypeptide binding]; other site 591001005836 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001005837 catalytic residue [active] 591001005838 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 591001005839 4Fe-4S binding domain; Region: Fer4; pfam00037 591001005840 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 591001005841 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 591001005842 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 591001005843 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 591001005844 ABC transporter; Region: ABC_tran_2; pfam12848 591001005845 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 591001005846 anaerobic sulfite reductase subunit A; Provisional; Region: PRK15055 591001005847 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001005848 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 591001005849 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 591001005850 FAD binding pocket [chemical binding]; other site 591001005851 FAD binding motif [chemical binding]; other site 591001005852 phosphate binding motif [ion binding]; other site 591001005853 beta-alpha-beta structure motif; other site 591001005854 NAD binding pocket [chemical binding]; other site 591001005855 Iron coordination center [ion binding]; other site 591001005856 sulfite reductase, subunit C; Region: sulfite_red_C; TIGR02912 591001005857 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 591001005858 4Fe-4S binding domain; Region: Fer4; pfam00037 591001005859 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 591001005860 active site 591001005861 metal binding site [ion binding]; metal-binding site 591001005862 homotetramer interface [polypeptide binding]; other site 591001005863 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 591001005864 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 591001005865 N-terminal plug; other site 591001005866 ligand-binding site [chemical binding]; other site 591001005867 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 591001005868 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 591001005869 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 591001005870 alphaNTD homodimer interface [polypeptide binding]; other site 591001005871 alphaNTD - beta interaction site [polypeptide binding]; other site 591001005872 alphaNTD - beta' interaction site [polypeptide binding]; other site 591001005873 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 591001005874 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 591001005875 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 591001005876 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 591001005877 RNA binding surface [nucleotide binding]; other site 591001005878 30S ribosomal protein S11; Validated; Region: PRK05309 591001005879 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 591001005880 30S ribosomal protein S13; Region: bact_S13; TIGR03631 591001005881 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 591001005882 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 591001005883 rRNA binding site [nucleotide binding]; other site 591001005884 predicted 30S ribosome binding site; other site 591001005885 adenylate kinase; Reviewed; Region: adk; PRK00279 591001005886 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 591001005887 AMP-binding site [chemical binding]; other site 591001005888 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 591001005889 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 591001005890 SecY translocase; Region: SecY; pfam00344 591001005891 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 591001005892 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 591001005893 23S rRNA binding site [nucleotide binding]; other site 591001005894 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 591001005895 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 591001005896 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 591001005897 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 591001005898 5S rRNA interface [nucleotide binding]; other site 591001005899 L27 interface [polypeptide binding]; other site 591001005900 23S rRNA interface [nucleotide binding]; other site 591001005901 L5 interface [polypeptide binding]; other site 591001005902 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 591001005903 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 591001005904 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 591001005905 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 591001005906 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 591001005907 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 591001005908 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 591001005909 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 591001005910 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 591001005911 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 591001005912 RNA binding site [nucleotide binding]; other site 591001005913 Protein of unknown function (DUF2614); Region: DUF2614; cl07936 591001005914 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 591001005915 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 591001005916 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 591001005917 23S rRNA interface [nucleotide binding]; other site 591001005918 putative translocon interaction site; other site 591001005919 signal recognition particle (SRP54) interaction site; other site 591001005920 L23 interface [polypeptide binding]; other site 591001005921 trigger factor interaction site; other site 591001005922 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 591001005923 23S rRNA interface [nucleotide binding]; other site 591001005924 5S rRNA interface [nucleotide binding]; other site 591001005925 putative antibiotic binding site [chemical binding]; other site 591001005926 L25 interface [polypeptide binding]; other site 591001005927 L27 interface [polypeptide binding]; other site 591001005928 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 591001005929 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 591001005930 G-X-X-G motif; other site 591001005931 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 591001005932 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 591001005933 putative translocon binding site; other site 591001005934 protein-rRNA interface [nucleotide binding]; other site 591001005935 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 591001005936 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 591001005937 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 591001005938 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 591001005939 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 591001005940 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 591001005941 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 591001005942 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 591001005943 elongation factor Tu; Reviewed; Region: PRK00049 591001005944 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 591001005945 G1 box; other site 591001005946 GEF interaction site [polypeptide binding]; other site 591001005947 GTP/Mg2+ binding site [chemical binding]; other site 591001005948 Switch I region; other site 591001005949 G2 box; other site 591001005950 G3 box; other site 591001005951 Switch II region; other site 591001005952 G4 box; other site 591001005953 G5 box; other site 591001005954 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 591001005955 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 591001005956 Antibiotic Binding Site [chemical binding]; other site 591001005957 elongation factor G; Reviewed; Region: PRK00007 591001005958 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 591001005959 G1 box; other site 591001005960 putative GEF interaction site [polypeptide binding]; other site 591001005961 GTP/Mg2+ binding site [chemical binding]; other site 591001005962 Switch I region; other site 591001005963 G2 box; other site 591001005964 G3 box; other site 591001005965 Switch II region; other site 591001005966 G4 box; other site 591001005967 G5 box; other site 591001005968 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 591001005969 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 591001005970 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 591001005971 30S ribosomal protein S7; Validated; Region: PRK05302 591001005972 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 591001005973 S17 interaction site [polypeptide binding]; other site 591001005974 S8 interaction site; other site 591001005975 16S rRNA interaction site [nucleotide binding]; other site 591001005976 streptomycin interaction site [chemical binding]; other site 591001005977 23S rRNA interaction site [nucleotide binding]; other site 591001005978 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 591001005979 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 591001005980 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 591001005981 Protein of unknown function (DUF3815); Region: DUF3815; pfam12821 591001005982 Uncharacterized conserved protein [Function unknown]; Region: COG2966 591001005983 Protein of unknown function (DUF1212); Region: DUF1212; pfam06738 591001005984 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_3; cd10035 591001005985 putative uracil binding site [chemical binding]; other site 591001005986 putative active site [active] 591001005987 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 591001005988 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 591001005989 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 591001005990 ABC transporter; Region: ABC_tran_2; pfam12848 591001005991 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 591001005992 ABC transporter; Region: ABC_tran_2; pfam12848 591001005993 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 591001005994 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 591001005995 NAD binding site [chemical binding]; other site 591001005996 homodimer interface [polypeptide binding]; other site 591001005997 active site 591001005998 substrate binding site [chemical binding]; other site 591001005999 phosphomannomutase CpsG; Provisional; Region: PRK15414 591001006000 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 591001006001 active site 591001006002 substrate binding site [chemical binding]; other site 591001006003 metal binding site [ion binding]; metal-binding site 591001006004 Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and...; Region: INT_Tn1545_C; cd01199 591001006005 Int/Topo IB signature motif; other site 591001006006 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 591001006007 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 591001006008 non-specific DNA binding site [nucleotide binding]; other site 591001006009 salt bridge; other site 591001006010 sequence-specific DNA binding site [nucleotide binding]; other site 591001006011 Helix-turn-helix XRE-family like proteins; Region: HTH_XRE; smart00530 591001006012 sequence-specific DNA binding site [nucleotide binding]; other site 591001006013 salt bridge; other site 591001006014 Helix-turn-helix domain; Region: HTH_17; pfam12728 591001006015 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 591001006016 active site 591001006017 metal binding site [ion binding]; metal-binding site 591001006018 interdomain interaction site; other site 591001006019 Domain of unknown function (DUF927); Region: DUF927; cl12098 591001006020 Predicted transcriptional regulator [Transcription]; Region: COG1959 591001006021 Transcriptional regulator; Region: Rrf2; cl17282 591001006022 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 591001006023 putative glutamate synthase (NADPH) small subunit; Provisional; Region: PRK12771 591001006024 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 591001006025 Alanine dehydrogenase/PNT, C-terminal domain; Region: AlaDh_PNT_C; smart01002 591001006026 bidirectional hydrogenase complex protein HoxU; Validated; Region: PRK07569 591001006027 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 591001006028 catalytic loop [active] 591001006029 iron binding site [ion binding]; other site 591001006030 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 591001006031 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 591001006032 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 591001006033 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 591001006034 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 591001006035 putative substrate binding pocket [chemical binding]; other site 591001006036 AC domain interface; other site 591001006037 catalytic triad [active] 591001006038 AB domain interface; other site 591001006039 interchain disulfide; other site 591001006040 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 591001006041 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 591001006042 putative active site [active] 591001006043 putative metal binding site [ion binding]; other site 591001006044 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 591001006045 Predicted peptidase [General function prediction only]; Region: COG4099 591001006046 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 591001006047 Clp amino terminal domain; Region: Clp_N; pfam02861 591001006048 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001006049 Walker A motif; other site 591001006050 ATP binding site [chemical binding]; other site 591001006051 Walker B motif; other site 591001006052 arginine finger; other site 591001006053 Protein-interacting V-domain of mammalian Alix and related domains; Region: V_Alix_like; cl14654 591001006054 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001006055 Walker A motif; other site 591001006056 ATP binding site [chemical binding]; other site 591001006057 Walker B motif; other site 591001006058 arginine finger; other site 591001006059 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 591001006060 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 591001006061 putative active site [active] 591001006062 putative metal binding residues [ion binding]; other site 591001006063 signature motif; other site 591001006064 putative triphosphate binding site [ion binding]; other site 591001006065 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 591001006066 metal binding site 2 [ion binding]; metal-binding site 591001006067 putative DNA binding helix; other site 591001006068 metal binding site 1 [ion binding]; metal-binding site 591001006069 dimer interface [polypeptide binding]; other site 591001006070 structural Zn2+ binding site [ion binding]; other site 591001006071 Dicarboxylate carrier protein MatC N-terminus; Region: MatC_N; pfam07158 591001006072 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001006073 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006074 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006075 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 591001006076 dimerization interface [polypeptide binding]; other site 591001006077 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006078 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006079 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 591001006080 dimerization interface [polypeptide binding]; other site 591001006081 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 591001006082 isocitrate dehydrogenase; Validated; Region: PRK06451 591001006083 Dicarboxylate carrier protein MatC N-terminus; Region: MatC_N; pfam07158 591001006084 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001006085 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 591001006086 aconitate hydratase; Validated; Region: PRK07229 591001006087 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 591001006088 substrate binding site [chemical binding]; other site 591001006089 ligand binding site [chemical binding]; other site 591001006090 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 591001006091 substrate binding site [chemical binding]; other site 591001006092 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006093 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006094 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 591001006095 dimerization interface [polypeptide binding]; other site 591001006096 putative hydratase; Provisional; Region: PRK11413 591001006097 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 591001006098 substrate binding site [chemical binding]; other site 591001006099 ligand binding site [chemical binding]; other site 591001006100 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 591001006101 substrate binding site [chemical binding]; other site 591001006102 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2828 591001006103 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 591001006104 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 591001006105 active site 591001006106 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 591001006107 FMN binding site [chemical binding]; other site 591001006108 dimer interface [polypeptide binding]; other site 591001006109 putative metallo-dependent hydrolase; Provisional; Region: PRK12394 591001006110 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 591001006111 active site 591001006112 DctM-like transporters; Region: DctM; pfam06808 591001006113 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 591001006114 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 591001006115 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 591001006116 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 591001006117 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006118 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006119 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 591001006120 dimerization interface [polypeptide binding]; other site 591001006121 Uncharacterized protein with conserved CXXC pairs [Function unknown]; Region: COG3862 591001006122 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 591001006123 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 591001006124 Predicted dehydrogenase [General function prediction only]; Region: COG0579 591001006125 hydroxyglutarate oxidase; Provisional; Region: PRK11728 591001006126 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 591001006127 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 591001006128 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; cd00625 591001006129 transmembrane helices; other site 591001006130 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 591001006131 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 591001006132 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 591001006133 Domain of unknown function (DUF362); Region: DUF362; pfam04015 591001006134 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 591001006135 homotrimer interaction site [polypeptide binding]; other site 591001006136 putative active site [active] 591001006137 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 591001006138 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 591001006139 active site 591001006140 putative substrate binding pocket [chemical binding]; other site 591001006141 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 591001006142 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 591001006143 Na binding site [ion binding]; other site 591001006144 peptidase; Reviewed; Region: PRK13004 591001006145 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like4; cd05649 591001006146 putative metal binding site [ion binding]; other site 591001006147 putative dimer interface [polypeptide binding]; other site 591001006148 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 591001006149 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cd00640 591001006150 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 591001006151 catalytic residue [active] 591001006152 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 591001006153 GAF domain; Region: GAF; cl17456 591001006154 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 591001006155 Walker A motif; other site 591001006156 ATP binding site [chemical binding]; other site 591001006157 Walker B motif; other site 591001006158 arginine finger; other site 591001006159 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 591001006160 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 591001006161 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 591001006162 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 591001006163 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 591001006164 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 591001006165 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001006166 Walker A/P-loop; other site 591001006167 ATP binding site [chemical binding]; other site 591001006168 Q-loop/lid; other site 591001006169 ABC transporter signature motif; other site 591001006170 Walker B; other site 591001006171 D-loop; other site 591001006172 H-loop/switch region; other site 591001006173 TOBE domain; Region: TOBE_2; pfam08402 591001006174 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 591001006175 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001006176 dimer interface [polypeptide binding]; other site 591001006177 conserved gate region; other site 591001006178 putative PBP binding loops; other site 591001006179 ABC-ATPase subunit interface; other site 591001006180 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 591001006181 dimer interface [polypeptide binding]; other site 591001006182 conserved gate region; other site 591001006183 putative PBP binding loops; other site 591001006184 ABC-ATPase subunit interface; other site 591001006185 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 591001006186 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 591001006187 Walker A/P-loop; other site 591001006188 ATP binding site [chemical binding]; other site 591001006189 Q-loop/lid; other site 591001006190 ABC transporter signature motif; other site 591001006191 Walker B; other site 591001006192 D-loop; other site 591001006193 H-loop/switch region; other site 591001006194 TOBE domain; Region: TOBE_2; pfam08402 591001006195 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 591001006196 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 591001006197 L-2-amino-thiazoline-4-carboxylic acid hydrolase; Region: ATC_hydrolase; pfam14196 591001006198 formimidoylglutamase; Provisional; Region: PRK13775 591001006199 Agmatinase-like family; Region: Agmatinase-like; cd09990 591001006200 active site 591001006201 oligomer interface [polypeptide binding]; other site 591001006202 Mn binding site [ion binding]; other site 591001006203 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 591001006204 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 591001006205 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 591001006206 Transcriptional regulator [Transcription]; Region: IclR; COG1414 591001006207 Bacterial transcriptional regulator; Region: IclR; pfam01614 591001006208 allantoate amidohydrolase; Reviewed; Region: PRK09290 591001006209 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 591001006210 active site 591001006211 metal binding site [ion binding]; metal-binding site 591001006212 dimer interface [polypeptide binding]; other site 591001006213 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 591001006214 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 591001006215 metal binding site [ion binding]; metal-binding site 591001006216 dimer interface [polypeptide binding]; other site 591001006217 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 591001006218 Creatinine amidohydrolase; Region: Creatininase; pfam02633 591001006219 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006220 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006221 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 591001006222 dimerization interface [polypeptide binding]; other site 591001006223 Transcriptional regulators [Transcription]; Region: FadR; COG2186 591001006224 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 591001006225 DNA-binding site [nucleotide binding]; DNA binding site 591001006226 FCD domain; Region: FCD; pfam07729 591001006227 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 591001006228 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 591001006229 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 591001006230 DctM-like transporters; Region: DctM; pfam06808 591001006231 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 591001006232 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 591001006233 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 591001006234 active site pocket [active] 591001006235 putative transposase OrfB; Reviewed; Region: PHA02517 591001006236 HTH-like domain; Region: HTH_21; pfam13276 591001006237 Integrase core domain; Region: rve; pfam00665 591001006238 Integrase core domain; Region: rve_2; pfam13333 591001006239 Tripartite tricarboxylate transporter TctA family; Region: TctA; cl00772 591001006240 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 591001006241 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 591001006242 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006243 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006244 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 591001006245 dimerization interface [polypeptide binding]; other site 591001006246 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 591001006247 AAA domain; Region: AAA_14; pfam13173 591001006248 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 591001006249 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 591001006250 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 591001006251 transmembrane helices; other site 591001006252 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 591001006253 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 591001006254 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 591001006255 ligand binding site [chemical binding]; other site 591001006256 NAD binding site [chemical binding]; other site 591001006257 dimerization interface [polypeptide binding]; other site 591001006258 catalytic site [active] 591001006259 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 591001006260 hypothetical protein; Validated; Region: PRK06201 591001006261 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 591001006262 Transcriptional regulator [Transcription]; Region: LysR; COG0583 591001006263 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 591001006264 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 591001006265 dimerization interface [polypeptide binding]; other site 591001006266 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 591001006267 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 591001006268 Domain of unknown function (DUF1932); Region: DUF1932; pfam09130 591001006269 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 591001006270 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 591001006271 ligand binding site [chemical binding]; other site 591001006272 NAD binding site [chemical binding]; other site 591001006273 dimerization interface [polypeptide binding]; other site 591001006274 catalytic site [active] 591001006275 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 591001006276 putative L-serine binding site [chemical binding]; other site 591001006277 RmuC family; Region: RmuC; pfam02646 591001006278 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 591001006279 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 591001006280 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 591001006281 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 591001006282 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 591001006283 motif II; other site 591001006284 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 591001006285 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 591001006286 trimer interface [polypeptide binding]; other site 591001006287 YadA-like C-terminal region; Region: YadA; pfam03895 591001006288 Homeobox associated leucine zipper; Region: HALZ; pfam02183 591001006289 RelB antitoxin; Region: RelB; cl01171 591001006290 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 591001006291 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 591001006292 AAA domain; Region: AAA_14; pfam13173 591001006293 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 591001006294 Di- and tripeptidases [Amino acid transport and metabolism]; Region: PepD; COG2195 591001006295 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 591001006296 metal binding site [ion binding]; metal-binding site 591001006297 dimer interface [polypeptide binding]; other site 591001006298 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 591001006299 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 591001006300 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 591001006301 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 591001006302 RNA binding site [nucleotide binding]; other site 591001006303 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 591001006304 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 591001006305 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 591001006306 Walker A/P-loop; other site 591001006307 ATP binding site [chemical binding]; other site 591001006308 Q-loop/lid; other site 591001006309 ABC transporter signature motif; other site 591001006310 Walker B; other site 591001006311 D-loop; other site 591001006312 H-loop/switch region; other site 591001006313 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 591001006314 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 591001006315 Walker A/P-loop; other site 591001006316 ATP binding site [chemical binding]; other site 591001006317 Q-loop/lid; other site 591001006318 ABC transporter signature motif; other site 591001006319 Walker B; other site 591001006320 D-loop; other site 591001006321 H-loop/switch region; other site 591001006322 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 591001006323 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 591001006324 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 591001006325 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 591001006326 putative dimer interface [polypeptide binding]; other site 591001006327 putative active site [active] 591001006328 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 591001006329 fumarate hydratase; Reviewed; Region: fumC; PRK00485 591001006330 Class II fumarases; Region: Fumarase_classII; cd01362 591001006331 active site 591001006332 tetramer interface [polypeptide binding]; other site 591001006333 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 591001006334 DctM-like transporters; Region: DctM; pfam06808 591001006335 Domain of unknown function (DUF1850); Region: DUF1850; pfam08905 591001006336 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 591001006337 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 591001006338 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 591001006339 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 591001006340 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 591001006341 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]; Region: COG4545 591001006342 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1672 591001006343 AAA domain; Region: AAA_14; pfam13173 591001006344 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; cl17220 591001006345 putative DNA binding site [nucleotide binding]; other site 591001006346 putative Zn2+ binding site [ion binding]; other site 591001006347 Archaea bacterial proteins of unknown function; Region: DUF234; pfam03008 591001006348 Peptidase C26; Region: Peptidase_C26; pfam07722 591001006349 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 591001006350 conserved cys residue [active] 591001006351 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 591001006352 RNA polymerase sigma-54 factor; Region: rpoN_sigma; TIGR02395 591001006353 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 591001006354 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 591001006355 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 591001006356 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 591001006357 pyridoxal 5'-phosphate binding site [chemical binding]; other site 591001006358 homodimer interface [polypeptide binding]; other site 591001006359 catalytic residue [active] 591001006360 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 591001006361 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 591001006362 Transcriptional regulators [Transcription]; Region: PurR; COG1609 591001006363 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 591001006364 DNA binding site [nucleotide binding] 591001006365 domain linker motif; other site 591001006366 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 591001006367 dimerization interface [polypeptide binding]; other site 591001006368 ligand binding site [chemical binding]; other site 591001006369 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 591001006370 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 591001006371 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 591001006372 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 591001006373 inhibitor site; inhibition site 591001006374 active site 591001006375 dimer interface [polypeptide binding]; other site 591001006376 catalytic residue [active] 591001006377 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 591001006378 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 591001006379 active site 591001006380 metal binding site [ion binding]; metal-binding site 591001006381 Protein of unknown function (DUF554); Region: DUF554; pfam04474 591001006382 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 591001006383 ParB-like nuclease domain; Region: ParB; smart00470 591001006384 KorB domain; Region: KorB; pfam08535 591001006385 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 591001006386 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 591001006387 P-loop; other site 591001006388 Magnesium ion binding site [ion binding]; other site 591001006389 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 591001006390 Magnesium ion binding site [ion binding]; other site 591001006391 peptidase T; Region: peptidase-T; TIGR01882 591001006392 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 591001006393 metal binding site [ion binding]; metal-binding site 591001006394 dimer interface [polypeptide binding]; other site 591001006395 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 591001006396 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 591001006397 S-adenosylmethionine binding site [chemical binding]; other site 591001006398 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 591001006399 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 591001006400 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 591001006401 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 591001006402 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 591001006403 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 591001006404 G4 box; other site 591001006405 GTP/Mg2+ binding site [chemical binding]; other site 591001006406 G5 box; other site 591001006407 trmE is a tRNA modification GTPase; Region: trmE; cd04164 591001006408 G1 box; other site 591001006409 G1 box; other site 591001006410 GTP/Mg2+ binding site [chemical binding]; other site 591001006411 Switch I region; other site 591001006412 Switch I region; other site 591001006413 G2 box; other site 591001006414 G2 box; other site 591001006415 Switch II region; other site 591001006416 G3 box; other site 591001006417 G3 box; other site 591001006418 Switch II region; other site 591001006419 G4 box; other site 591001006420 G5 box; other site 591001006421 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 591001006422 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 591001006423 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 591001006424 G-X-X-G motif; other site 591001006425 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 591001006426 RxxxH motif; other site 591001006427 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 591001006428 Haemolytic domain; Region: Haemolytic; pfam01809 591001006429 Ribonuclease P; Region: Ribonuclease_P; cl00457 591001006430 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 591001006431 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 591001006432 M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily; Region: M20_Acy1L2_AbgB; cd05673 591001006433 amidohydrolase; Region: amidohydrolases; TIGR01891 591001006434 putative metal binding site [ion binding]; other site 591001006435 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 591001006436 G1 box; other site 591001006437 GTP/Mg2+ binding site [chemical binding]; other site 591001006438 G2 box; other site 591001006439 Switch I region; other site 591001006440 G3 box; other site 591001006441 Switch II region; other site 591001006442 G4 box; other site 591001006443 G5 box; other site 591001006444 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 591001006445 G1 box; other site 591001006446 GTP/Mg2+ binding site [chemical binding]; other site 591001006447 G2 box; other site 591001006448 Switch I region; other site 591001006449 G3 box; other site 591001006450 Switch II region; other site 591001006451 G4 box; other site 591001006452 G5 box; other site 591001006453 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 591001006454 active site 591001006455 homodimer interface [polypeptide binding]; other site 591001006456 Peptidase family M48; Region: Peptidase_M48; cl12018 591001006457 xanthine permease; Region: pbuX; TIGR03173 591001006458 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 591001006459 active site 591001006460 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001006461 metal binding site [ion binding]; metal-binding site 591001006462 active site 591001006463 I-site; other site 591001006464 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 591001006465 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 591001006466 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001006467 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 591001006468 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 591001006469 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 591001006470 metal binding site [ion binding]; metal-binding site 591001006471 active site 591001006472 I-site; other site 591001006473 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 591001006474 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 591001006475 catalytic triad [active]