-- dump date 20111121_015458 -- class Genbank::misc_feature -- table misc_feature_note -- id note 479436000001 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000002 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 479436000003 Walker A motif; other site 479436000004 ATP binding site [chemical binding]; other site 479436000005 Walker B motif; other site 479436000006 arginine finger; other site 479436000007 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 479436000008 DnaA box-binding interface [nucleotide binding]; other site 479436000009 DNA polymerase III subunit beta; Validated; Region: PRK05643 479436000010 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 479436000011 putative DNA binding surface [nucleotide binding]; other site 479436000012 dimer interface [polypeptide binding]; other site 479436000013 beta-clamp/clamp loader binding surface; other site 479436000014 beta-clamp/translesion DNA polymerase binding surface; other site 479436000015 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 479436000016 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 479436000017 RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication...; Region: ABC_RecF; cd03242 479436000018 Walker A/P-loop; other site 479436000019 ATP binding site [chemical binding]; other site 479436000020 Q-loop/lid; other site 479436000021 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000022 ABC transporter signature motif; other site 479436000023 Walker B; other site 479436000024 D-loop; other site 479436000025 H-loop/switch region; other site 479436000026 Protein of unknown function (DUF721); Region: DUF721; cl02324 479436000027 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 479436000028 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 479436000029 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 479436000030 anchoring element; other site 479436000031 dimer interface [polypeptide binding]; other site 479436000032 ATP binding site [chemical binding]; other site 479436000033 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 479436000034 active site 479436000035 putative metal-binding site [ion binding]; other site 479436000036 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 479436000037 Amino acid permease; Region: AA_permease; cl00524 479436000038 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 479436000039 Domain of unknown function (DUF74); Region: DUF74; cl00426 479436000040 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 479436000041 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 479436000042 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 479436000043 Domain of unknown function DUF21; Region: DUF21; pfam01595 479436000044 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 479436000045 Transporter associated domain; Region: CorC_HlyC; cl08393 479436000046 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 479436000047 S-adenosylmethionine binding site [chemical binding]; other site 479436000048 Sulfatase; Region: Sulfatase; cl10460 479436000049 putative glycosyl transferase; Provisional; Region: PRK10073 479436000050 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 479436000051 active site 479436000052 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 479436000053 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 479436000054 putative metal binding site; other site 479436000055 Protein of unknown function (DUF535); Region: DUF535; cl01128 479436000056 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 479436000057 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 479436000058 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 479436000059 O-Antigen ligase; Region: Wzy_C; cl04850 479436000060 Undecaprenyl-phosphate galactose phosphotransferase, WbaP; Region: WbaP_sugtrans; TIGR03022 479436000061 Bacterial sugar transferase; Region: Bac_transf; cl00939 479436000062 OpgC protein; Region: OpgC_C; cl00792 479436000063 Acyltransferase family; Region: Acyl_transf_3; pfam01757 479436000064 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000065 UDP-galactopyranose mutase [Cell envelope biogenesis, outer membrane]; Region: Glf; COG0562 479436000066 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000067 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 479436000068 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 479436000069 putative ADP-binding pocket [chemical binding]; other site 479436000070 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Region: deacetyl_PgaB; TIGR03938 479436000071 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 479436000072 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436000073 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 479436000074 LicD family; Region: LicD; cl01378 479436000075 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 479436000076 substrate binding site; other site 479436000077 dimer interface; other site 479436000078 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 479436000079 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 479436000080 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000081 NAD(P) binding site [chemical binding]; other site 479436000082 active site 479436000083 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 479436000084 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000085 NAD(P) binding site [chemical binding]; other site 479436000086 active site 479436000087 Acyltransferase family; Region: Acyl_transf_3; pfam01757 479436000088 OpgC protein; Region: OpgC_C; cl00792 479436000089 Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]; Region: LytB; COG2247 479436000090 Procyclic acidic repetitive protein (PARP); Region: Trypan_PARP; pfam05887 479436000091 putative scaffolding protein; Region: PHA01929 479436000092 Autotransporter beta-domain; Region: Autotransporter; cl02365 479436000093 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 479436000094 Autotransporter adhesin [Intracellular trafficking and secretion / Extracellular structures]; Region: Hia; COG5295 479436000095 Haemagglutinin; Region: HIM; pfam05662 479436000096 YadA-like C-terminal region; Region: YadA; pfam03895 479436000097 S-layer homology domain; Region: SLH; pfam00395 479436000098 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 479436000099 Haemagglutinin; Region: HIM; pfam05662 479436000100 Haemagglutinin; Region: HIM; pfam05662 479436000101 Haemagglutinin; Region: HIM; pfam05662 479436000102 YadA-like C-terminal region; Region: YadA; pfam03895 479436000103 YadA-like C-terminal region; Region: YadA; pfam03895 479436000104 Haemagglutinin; Region: HIM; pfam05662 479436000105 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 479436000106 YadA-like C-terminal region; Region: YadA; pfam03895 479436000107 Haemagglutinin; Region: HIM; pfam05662 479436000108 Haemagglutinin; Region: HIM; pfam05662 479436000109 YadA-like C-terminal region; Region: YadA; pfam03895 479436000110 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 479436000111 Haemagglutinin; Region: HIM; pfam05662 479436000112 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 479436000113 YadA-like C-terminal region; Region: YadA; pfam03895 479436000114 Haemagglutinin; Region: HIM; pfam05662 479436000115 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 479436000116 YadA-like C-terminal region; Region: YadA; pfam03895 479436000117 flagellin; Validated; Region: PRK08026 479436000118 Haemagglutinin; Region: HIM; pfam05662 479436000119 YadA-like C-terminal region; Region: YadA; pfam03895 479436000120 Pirin-related protein [General function prediction only]; Region: COG1741 479436000121 Cupin domain; Region: Cupin_2; cl09118 479436000122 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 479436000123 CGGC domain; Region: CGGC; cl02356 479436000124 Peptidase family M48; Region: Peptidase_M48; cl12018 479436000125 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 479436000126 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 479436000127 Gram-negative bacterial tonB protein; Region: TonB; cl10048 479436000128 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 479436000129 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 479436000130 N-terminal plug; other site 479436000131 ligand-binding site [chemical binding]; other site 479436000132 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 479436000133 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 479436000134 intersubunit interface [polypeptide binding]; other site 479436000135 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 479436000136 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 479436000137 ABC-ATPase subunit interface; other site 479436000138 dimer interface [polypeptide binding]; other site 479436000139 putative PBP binding regions; other site 479436000140 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436000141 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 479436000142 Walker A/P-loop; other site 479436000143 ATP binding site [chemical binding]; other site 479436000144 Q-loop/lid; other site 479436000145 ABC transporter signature motif; other site 479436000146 Walker B; other site 479436000147 D-loop; other site 479436000148 H-loop/switch region; other site 479436000149 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 479436000150 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 479436000151 N-terminal plug; other site 479436000152 ligand-binding site [chemical binding]; other site 479436000153 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 479436000154 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 479436000155 N-terminal plug; other site 479436000156 ligand-binding site [chemical binding]; other site 479436000157 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 479436000158 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 479436000159 intersubunit interface [polypeptide binding]; other site 479436000160 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 479436000161 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 479436000162 ABC-ATPase subunit interface; other site 479436000163 dimer interface [polypeptide binding]; other site 479436000164 putative PBP binding regions; other site 479436000165 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436000166 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 479436000167 Walker A/P-loop; other site 479436000168 ATP binding site [chemical binding]; other site 479436000169 Q-loop/lid; other site 479436000170 ABC transporter signature motif; other site 479436000171 Walker B; other site 479436000172 D-loop; other site 479436000173 H-loop/switch region; other site 479436000174 magnesium chelatase ATPase subunit I; Region: BchI-ChlI; TIGR02030 479436000175 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000176 cobaltochelatase subunit; Region: Cob-chelat-sub; TIGR02442 479436000177 Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is...; Region: vWA_Magnesium_chelatase; cd01451 479436000178 metal ion-dependent adhesion site (MIDAS); other site 479436000179 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 479436000180 CobN/Magnesium Chelatase; Region: CobN-Mg_chel; pfam02514 479436000181 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 479436000182 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 479436000183 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 479436000184 intersubunit interface [polypeptide binding]; other site 479436000185 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 479436000186 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 479436000187 N-terminal plug; other site 479436000188 ligand-binding site [chemical binding]; other site 479436000189 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 479436000190 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 479436000191 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000192 homodimer interface [polypeptide binding]; other site 479436000193 catalytic residue [active] 479436000194 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 479436000195 dimerization interface [polypeptide binding]; other site 479436000196 putative DNA binding site [nucleotide binding]; other site 479436000197 putative Zn2+ binding site [ion binding]; other site 479436000198 putative oxidoreductase FixC; Provisional; Region: PRK10157 479436000199 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000200 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 479436000201 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 479436000202 Ligand binding site [chemical binding]; other site 479436000203 Electron transfer flavoprotein domain; Region: ETF; pfam01012 479436000204 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 479436000205 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 479436000206 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 479436000207 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 479436000208 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000209 NAD(P) binding site [chemical binding]; other site 479436000210 active site 479436000211 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 479436000212 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 479436000213 dimer interface [polypeptide binding]; other site 479436000214 conserved gate region; other site 479436000215 putative PBP binding loops; other site 479436000216 ABC-ATPase subunit interface; other site 479436000217 nickel transporter permease NikC; Provisional; Region: nikC; PRK10417 479436000218 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 479436000219 dimer interface [polypeptide binding]; other site 479436000220 conserved gate region; other site 479436000221 putative PBP binding loops; other site 479436000222 ABC-ATPase subunit interface; other site 479436000223 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 479436000224 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_3; cd08490 479436000225 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 479436000226 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 479436000227 Walker A/P-loop; other site 479436000228 ATP binding site [chemical binding]; other site 479436000229 Q-loop/lid; other site 479436000230 ABC transporter signature motif; other site 479436000231 Walker B; other site 479436000232 D-loop; other site 479436000233 H-loop/switch region; other site 479436000234 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 479436000235 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 479436000236 Walker A/P-loop; other site 479436000237 ATP binding site [chemical binding]; other site 479436000238 Q-loop/lid; other site 479436000239 ABC transporter signature motif; other site 479436000240 Walker B; other site 479436000241 D-loop; other site 479436000242 H-loop/switch region; other site 479436000243 2-isopropylmalate synthase; Validated; Region: PRK00915 479436000244 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 479436000245 active site 479436000246 catalytic residues [active] 479436000247 metal binding site [ion binding]; metal-binding site 479436000248 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 479436000249 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 479436000250 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 479436000251 substrate binding site [chemical binding]; other site 479436000252 ligand binding site [chemical binding]; other site 479436000253 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 479436000254 substrate binding site [chemical binding]; other site 479436000255 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 479436000256 tartrate dehydrogenase; Provisional; Region: PRK08194 479436000257 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional; Region: PRK11921 479436000258 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436000259 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 479436000260 Haemagglutinin; Region: HIM; pfam05662 479436000261 YadA-like C-terminal region; Region: YadA; pfam03895 479436000262 S-layer homology domain; Region: SLH; pfam00395 479436000263 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 479436000264 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 479436000265 Coenzyme A binding pocket [chemical binding]; other site 479436000266 Protein of unknown function (DUF969); Region: DUF969; cl01573 479436000267 Protein of unknown function (DUF979); Region: DUF979; cl01572 479436000268 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 479436000269 putative substrate binding pocket [chemical binding]; other site 479436000270 AC domain interface; other site 479436000271 catalytic triad [active] 479436000272 AB domain interface; other site 479436000273 interchain disulfide; other site 479436000274 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 479436000275 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 479436000276 ligand binding site [chemical binding]; other site 479436000277 dimerization interface [polypeptide binding]; other site 479436000278 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 479436000279 TM-ABC transporter signature motif; other site 479436000280 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 479436000281 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000282 Walker A/P-loop; other site 479436000283 ATP binding site [chemical binding]; other site 479436000284 Q-loop/lid; other site 479436000285 ABC transporter signature motif; other site 479436000286 Walker B; other site 479436000287 D-loop; other site 479436000288 H-loop/switch region; other site 479436000289 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses; Region: ABC_Carb_Monos_II; cd03215 479436000290 RbsD / FucU transport protein family; Region: RbsD_FucU; cl00809 479436000291 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 479436000292 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 479436000293 substrate binding site [chemical binding]; other site 479436000294 dimer interface [polypeptide binding]; other site 479436000295 ATP binding site [chemical binding]; other site 479436000296 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000297 NAD(P) binding site [chemical binding]; other site 479436000298 active site 479436000299 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 479436000300 catalytic triad [active] 479436000301 conserved cis-peptide bond; other site 479436000302 Phd_YefM; Region: PhdYeFM; cl09153 479436000303 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 479436000304 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 479436000305 hypothetical protein; Provisional; Region: PRK01184 479436000306 HsdM N-terminal domain; Region: HsdM_N; pfam12161 479436000307 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 479436000308 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 479436000309 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 479436000310 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 479436000311 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 479436000312 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000313 Domain of unknown function (DUF947); Region: DUF947; pfam06102 479436000314 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 479436000315 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 479436000316 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 479436000317 Walker A/P-loop; other site 479436000318 ATP binding site [chemical binding]; other site 479436000319 Q-loop/lid; other site 479436000320 ABC transporter signature motif; other site 479436000321 Walker B; other site 479436000322 D-loop; other site 479436000323 H-loop/switch region; other site 479436000324 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 479436000325 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 479436000326 Walker A/P-loop; other site 479436000327 ATP binding site [chemical binding]; other site 479436000328 Q-loop/lid; other site 479436000329 ABC transporter signature motif; other site 479436000330 Walker B; other site 479436000331 D-loop; other site 479436000332 H-loop/switch region; other site 479436000333 Cobalt transport protein; Region: CbiQ; cl00463 479436000334 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 479436000335 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 479436000336 Coenzyme A binding pocket [chemical binding]; other site 479436000337 histidinol-phosphatase; Reviewed; Region: PRK08123 479436000338 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 479436000339 dimer interface [polypeptide binding]; other site 479436000340 motif 1; other site 479436000341 active site 479436000342 motif 2; other site 479436000343 motif 3; other site 479436000344 ATP phosphoribosyltransferase; Region: HisG; cl15266 479436000345 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 479436000346 histidinol dehydrogenase; Region: hisD; TIGR00069 479436000347 NAD binding site [chemical binding]; other site 479436000348 dimerization interface [polypeptide binding]; other site 479436000349 product binding site; other site 479436000350 substrate binding site [chemical binding]; other site 479436000351 zinc binding site [ion binding]; other site 479436000352 catalytic residues [active] 479436000353 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 479436000354 putative active site pocket [active] 479436000355 4-fold oligomerization interface [polypeptide binding]; other site 479436000356 metal binding residues [ion binding]; metal-binding site 479436000357 3-fold/trimer interface [polypeptide binding]; other site 479436000358 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 479436000359 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 479436000360 catalytic residues [active] 479436000361 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 479436000362 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 479436000363 substrate binding site [chemical binding]; other site 479436000364 glutamase interaction surface [polypeptide binding]; other site 479436000365 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 479436000366 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 479436000367 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 479436000368 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 479436000369 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000370 homodimer interface [polypeptide binding]; other site 479436000371 catalytic residue [active] 479436000372 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 479436000373 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 479436000374 putative active site [active] 479436000375 oxyanion strand; other site 479436000376 catalytic triad [active] 479436000377 Carbon starvation protein CstA; Region: CstA; cl00856 479436000378 Tat binding protein 1(TBP-1)-interacting protein (TBPIP); Region: TBPIP; pfam07106 479436000379 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 479436000380 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 479436000381 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 479436000382 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 479436000383 dimer interface [polypeptide binding]; other site 479436000384 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000385 catalytic residue [active] 479436000386 serine O-acetyltransferase; Region: cysE; TIGR01172 479436000387 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 479436000388 trimer interface [polypeptide binding]; other site 479436000389 active site 479436000390 substrate binding site [chemical binding]; other site 479436000391 CoA binding site [chemical binding]; other site 479436000392 Ferritin-like domain; Region: Ferritin; pfam00210 479436000393 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 479436000394 dimerization interface [polypeptide binding]; other site 479436000395 DPS ferroxidase diiron center [ion binding]; other site 479436000396 ion pore; other site 479436000397 MAEBL; Provisional; Region: PTZ00121 479436000398 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 479436000399 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 479436000400 Protein of unknown function (DUF328); Region: DUF328; cl01143 479436000401 biotin synthase; Provisional; Region: PRK07094 479436000402 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 479436000403 FeS/SAM binding site; other site 479436000404 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 479436000405 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so...; Region: EF-G_bact; cd04170 479436000406 elongation factor G; Reviewed; Region: PRK12740 479436000407 G1 box; other site 479436000408 putative GEF interaction site [polypeptide binding]; other site 479436000409 GTP/Mg2+ binding site [chemical binding]; other site 479436000410 Switch I region; other site 479436000411 G2 box; other site 479436000412 G3 box; other site 479436000413 Switch II region; other site 479436000414 G4 box; other site 479436000415 G5 box; other site 479436000416 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 479436000417 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 479436000418 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 479436000419 Domain of unknown function (DUF386); Region: DUF386; cl01047 479436000420 EamA-like transporter family; Region: EamA; cl01037 479436000421 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 479436000422 EamA-like transporter family; Region: EamA; cl01037 479436000423 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 479436000424 EamA-like transporter family; Region: EamA; cl01037 479436000425 EamA-like transporter family; Region: EamA; cl01037 479436000426 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 479436000427 M20 Peptidases Aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase from bacteria and archaea; Region: M20_Acy1_IAAspH_bact; cd05665 479436000428 putative metal binding site [ion binding]; other site 479436000429 dimer interface [polypeptide binding]; other site 479436000430 allantoate amidohydrolase; Reviewed; Region: PRK09290 479436000431 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 479436000432 active site 479436000433 metal binding site [ion binding]; metal-binding site 479436000434 dimer interface [polypeptide binding]; other site 479436000435 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 479436000436 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 479436000437 drug efflux system protein MdtG; Provisional; Region: PRK09874 479436000438 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 479436000439 putative substrate translocation pore; other site 479436000440 anthranilate synthase component I; Provisional; Region: PRK13565 479436000441 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 479436000442 chorismate binding enzyme; Region: Chorismate_bind; cl10555 479436000443 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 479436000444 Glutamine amidotransferase class-I; Region: GATase; pfam00117 479436000445 glutamine binding [chemical binding]; other site 479436000446 catalytic triad [active] 479436000447 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 479436000448 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 479436000449 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 479436000450 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 479436000451 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 479436000452 active site 479436000453 ribulose/triose binding site [chemical binding]; other site 479436000454 phosphate binding site [ion binding]; other site 479436000455 substrate (anthranilate) binding pocket [chemical binding]; other site 479436000456 product (indole) binding pocket [chemical binding]; other site 479436000457 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 479436000458 active site 479436000459 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 479436000460 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 479436000461 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000462 catalytic residue [active] 479436000463 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 479436000464 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 479436000465 substrate binding site [chemical binding]; other site 479436000466 active site 479436000467 catalytic residues [active] 479436000468 heterodimer interface [polypeptide binding]; other site 479436000469 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436000470 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436000471 Uncharacterised protein family UPF0547; Region: UPF0547; pfam10571 479436000472 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436000473 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 479436000474 non-specific DNA binding site [nucleotide binding]; other site 479436000475 salt bridge; other site 479436000476 sequence-specific DNA binding site [nucleotide binding]; other site 479436000477 CAAX amino terminal protease self- immunity; Region: Abi; cl00558 479436000478 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 479436000479 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 479436000480 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000481 Walker A/P-loop; other site 479436000482 ATP binding site [chemical binding]; other site 479436000483 Q-loop/lid; other site 479436000484 ABC transporter signature motif; other site 479436000485 Walker B; other site 479436000486 D-loop; other site 479436000487 H-loop/switch region; other site 479436000488 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 479436000489 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 479436000490 FeS/SAM binding site; other site 479436000491 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 479436000492 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 479436000493 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436000494 active site 479436000495 HIGH motif; other site 479436000496 nucleotide binding site [chemical binding]; other site 479436000497 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 479436000498 active site 479436000499 KMSKS motif; other site 479436000500 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 479436000501 tRNA binding surface [nucleotide binding]; other site 479436000502 anticodon binding site; other site 479436000503 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 479436000504 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 479436000505 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 479436000506 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 479436000507 substrate binding pocket [chemical binding]; other site 479436000508 membrane-bound complex binding site; other site 479436000509 hinge residues; other site 479436000510 M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily; Region: M20_ACY1L2_like; cd05672 479436000511 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 479436000512 metal binding site [ion binding]; metal-binding site 479436000513 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 479436000514 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 479436000515 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436000516 reductive dehalogenase; Region: RDH; TIGR02486 479436000517 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 479436000518 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 479436000519 active site 479436000520 catalytic tetrad [active] 479436000521 GMP synthase; Reviewed; Region: guaA; PRK00074 479436000522 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 479436000523 AMP/PPi binding site [chemical binding]; other site 479436000524 candidate oxyanion hole; other site 479436000525 catalytic triad [active] 479436000526 potential glutamine specificity residues [chemical binding]; other site 479436000527 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 479436000528 ATP Binding subdomain [chemical binding]; other site 479436000529 Ligand Binding sites [chemical binding]; other site 479436000530 Dimerization subdomain; other site 479436000531 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 479436000532 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 479436000533 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 479436000534 ATP binding site [chemical binding]; other site 479436000535 Mg2+ binding site [ion binding]; other site 479436000536 G-X-G motif; other site 479436000537 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 479436000538 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436000539 cofactor binding site; other site 479436000540 DNA binding site [nucleotide binding] 479436000541 substrate interaction site [chemical binding]; other site 479436000542 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436000543 Restriction endonuclease; Region: Mrr_cat; cl00747 479436000544 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 479436000545 S-adenosylmethionine binding site [chemical binding]; other site 479436000546 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 479436000547 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 479436000548 putative acetyltransferase; Provisional; Region: PRK03624 479436000549 Coenzyme A binding pocket [chemical binding]; other site 479436000550 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 479436000551 Coenzyme A binding pocket [chemical binding]; other site 479436000552 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 479436000553 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 479436000554 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 479436000555 intersubunit interface [polypeptide binding]; other site 479436000556 ferrichrome/ferrioxamine B periplasmic transporter; Provisional; Region: PRK14048 479436000557 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 479436000558 intersubunit interface [polypeptide binding]; other site 479436000559 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 479436000560 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 479436000561 ABC-ATPase subunit interface; other site 479436000562 dimer interface [polypeptide binding]; other site 479436000563 putative PBP binding regions; other site 479436000564 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436000565 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 479436000566 Walker A/P-loop; other site 479436000567 ATP binding site [chemical binding]; other site 479436000568 Q-loop/lid; other site 479436000569 ABC transporter signature motif; other site 479436000570 Walker B; other site 479436000571 D-loop; other site 479436000572 H-loop/switch region; other site 479436000573 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 479436000574 ABC-ATPase subunit interface; other site 479436000575 dimer interface [polypeptide binding]; other site 479436000576 putative PBP binding regions; other site 479436000577 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 479436000578 ABC-ATPase subunit interface; other site 479436000579 dimer interface [polypeptide binding]; other site 479436000580 putative PBP binding regions; other site 479436000581 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 479436000582 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 479436000583 Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins...; Region: TroA; cd01016 479436000584 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 479436000585 metal binding site [ion binding]; metal-binding site 479436000586 intersubunit interface [polypeptide binding]; other site 479436000587 Gram-negative bacterial tonB protein; Region: TonB; cl10048 479436000588 Gram-negative bacterial tonB protein; Region: TonB; cl10048 479436000589 Uncharacterized conserved protein [Function unknown]; Region: COG2461 479436000590 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 479436000591 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_HprK; cl00270 479436000592 active site 479436000593 metal-binding site [ion binding] 479436000594 nucleotide-binding site [chemical binding]; other site 479436000595 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436000596 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436000597 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 479436000598 dimerization interface [polypeptide binding]; other site 479436000599 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 479436000600 Prismane/CO dehydrogenase family; Region: Prismane; pfam03063 479436000601 ACS interaction site; other site 479436000602 CODH interaction site; other site 479436000603 metal cluster binding site [ion binding]; other site 479436000604 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436000605 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 479436000606 biotin synthase; Validated; Region: PRK06256 479436000607 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 479436000608 FeS/SAM binding site; other site 479436000609 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 479436000610 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 479436000611 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 479436000612 active site 479436000613 metal binding site [ion binding]; metal-binding site 479436000614 DNA binding site [nucleotide binding] 479436000615 Uncharacterized conserved protein [Function unknown]; Region: COG4717 479436000616 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000617 Walker A/P-loop; other site 479436000618 ATP binding site [chemical binding]; other site 479436000619 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 479436000620 Uncharacterized conserved protein [Function unknown]; Region: COG4717 479436000621 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 479436000622 substrate binding site [chemical binding]; other site 479436000623 active site 479436000624 Ferrochelatase; Region: Ferrochelatase; pfam00762 479436000625 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 479436000626 active site 479436000627 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 479436000628 active site 479436000629 N-terminal domain interface [polypeptide binding]; other site 479436000630 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000631 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000632 Chlorite dismutase; Region: Chlor_dismutase; cl01280 479436000633 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 479436000634 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 479436000635 putative substrate translocation pore; other site 479436000636 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 479436000637 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 479436000638 ligand binding site [chemical binding]; other site 479436000639 flexible hinge region; other site 479436000640 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 479436000641 putative switch regulator; other site 479436000642 non-specific DNA interactions [nucleotide binding]; other site 479436000643 DNA binding site [nucleotide binding] 479436000644 sequence specific DNA binding site [nucleotide binding]; other site 479436000645 putative cAMP binding site [chemical binding]; other site 479436000646 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 479436000647 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 479436000648 [4Fe-4S] binding site [ion binding]; other site 479436000649 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 479436000650 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 479436000651 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 479436000652 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 479436000653 molybdopterin cofactor binding site; other site 479436000654 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 479436000655 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 479436000656 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; cl00959 479436000657 S-layer homology domain; Region: SLH; pfam00395 479436000658 drug efflux system protein MdtG; Provisional; Region: PRK09874 479436000659 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 479436000660 putative substrate translocation pore; other site 479436000661 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436000662 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436000663 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 479436000664 LysE type translocator; Region: LysE; cl00565 479436000665 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 479436000666 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeD; cd03379 479436000667 active site clefts [active] 479436000668 zinc binding site [ion binding]; other site 479436000669 dimer interface [polypeptide binding]; other site 479436000670 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 479436000671 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000672 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000673 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 479436000674 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06916 479436000675 inhibitor-cofactor binding pocket; inhibition site 479436000676 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000677 catalytic residue [active] 479436000678 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 479436000679 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 479436000680 metal binding site 2 [ion binding]; metal-binding site 479436000681 putative DNA binding helix; other site 479436000682 metal binding site 1 [ion binding]; metal-binding site 479436000683 dimer interface [polypeptide binding]; other site 479436000684 structural Zn2+ binding site [ion binding]; other site 479436000685 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 479436000686 ABC-ATPase subunit interface; other site 479436000687 dimer interface [polypeptide binding]; other site 479436000688 putative PBP binding regions; other site 479436000689 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 479436000690 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 479436000691 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 479436000692 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 479436000693 metal binding site [ion binding]; metal-binding site 479436000694 Peptidase propeptide and YPEB domain; Region: PepSY; cl15480 479436000695 alanine racemase; Reviewed; Region: alr; PRK00053 479436000696 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 479436000697 active site 479436000698 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 479436000699 dimer interface [polypeptide binding]; other site 479436000700 substrate binding site [chemical binding]; other site 479436000701 catalytic residues [active] 479436000702 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 479436000703 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000704 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 479436000705 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436000706 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 479436000707 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 479436000708 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436000709 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 479436000710 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 479436000711 FeS/SAM binding site; other site 479436000712 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 479436000713 Pyruvate formate lyase 1; Region: PFL1; cd01678 479436000714 coenzyme A binding site [chemical binding]; other site 479436000715 active site 479436000716 catalytic residues [active] 479436000717 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 479436000718 non-specific DNA binding site [nucleotide binding]; other site 479436000719 salt bridge; other site 479436000720 sequence-specific DNA binding site [nucleotide binding]; other site 479436000721 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 479436000722 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 479436000723 Walker A/P-loop; other site 479436000724 ATP binding site [chemical binding]; other site 479436000725 Q-loop/lid; other site 479436000726 ABC transporter signature motif; other site 479436000727 Walker B; other site 479436000728 D-loop; other site 479436000729 H-loop/switch region; other site 479436000730 NIL domain; Region: NIL; cl09633 479436000731 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 479436000732 dimer interface [polypeptide binding]; other site 479436000733 conserved gate region; other site 479436000734 ABC-ATPase subunit interface; other site 479436000735 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 479436000736 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 479436000737 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; cl15357 479436000738 transmembrane helices; other site 479436000739 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 479436000740 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 479436000741 Cys/Met metabolism PLP-dependent enzyme; Region: Cys_Met_Meta_PP; pfam01053 479436000742 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 479436000743 homodimer interface [polypeptide binding]; other site 479436000744 substrate-cofactor binding pocket; other site 479436000745 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000746 catalytic residue [active] 479436000747 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 479436000748 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 479436000749 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000750 homodimer interface [polypeptide binding]; other site 479436000751 catalytic residue [active] 479436000752 Homoserine O-succinyltransferase; Region: HTS; pfam04204 479436000753 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 479436000754 proposed active site lysine [active] 479436000755 conserved cys residue [active] 479436000756 OAH/OAS sulfhydrylase; Region: OAH_OAS_sulfhy; TIGR01326 479436000757 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 479436000758 homodimer interface [polypeptide binding]; other site 479436000759 substrate-cofactor binding pocket; other site 479436000760 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000761 catalytic residue [active] 479436000762 Peptidase propeptide and YPEB domain; Region: PepSY; cl15480 479436000763 Peptidase propeptide and YPEB domain; Region: PepSY; cl15480 479436000764 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 479436000765 Domain of unknown function (DUF1980); Region: DUF1980; cl01492 479436000766 Domain of unknown function (DUF1980); Region: DUF1980; cl01492 479436000767 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 479436000768 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000769 Predicted permease; Region: DUF318; cl00487 479436000770 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 479436000771 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000772 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; cl08458 479436000773 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 479436000774 metal binding site [ion binding]; metal-binding site 479436000775 dimer interface [polypeptide binding]; other site 479436000776 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 479436000777 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 479436000778 active site 479436000779 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 479436000780 NAD synthase; Region: NAD_synthase; pfam02540 479436000781 homodimer interface [polypeptide binding]; other site 479436000782 NAD binding pocket [chemical binding]; other site 479436000783 ATP binding pocket [chemical binding]; other site 479436000784 Mg binding site [ion binding]; other site 479436000785 active-site loop [active] 479436000786 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 479436000787 active site 479436000788 homodimer interface [polypeptide binding]; other site 479436000789 homotetramer interface [polypeptide binding]; other site 479436000790 Adenosylcobinamide amidohydrolase; Region: CbiZ; cl00808 479436000791 mechanosensitive channel MscS; Provisional; Region: PRK10334 479436000792 Mechanosensitive ion channel; Region: MS_channel; pfam00924 479436000793 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 479436000794 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 479436000795 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 479436000796 Uncharacterized Fe-S protein [Energy production and conversion]; Region: COG1600 479436000797 FAD binding domain in molybdopterin dehydrogenase; Region: FAD_binding_5; pfam00941 479436000798 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; cl08390 479436000799 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 479436000800 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 479436000801 catalytic loop [active] 479436000802 iron binding site [ion binding]; other site 479436000803 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 479436000804 xanthine dehydrogenase subunit XdhA; Provisional; Region: PRK09970 479436000805 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 479436000806 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 479436000807 probable selenium-dependent hydroxylase accessory protein YqeC; Region: TIGR03172 479436000808 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 479436000809 Ligand binding site; other site 479436000810 selenium-dependent molybdenum hydroxylase system protein, YqeB family; Region: matur_yqeB; TIGR03309 479436000811 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 479436000812 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 479436000813 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl14614 479436000814 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 479436000815 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 479436000816 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 479436000817 YbbR-like protein; Region: YbbR; pfam07949 479436000818 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 479436000819 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000820 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 479436000821 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 479436000822 active site 479436000823 substrate binding site [chemical binding]; other site 479436000824 metal binding site [ion binding]; metal-binding site 479436000825 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 479436000826 aspartate racemase; Region: asp_race; TIGR00035 479436000827 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 479436000828 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 479436000829 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 479436000830 glutaminase active site [active] 479436000831 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 479436000832 dimer interface [polypeptide binding]; other site 479436000833 active site 479436000834 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 479436000835 dimer interface [polypeptide binding]; other site 479436000836 active site 479436000837 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 479436000838 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 479436000839 active site 479436000840 HIGH motif; other site 479436000841 dimer interface [polypeptide binding]; other site 479436000842 KMSKS motif; other site 479436000843 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 479436000844 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 479436000845 substrate binding pocket [chemical binding]; other site 479436000846 membrane-bound complex binding site; other site 479436000847 hinge residues; other site 479436000848 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 479436000849 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 479436000850 dimer interface [polypeptide binding]; other site 479436000851 conserved gate region; other site 479436000852 putative PBP binding loops; other site 479436000853 ABC-ATPase subunit interface; other site 479436000854 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 479436000855 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 479436000856 Walker A/P-loop; other site 479436000857 ATP binding site [chemical binding]; other site 479436000858 Q-loop/lid; other site 479436000859 ABC transporter signature motif; other site 479436000860 Walker B; other site 479436000861 D-loop; other site 479436000862 H-loop/switch region; other site 479436000863 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 479436000864 Ligand Binding Site [chemical binding]; other site 479436000865 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 479436000866 dimerization interface [polypeptide binding]; other site 479436000867 putative DNA binding site [nucleotide binding]; other site 479436000868 putative Zn2+ binding site [ion binding]; other site 479436000869 Membrane transport protein; Region: Mem_trans; cl09117 479436000870 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 479436000871 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 479436000872 dimer interface [polypeptide binding]; other site 479436000873 conserved gate region; other site 479436000874 putative PBP binding loops; other site 479436000875 ABC-ATPase subunit interface; other site 479436000876 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 479436000877 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000878 Walker A/P-loop; other site 479436000879 ATP binding site [chemical binding]; other site 479436000880 Q-loop/lid; other site 479436000881 ABC transporter signature motif; other site 479436000882 Walker B; other site 479436000883 D-loop; other site 479436000884 H-loop/switch region; other site 479436000885 Sodium:solute symporter family; Region: SSF; cl00456 479436000886 Thiamine-precursor transporter protein (ThiW); Region: ThiW; cl01952 479436000887 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 479436000888 dimer interface [polypeptide binding]; other site 479436000889 substrate binding site [chemical binding]; other site 479436000890 ATP binding site [chemical binding]; other site 479436000891 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 479436000892 substrate binding site [chemical binding]; other site 479436000893 multimerization interface [polypeptide binding]; other site 479436000894 ATP binding site [chemical binding]; other site 479436000895 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 479436000896 thiamine phosphate binding site [chemical binding]; other site 479436000897 active site 479436000898 pyrophosphate binding site [ion binding]; other site 479436000899 Rubrerythrin [Energy production and conversion]; Region: COG1592 479436000900 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 479436000901 binuclear metal center [ion binding]; other site 479436000902 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 479436000903 iron binding site [ion binding]; other site 479436000904 Bacterial protein of unknown function (DUF951); Region: DUF951; cl01864 479436000905 selenophosphate synthetase; Provisional; Region: PRK00943 479436000906 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 479436000907 dimerization interface [polypeptide binding]; other site 479436000908 putative ATP binding site [chemical binding]; other site 479436000909 SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response...; Region: SirA_like_N; cd03421 479436000910 selenium metabolism protein YedF; Region: selenium_YedF; TIGR03527 479436000911 CPxP motif; other site 479436000912 DsrE/DsrF-like family; Region: DrsE; cl00672 479436000913 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 479436000914 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 479436000915 dimer interface [polypeptide binding]; other site 479436000916 FMN binding site [chemical binding]; other site 479436000917 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 479436000918 GTP-binding protein YchF; Reviewed; Region: PRK09601 479436000919 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 479436000920 G1 box; other site 479436000921 GTP/Mg2+ binding site [chemical binding]; other site 479436000922 Switch I region; other site 479436000923 G2 box; other site 479436000924 Switch II region; other site 479436000925 G3 box; other site 479436000926 G4 box; other site 479436000927 G5 box; other site 479436000928 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 479436000929 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 479436000930 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 479436000931 S-adenosylmethionine binding site [chemical binding]; other site 479436000932 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436000933 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436000934 Walker A/P-loop; other site 479436000935 ATP binding site [chemical binding]; other site 479436000936 Q-loop/lid; other site 479436000937 ABC transporter signature motif; other site 479436000938 Walker B; other site 479436000939 D-loop; other site 479436000940 H-loop/switch region; other site 479436000941 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 479436000942 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 479436000943 ABC-ATPase subunit interface; other site 479436000944 dimer interface [polypeptide binding]; other site 479436000945 putative PBP binding regions; other site 479436000946 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 479436000947 Periplasmic binding protein TroA_e. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_e; cd01142 479436000948 putative ligand binding residues [chemical binding]; other site 479436000949 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 479436000950 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436000951 Autotransporter beta-domain; Region: Autotransporter; cl02365 479436000952 LL-diaminopimelate aminotransferase; Region: DAPAT_plant; TIGR03542 479436000953 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 479436000954 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436000955 homodimer interface [polypeptide binding]; other site 479436000956 catalytic residue [active] 479436000957 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 479436000958 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436000959 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 479436000960 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 479436000961 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 479436000962 putative substrate translocation pore; other site 479436000963 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 479436000964 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 479436000965 dimer interface [polypeptide binding]; other site 479436000966 ssDNA binding site [nucleotide binding]; other site 479436000967 tetramer (dimer of dimers) interface [polypeptide binding]; other site 479436000968 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 479436000969 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 479436000970 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 479436000971 4Fe-4S binding domain; Region: Fer4_5; pfam12801 479436000972 4Fe-4S binding domain; Region: Fer4_5; pfam12801 479436000973 nitrogenase cofactor biosynthesis protein NifB; Region: nifB; TIGR01290 479436000974 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 479436000975 FeS/SAM binding site; other site 479436000976 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 479436000977 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 479436000978 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 479436000979 catalytic residue [active] 479436000980 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 479436000981 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 479436000982 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 479436000983 S-adenosylmethionine binding site [chemical binding]; other site 479436000984 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 479436000985 Permease family; Region: Xan_ur_permease; cl00967 479436000986 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 479436000987 SigmaW regulon antibacterial; Region: YdfA_immunity; cl12057 479436000988 DNA-binding transcriptional regulator TyrR; Provisional; Region: PRK10820 479436000989 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 479436000990 putative active site [active] 479436000991 Major Facilitator Superfamily; Region: MFS_1; pfam07690 479436000992 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 479436000993 putative substrate translocation pore; other site 479436000994 peptidase T; Region: peptidase-T; TIGR01882 479436000995 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 479436000996 metal binding site [ion binding]; metal-binding site 479436000997 dimer interface [polypeptide binding]; other site 479436000998 OPT oligopeptide transporter protein; Region: OPT; cl14607 479436000999 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 479436001000 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 479436001001 substrate binding pocket [chemical binding]; other site 479436001002 membrane-bound complex binding site; other site 479436001003 hinge residues; other site 479436001004 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 479436001005 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 479436001006 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 479436001007 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436001008 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 479436001009 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 479436001010 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 479436001011 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 479436001012 dimerization interface [polypeptide binding]; other site 479436001013 ATP binding site [chemical binding]; other site 479436001014 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 479436001015 dimerization interface [polypeptide binding]; other site 479436001016 ATP binding site [chemical binding]; other site 479436001017 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 479436001018 putative active site [active] 479436001019 catalytic triad [active] 479436001020 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436001021 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436001022 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 479436001023 dimerization interface [polypeptide binding]; other site 479436001024 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001025 AIR carboxylase; Region: AIRC; cl00310 479436001026 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 479436001027 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 479436001028 ATP binding site [chemical binding]; other site 479436001029 active site 479436001030 substrate binding site [chemical binding]; other site 479436001031 amidophosphoribosyltransferase; Provisional; Region: PRK05793 479436001032 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 479436001033 active site 479436001034 tetramer interface [polypeptide binding]; other site 479436001035 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001036 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001037 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 479436001038 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 479436001039 dimerization interface [polypeptide binding]; other site 479436001040 putative ATP binding site [chemical binding]; other site 479436001041 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 479436001042 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 479436001043 active site 479436001044 substrate binding site [chemical binding]; other site 479436001045 cosubstrate binding site; other site 479436001046 catalytic site [active] 479436001047 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 479436001048 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 479436001049 purine monophosphate binding site [chemical binding]; other site 479436001050 dimer interface [polypeptide binding]; other site 479436001051 putative catalytic residues [active] 479436001052 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 479436001053 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 479436001054 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 479436001055 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 479436001056 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 479436001057 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 479436001058 Isochorismate synthase [Coenzyme metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: MenF; COG1169 479436001059 chorismate binding enzyme; Region: Chorismate_bind; cl10555 479436001060 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase [Coenzyme metabolism]; Region: MenD; COG1165 479436001061 Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1- carboxylate synthase (MenD) and related proteins; Region: TPP_PYR_MenD; cd07037 479436001062 dimer interface [polypeptide binding]; other site 479436001063 tetramer interface [polypeptide binding]; other site 479436001064 PYR/PP interface [polypeptide binding]; other site 479436001065 TPP binding site [chemical binding]; other site 479436001066 Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key...; Region: TPP_SHCHC_synthase; cd02009 479436001067 TPP-binding site; other site 479436001068 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase; Region: menH_SHCHC; TIGR03695 479436001069 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 479436001070 dihydroxynaphthoic acid synthetase; Validated; Region: PRK07396 479436001071 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 479436001072 substrate binding site [chemical binding]; other site 479436001073 oxyanion hole (OAH) forming residues; other site 479436001074 trimer interface [polypeptide binding]; other site 479436001075 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 479436001076 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 479436001077 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 479436001078 o-succinylbenzoic acid (OSB) synthetase; Region: menC_lowGC/arch; TIGR01928 479436001079 metal binding site [ion binding]; metal-binding site 479436001080 substrate binding pocket [chemical binding]; other site 479436001081 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 479436001082 CoenzymeA binding site [chemical binding]; other site 479436001083 subunit interaction site [polypeptide binding]; other site 479436001084 PHB binding site; other site 479436001085 Protein of unknown function (DUF2939); Region: DUF2939; pfam11159 479436001086 Virulence protein [General function prediction only]; Region: COG3943 479436001087 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 479436001088 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 479436001089 non-specific DNA binding site [nucleotide binding]; other site 479436001090 salt bridge; other site 479436001091 sequence-specific DNA binding site [nucleotide binding]; other site 479436001092 Uncharacterized protein conserved in bacteria (DUF2188); Region: DUF2188; cl11557 479436001093 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 479436001094 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 479436001095 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 479436001096 Predicted amidohydrolase [General function prediction only]; Region: COG0388 479436001097 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_5; cd07583 479436001098 putative active site [active] 479436001099 catalytic triad [active] 479436001100 putative dimer interface [polypeptide binding]; other site 479436001101 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 479436001102 Exopolysaccharide biosynthesis protein related to N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [Carbohydrate transport and metabolism]; Region: EpsL; COG4632 479436001103 Predicted periplasmic protein (DUF2233); Region: DUF2233; cl10481 479436001104 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 479436001105 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 479436001106 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 479436001107 putative active site [active] 479436001108 oxaloacetate decarboxylase; Provisional; Region: PRK12331 479436001109 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 479436001110 active site 479436001111 catalytic residues [active] 479436001112 metal binding site [ion binding]; metal-binding site 479436001113 homodimer binding site [polypeptide binding]; other site 479436001114 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 479436001115 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 479436001116 dimer interface [polypeptide binding]; other site 479436001117 phosphorylation site [posttranslational modification] 479436001118 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 479436001119 ATP binding site [chemical binding]; other site 479436001120 G-X-G motif; other site 479436001121 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 479436001122 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 479436001123 active site 479436001124 phosphorylation site [posttranslational modification] 479436001125 intermolecular recognition site; other site 479436001126 dimerization interface [polypeptide binding]; other site 479436001127 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 479436001128 DNA binding site [nucleotide binding] 479436001129 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 479436001130 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 479436001131 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 479436001132 protein binding site [polypeptide binding]; other site 479436001133 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436001134 Protein of unknown function (DUF1700); Region: DUF1700; cl01933 479436001135 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001136 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 479436001137 active site 479436001138 dimer interface [polypeptide binding]; other site 479436001139 an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; Region: DNA_pol_III_epsilon_like; cd06130 479436001140 active site 479436001141 substrate binding site [chemical binding]; other site 479436001142 catalytic site [active] 479436001143 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 479436001144 intersubunit interface [polypeptide binding]; other site 479436001145 active site 479436001146 catalytic residue [active] 479436001147 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 479436001148 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 479436001149 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 479436001150 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; cl06734 479436001151 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 479436001152 active site 479436001153 catalytic motif [active] 479436001154 Zn binding site [ion binding]; other site 479436001155 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 479436001156 UbiA prenyltransferase family; Region: UbiA; cl00337 479436001157 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 479436001158 homotrimer interaction site [polypeptide binding]; other site 479436001159 putative active site [active] 479436001160 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 479436001161 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 479436001162 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 479436001163 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 479436001164 putative substrate translocation pore; other site 479436001165 Major Facilitator Superfamily; Region: MFS_1; pfam07690 479436001166 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 479436001167 nucleoside/Zn binding site; other site 479436001168 dimer interface [polypeptide binding]; other site 479436001169 catalytic motif [active] 479436001170 Predicted membrane protein [Function unknown]; Region: COG2860 479436001171 UPF0126 domain; Region: UPF0126; pfam03458 479436001172 UPF0126 domain; Region: UPF0126; pfam03458 479436001173 Acyltransferase family; Region: Acyl_transf_3; pfam01757 479436001174 OpgC protein; Region: OpgC_C; cl00792 479436001175 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 479436001176 homodimer interface [polypeptide binding]; other site 479436001177 substrate-cofactor binding pocket; other site 479436001178 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436001179 Aminotransferase class IV; Region: Aminotran_4; pfam01063 479436001180 catalytic residue [active] 479436001181 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 479436001182 MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC...; Region: ABC_MetN_methionine_transporter; cd03258 479436001183 Walker A/P-loop; other site 479436001184 ATP binding site [chemical binding]; other site 479436001185 Q-loop/lid; other site 479436001186 ABC transporter signature motif; other site 479436001187 Walker B; other site 479436001188 D-loop; other site 479436001189 H-loop/switch region; other site 479436001190 NIL domain; Region: NIL; cl09633 479436001191 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 479436001192 dimer interface [polypeptide binding]; other site 479436001193 conserved gate region; other site 479436001194 ABC-ATPase subunit interface; other site 479436001195 Trp repressor protein; Region: Trp_repressor; cl01121 479436001196 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 479436001197 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 479436001198 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 479436001199 classical (c) SDRs; Region: SDR_c; cd05233 479436001200 NAD(P) binding site [chemical binding]; other site 479436001201 active site 479436001202 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 479436001203 Protein of unknown function (DUF1232); Region: DUF1232; cl01318 479436001204 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 479436001205 active site 479436001206 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 479436001207 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; cl00644 479436001208 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 479436001209 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 479436001210 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 479436001211 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 479436001212 ribonuclease PH; Reviewed; Region: rph; PRK00173 479436001213 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 479436001214 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 479436001215 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 479436001216 active site 479436001217 dimerization interface [polypeptide binding]; other site 479436001218 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 479436001219 active site 479436001220 metal binding site [ion binding]; metal-binding site 479436001221 homotetramer interface [polypeptide binding]; other site 479436001222 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 479436001223 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 479436001224 Malic enzyme, N-terminal domain; Region: malic; pfam00390 479436001225 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001226 NAD(P) binding pocket [chemical binding]; other site 479436001227 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 479436001228 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 479436001229 Int/Topo IB signature motif; other site 479436001230 TrwC relaxase; Region: TrwC; cl08490 479436001231 Ti-type conjugative transfer relaxase TraA; Region: TraA_Ti; TIGR02768 479436001232 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001233 active site 479436001234 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001235 AAA-like domain; Region: AAA_10; pfam12846 479436001236 Walker A motif; other site 479436001237 ATP binding site [chemical binding]; other site 479436001238 Walker B motif; other site 479436001239 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 479436001240 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 479436001241 non-specific DNA binding site [nucleotide binding]; other site 479436001242 salt bridge; other site 479436001243 sequence-specific DNA binding site [nucleotide binding]; other site 479436001244 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436001245 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436001246 type III restriction-modification system StyLTI enzyme res; Provisional; Region: PRK15483 479436001247 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001248 Protein of unknown function (DUF342); Region: DUF342; pfam03961 479436001249 YadA-like C-terminal region; Region: YadA; pfam03895 479436001250 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 479436001251 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 479436001252 Walker A motif; other site 479436001253 ATP binding site [chemical binding]; other site 479436001254 Walker B motif; other site 479436001255 arginine finger; other site 479436001256 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 479436001257 Walker A motif; other site 479436001258 ATP binding site [chemical binding]; other site 479436001259 Walker B motif; other site 479436001260 arginine finger; other site 479436001261 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 479436001262 ThiC family; Region: ThiC; cl08031 479436001263 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 479436001264 thiS-thiF/thiG interaction site; other site 479436001265 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 479436001266 ThiS interaction site; other site 479436001267 putative active site [active] 479436001268 tetramer interface [polypeptide binding]; other site 479436001269 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 479436001270 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 479436001271 FeS/SAM binding site; other site 479436001272 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 479436001273 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001274 ATP binding site [chemical binding]; other site 479436001275 substrate interface [chemical binding]; other site 479436001276 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 479436001277 thiamine phosphate binding site [chemical binding]; other site 479436001278 active site 479436001279 pyrophosphate binding site [ion binding]; other site 479436001280 LamB/YcsF family; Region: LamB_YcsF; cl00664 479436001281 Natural resistance-associated macrophage protein; Region: Nramp; cl00836 479436001282 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 479436001283 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 479436001284 Allophanate hydrolase subunit 2; Region: AHS2; cl00865 479436001285 Haemagglutinin; Region: HIM; pfam05662 479436001286 YadA-like C-terminal region; Region: YadA; pfam03895 479436001287 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 479436001288 MatE; Region: MatE; cl10513 479436001289 MatE; Region: MatE; cl10513 479436001290 Surface antigen; Region: Surface_Ag_2; cl01155 479436001291 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 479436001292 ligand binding site [chemical binding]; other site 479436001293 Domain of unknown function DUF20; Region: UPF0118; cl00465 479436001294 Peptidase propeptide and YPEB domain; Region: PepSY; cl15480 479436001295 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 479436001296 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 479436001297 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001298 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 479436001299 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 479436001300 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 479436001301 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 479436001302 S-adenosylmethionine binding site [chemical binding]; other site 479436001303 Protein of unknown function (DUF541); Region: SIMPL; cl01077 479436001304 Polysaccharide deacetylase; Region: Polysacc_deac_1; cl12061 479436001305 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 479436001306 MPT binding site; other site 479436001307 trimer interface [polypeptide binding]; other site 479436001308 Predicted transcriptional regulator [Transcription]; Region: COG1959 479436001309 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436001310 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 479436001311 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 479436001312 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 479436001313 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 479436001314 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 479436001315 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 479436001316 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001317 Walker A/P-loop; other site 479436001318 ATP binding site [chemical binding]; other site 479436001319 Q-loop/lid; other site 479436001320 ABC transporter signature motif; other site 479436001321 Walker B; other site 479436001322 D-loop; other site 479436001323 H-loop/switch region; other site 479436001324 ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]; Region: CydC; COG4987 479436001325 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001326 Walker A/P-loop; other site 479436001327 ATP binding site [chemical binding]; other site 479436001328 Q-loop/lid; other site 479436001329 ABC transporter signature motif; other site 479436001330 Walker B; other site 479436001331 D-loop; other site 479436001332 H-loop/switch region; other site 479436001333 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436001334 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 479436001335 dimer interface [polypeptide binding]; other site 479436001336 pyridoxal binding site [chemical binding]; other site 479436001337 ATP binding site [chemical binding]; other site 479436001338 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 479436001339 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 479436001340 dimer interface [polypeptide binding]; other site 479436001341 conserved gate region; other site 479436001342 putative PBP binding loops; other site 479436001343 ABC-ATPase subunit interface; other site 479436001344 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 479436001345 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 479436001346 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 479436001347 putative PBP binding loops; other site 479436001348 dimer interface [polypeptide binding]; other site 479436001349 ABC-ATPase subunit interface; other site 479436001350 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 479436001351 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 479436001352 Walker A/P-loop; other site 479436001353 ATP binding site [chemical binding]; other site 479436001354 Q-loop/lid; other site 479436001355 ABC transporter signature motif; other site 479436001356 Walker B; other site 479436001357 D-loop; other site 479436001358 H-loop/switch region; other site 479436001359 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 479436001360 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 479436001361 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 479436001362 Walker A/P-loop; other site 479436001363 ATP binding site [chemical binding]; other site 479436001364 Q-loop/lid; other site 479436001365 ABC transporter signature motif; other site 479436001366 Walker B; other site 479436001367 D-loop; other site 479436001368 H-loop/switch region; other site 479436001369 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 479436001370 Beta-lactamase class A [Defense mechanisms]; Region: PenP; COG2367 479436001371 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 479436001372 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 479436001373 peptide binding site [polypeptide binding]; other site 479436001374 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 479436001375 dimer interface [polypeptide binding]; other site 479436001376 catalytic triad [active] 479436001377 M20 Peptidase Aminoacylase 1-like protein 2-like, amidohydrolase subfamily; Region: M20_ACY1L2_like; cd05672 479436001378 amidohydrolase; Region: amidohydrolases; TIGR01891 479436001379 metal binding site [ion binding]; metal-binding site 479436001380 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 479436001381 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001382 Walker A/P-loop; other site 479436001383 ATP binding site [chemical binding]; other site 479436001384 Q-loop/lid; other site 479436001385 ABC transporter signature motif; other site 479436001386 Walker B; other site 479436001387 D-loop; other site 479436001388 H-loop/switch region; other site 479436001389 ABC transporter; Region: ABC_tran_2; pfam12848 479436001390 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 479436001391 GTP cyclohydrolase I; Provisional; Region: PLN03044 479436001392 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 479436001393 active site 479436001394 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 479436001395 dihydropteroate synthase; Region: DHPS; TIGR01496 479436001396 substrate binding pocket [chemical binding]; other site 479436001397 dimer interface [polypeptide binding]; other site 479436001398 inhibitor binding site; inhibition site 479436001399 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 479436001400 homooctamer interface [polypeptide binding]; other site 479436001401 active site 479436001402 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 479436001403 catalytic center binding site [active] 479436001404 ATP binding site [chemical binding]; other site 479436001405 L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; Region: HicDH_like; cd05291 479436001406 tetramer (dimer of dimers) interface [polypeptide binding]; other site 479436001407 L-lactate dehydrogenase; Region: L-LDH-NAD; TIGR01771 479436001408 NAD binding site [chemical binding]; other site 479436001409 dimer interface [polypeptide binding]; other site 479436001410 substrate binding site [chemical binding]; other site 479436001411 hypothetical protein; Provisional; Region: PRK08582 479436001412 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_hs4; cd05692 479436001413 RNA binding site [nucleotide binding]; other site 479436001414 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 479436001415 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 479436001416 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 479436001417 Ligand Binding Site [chemical binding]; other site 479436001418 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001419 FtsH Extracellular; Region: FtsH_ext; pfam06480 479436001420 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 479436001421 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 479436001422 Walker A motif; other site 479436001423 ATP binding site [chemical binding]; other site 479436001424 Walker B motif; other site 479436001425 arginine finger; other site 479436001426 Peptidase family M41; Region: Peptidase_M41; pfam01434 479436001427 Uncharacterized conserved protein [Function unknown]; Region: COG2966 479436001428 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 479436001429 Protein of unknown function (DUF1212); Region: DUF1212; cl01118 479436001430 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436001431 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 479436001432 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 479436001433 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 479436001434 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 479436001435 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 479436001436 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 479436001437 FMN binding site [chemical binding]; other site 479436001438 active site 479436001439 catalytic residues [active] 479436001440 substrate binding site [chemical binding]; other site 479436001441 domain; Region: GreA_GreB_N; pfam03449 479436001442 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 479436001443 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 479436001444 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 479436001445 dimer interface [polypeptide binding]; other site 479436001446 putative anticodon binding site; other site 479436001447 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 479436001448 motif 1; other site 479436001449 active site 479436001450 motif 2; other site 479436001451 motif 3; other site 479436001452 Permease family; Region: Xan_ur_permease; cl00967 479436001453 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 479436001454 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 479436001455 active site 479436001456 Cation efflux family; Region: Cation_efflux; cl00316 479436001457 seryl-tRNA synthetase; Provisional; Region: PRK05431 479436001458 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 479436001459 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 bound...; Region: SerRS_core; cd00770 479436001460 dimer interface [polypeptide binding]; other site 479436001461 active site 479436001462 motif 1; other site 479436001463 motif 2; other site 479436001464 motif 3; other site 479436001465 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 479436001466 active site 479436001467 intersubunit interactions; other site 479436001468 catalytic residue [active] 479436001469 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 479436001470 putative active site [active] 479436001471 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 479436001472 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 479436001473 hinge; other site 479436001474 active site 479436001475 rod shape-determining protein MreB; Provisional; Region: PRK13930 479436001476 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 479436001477 ATP binding site [chemical binding]; other site 479436001478 profilin binding site; other site 479436001479 Exopolysaccharide biosynthesis protein related to N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [Carbohydrate transport and metabolism]; Region: EpsL; COG4632 479436001480 SpoIVB peptidase S55; Region: Peptidase_S55; pfam05580 479436001481 Domain of unknown function DUF140; Region: DUF140; cl00510 479436001482 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 479436001483 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 479436001484 Walker A/P-loop; other site 479436001485 ATP binding site [chemical binding]; other site 479436001486 Q-loop/lid; other site 479436001487 ABC transporter signature motif; other site 479436001488 Walker B; other site 479436001489 D-loop; other site 479436001490 H-loop/switch region; other site 479436001491 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 479436001492 mce related protein; Region: MCE; cl15431 479436001493 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 479436001494 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 479436001495 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 479436001496 Family of unknown function (DUF490); Region: DUF490; pfam04357 479436001497 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 479436001498 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 479436001499 Surface antigen; Region: Bac_surface_Ag; cl03097 479436001500 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 479436001501 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 479436001502 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 479436001503 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 479436001504 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 479436001505 trimer interface [polypeptide binding]; other site 479436001506 active site 479436001507 UDP-GlcNAc binding site [chemical binding]; other site 479436001508 lipid binding site [chemical binding]; lipid-binding site 479436001509 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 479436001510 putative acyl-acceptor binding pocket; other site 479436001511 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 479436001512 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 479436001513 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 479436001514 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 479436001515 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 479436001516 active site 479436001517 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 479436001518 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 479436001519 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 479436001520 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 479436001521 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 479436001522 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 479436001523 Walker A/P-loop; other site 479436001524 ATP binding site [chemical binding]; other site 479436001525 Q-loop/lid; other site 479436001526 ABC transporter signature motif; other site 479436001527 Walker B; other site 479436001528 D-loop; other site 479436001529 H-loop/switch region; other site 479436001530 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 479436001531 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 479436001532 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 479436001533 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 479436001534 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 479436001535 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 479436001536 Ligand binding site; other site 479436001537 oligomer interface; other site 479436001538 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 479436001539 NeuB family; Region: NeuB; cl00496 479436001540 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 479436001541 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 479436001542 putative active site [active] 479436001543 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 479436001544 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 479436001545 active site 479436001546 motif I; other site 479436001547 motif II; other site 479436001548 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 479436001549 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 479436001550 putative acyl-acceptor binding pocket; other site 479436001551 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 479436001552 OstA-like protein; Region: OstA; cl00844 479436001553 OstA-like protein; Region: OstA; cl00844 479436001554 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 479436001555 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 479436001556 Walker A/P-loop; other site 479436001557 ATP binding site [chemical binding]; other site 479436001558 Q-loop/lid; other site 479436001559 ABC transporter signature motif; other site 479436001560 Walker B; other site 479436001561 D-loop; other site 479436001562 H-loop/switch region; other site 479436001563 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 479436001564 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 479436001565 Protein of unknown function (DUF3084); Region: DUF3084; pfam11283 479436001566 Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]; Region: COG4372 479436001567 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cl01482 479436001568 dimer interface [polypeptide binding]; other site 479436001569 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 479436001570 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 479436001571 Uncharacterized conserved protein [Function unknown]; Region: COG1284 479436001572 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 479436001573 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 479436001574 Catalytic site [active] 479436001575 S-layer homology domain; Region: SLH; pfam00395 479436001576 S-layer homology domain; Region: SLH; pfam00395 479436001577 S-layer homology domain; Region: SLH; pfam00395 479436001578 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 479436001579 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 479436001580 active site 479436001581 motif I; other site 479436001582 motif II; other site 479436001583 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001584 Predicted P-loop-containing kinase [General function prediction only]; Region: COG1660 479436001585 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 479436001586 Uncharacterised protein family UPF0052; Region: UPF0052; pfam01933 479436001587 phosphate binding site [ion binding]; other site 479436001588 putative substrate binding pocket [chemical binding]; other site 479436001589 dimer interface [polypeptide binding]; other site 479436001590 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 479436001591 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 479436001592 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 479436001593 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 479436001594 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001595 dihydroorotase; Validated; Region: pyrC; PRK09357 479436001596 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 479436001597 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 479436001598 active site 479436001599 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 479436001600 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 479436001601 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 479436001602 catalytic site [active] 479436001603 subunit interface [polypeptide binding]; other site 479436001604 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 479436001605 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 479436001606 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 479436001607 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 479436001608 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 479436001609 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 479436001610 IMP binding site; other site 479436001611 dimer interface [polypeptide binding]; other site 479436001612 interdomain contacts; other site 479436001613 partial ornithine binding site; other site 479436001614 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 479436001615 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 479436001616 FAD binding pocket [chemical binding]; other site 479436001617 FAD binding motif [chemical binding]; other site 479436001618 phosphate binding motif [ion binding]; other site 479436001619 beta-alpha-beta structure motif; other site 479436001620 NAD binding pocket [chemical binding]; other site 479436001621 Iron coordination center [ion binding]; other site 479436001622 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 479436001623 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 479436001624 heterodimer interface [polypeptide binding]; other site 479436001625 active site 479436001626 FMN binding site [chemical binding]; other site 479436001627 homodimer interface [polypeptide binding]; other site 479436001628 substrate binding site [chemical binding]; other site 479436001629 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436001630 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436001631 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 479436001632 dimerization interface [polypeptide binding]; other site 479436001633 Uncharacterized conserved protein [Function unknown]; Region: COG1739 479436001634 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 479436001635 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 479436001636 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 479436001637 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 479436001638 metal-binding site [ion binding] 479436001639 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 479436001640 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436001641 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 479436001642 pyridine nucleotide-disulfide oxidoreductase; Provisional; Region: PRK07251 479436001643 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001644 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 479436001645 Putative helix-turn-helix protein, YlxM / p13 like; Region: UPF0122; pfam04297 479436001646 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; cl15358 479436001647 signal recognition particle protein; Provisional; Region: PRK10867 479436001648 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 479436001649 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 479436001650 P loop; other site 479436001651 GTP binding site [chemical binding]; other site 479436001652 Signal peptide binding domain; Region: SRP_SPB; pfam02978 479436001653 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 479436001654 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837; cl00794 479436001655 Protein of unknown function (DUF2869); Region: DUF2869; pfam11068 479436001656 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 479436001657 RimM N-terminal domain; Region: RimM; pfam01782 479436001658 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 479436001659 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 479436001660 Glutathionylspermidine synthase; Region: GSP_synth; cl00503 479436001661 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 479436001662 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 479436001663 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 479436001664 Domain of unknown function DUF28; Region: DUF28; cl00361 479436001665 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 479436001666 active site 479436001667 putative DNA-binding cleft [nucleotide binding]; other site 479436001668 dimer interface [polypeptide binding]; other site 479436001669 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 479436001670 RuvA N terminal domain; Region: RuvA_N; pfam01330 479436001671 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 479436001672 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 479436001673 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 479436001674 Walker A motif; other site 479436001675 ATP binding site [chemical binding]; other site 479436001676 Walker B motif; other site 479436001677 arginine finger; other site 479436001678 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 479436001679 hypothetical protein; Reviewed; Region: PRK11901 479436001680 Stage II sporulation protein; Region: SpoIID; pfam08486 479436001681 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 479436001682 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 479436001683 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 479436001684 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 479436001685 Preprotein translocase subunit; Region: YajC; cl00806 479436001686 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 479436001687 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 479436001688 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 479436001689 Protein export membrane protein; Region: SecD_SecF; cl14618 479436001690 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 479436001691 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 479436001692 Protein export membrane protein; Region: SecD_SecF; cl14618 479436001693 Major Facilitator Superfamily; Region: MFS_1; pfam07690 479436001694 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 479436001695 putative substrate translocation pore; other site 479436001696 TOBE domain; Region: TOBE_2; cl01440 479436001697 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 479436001698 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 479436001699 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 479436001700 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 479436001701 3D domain; Region: 3D; cl01439 479436001702 pur operon repressor; Provisional; Region: PRK09213 479436001703 Bacterial purine repressor, N-terminal; Region: PuR_N; pfam09182 479436001704 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001705 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 479436001706 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 479436001707 Substrate binding site; other site 479436001708 Mg++ binding site; other site 479436001709 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 479436001710 active site 479436001711 substrate binding site [chemical binding]; other site 479436001712 CoA binding site [chemical binding]; other site 479436001713 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 479436001714 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436001715 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 479436001716 putative active site [active] 479436001717 catalytic residue [active] 479436001718 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 479436001719 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 479436001720 homodimer interface [polypeptide binding]; other site 479436001721 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436001722 catalytic residue [active] 479436001723 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 479436001724 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 479436001725 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 479436001726 TMP-binding site; other site 479436001727 ATP-binding site [chemical binding]; other site 479436001728 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 479436001729 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001730 PSP1 C-terminal conserved region; Region: PSP1; cl00770 479436001731 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 479436001732 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 479436001733 S-adenosylmethionine binding site [chemical binding]; other site 479436001734 Predicted methyltransferases [General function prediction only]; Region: COG0313 479436001735 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 479436001736 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 479436001737 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 479436001738 HIGH motif; other site 479436001739 active site 479436001740 KMSKS motif; other site 479436001741 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 479436001742 tRNA binding surface [nucleotide binding]; other site 479436001743 anticodon binding site; other site 479436001744 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 479436001745 dimer interface [polypeptide binding]; other site 479436001746 putative tRNA-binding site [nucleotide binding]; other site 479436001747 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 479436001748 active site 479436001749 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 479436001750 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 479436001751 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 479436001752 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 479436001753 Polyphosphate kinase; Region: PP_kinase; pfam02503 479436001754 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 479436001755 putative domain interface [polypeptide binding]; other site 479436001756 putative active site [active] 479436001757 catalytic site [active] 479436001758 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 479436001759 putative domain interface [polypeptide binding]; other site 479436001760 putative active site [active] 479436001761 catalytic site [active] 479436001762 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3583 479436001763 Domain of unknown function (DUF348); Region: DUF348; pfam03990 479436001764 G5 domain; Region: G5; pfam07501 479436001765 3D domain; Region: 3D; cl01439 479436001766 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 479436001767 SelR domain; Region: SelR; cl00369 479436001768 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 479436001769 substrate binding site [chemical binding]; other site 479436001770 THF binding site; other site 479436001771 zinc-binding site [ion binding]; other site 479436001772 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436001773 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436001774 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 479436001775 dimerization interface [polypeptide binding]; other site 479436001776 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 479436001777 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 479436001778 putative active site [active] 479436001779 putative metal binding site [ion binding]; other site 479436001780 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 479436001781 S-adenosylmethionine binding site [chemical binding]; other site 479436001782 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 479436001783 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 479436001784 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and...; Region: RF3; cd04169 479436001785 G1 box; other site 479436001786 putative GEF interaction site [polypeptide binding]; other site 479436001787 GTP/Mg2+ binding site [chemical binding]; other site 479436001788 Switch I region; other site 479436001789 G2 box; other site 479436001790 G3 box; other site 479436001791 Switch II region; other site 479436001792 G4 box; other site 479436001793 G5 box; other site 479436001794 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 479436001795 DNA topoisomerase III; Provisional; Region: PRK07726 479436001796 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 479436001797 active site 479436001798 putative interdomain interaction site [polypeptide binding]; other site 479436001799 putative metal-binding site [ion binding]; other site 479436001800 putative nucleotide binding site [chemical binding]; other site 479436001801 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 479436001802 domain I; other site 479436001803 DNA binding groove [nucleotide binding] 479436001804 phosphate binding site [ion binding]; other site 479436001805 domain II; other site 479436001806 domain III; other site 479436001807 nucleotide binding site [chemical binding]; other site 479436001808 catalytic site [active] 479436001809 domain IV; other site 479436001810 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 479436001811 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 479436001812 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 479436001813 ATP binding site [chemical binding]; other site 479436001814 Mg++ binding site [ion binding]; other site 479436001815 motif III; other site 479436001816 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 479436001817 nucleotide binding region [chemical binding]; other site 479436001818 ATP-binding site [chemical binding]; other site 479436001819 FeoA domain; Region: FeoA; cl00838 479436001820 Ferrous iron transport protein B; Region: FeoB_N; pfam02421 479436001821 Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this...; Region: FeoB; cd01879 479436001822 G1 box; other site 479436001823 GTP/Mg2+ binding site [chemical binding]; other site 479436001824 Switch I region; other site 479436001825 G2 box; other site 479436001826 G3 box; other site 479436001827 Switch II region; other site 479436001828 G4 box; other site 479436001829 G5 box; other site 479436001830 Nucleoside recognition; Region: Gate; cl00486 479436001831 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 479436001832 Nucleoside recognition; Region: Gate; cl00486 479436001833 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 479436001834 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 479436001835 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436001836 Predicted membrane protein [Function unknown]; Region: COG4684 479436001837 rSAM-modified six-cysteine peptide SCIFF; Region: six_Cys_in_45; TIGR03973 479436001838 six-Cys-in-45 modification radical SAM protein; Region: rSAM_six_Cys; TIGR03974 479436001839 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 479436001840 FeS/SAM binding site; other site 479436001841 radical SAM additional 4Fe4S-binding domain; Region: rSAM_more_4Fe4S; TIGR04085 479436001842 Acylphosphatase; Region: Acylphosphatase; cl00551 479436001843 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 479436001844 HypF finger; Region: zf-HYPF; pfam07503 479436001845 HypF finger; Region: zf-HYPF; pfam07503 479436001846 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 479436001847 HupF/HypC family; Region: HupF_HypC; cl00394 479436001848 Hydrogenase formation hypA family; Region: HypD; cl12072 479436001849 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypD; COG0409 479436001850 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 479436001851 dimerization interface [polypeptide binding]; other site 479436001852 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 479436001853 ATP binding site [chemical binding]; other site 479436001854 OstA-like protein; Region: OstA; cl00844 479436001855 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 479436001856 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 479436001857 active site 479436001858 tetramer interface; other site 479436001859 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 479436001860 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 479436001861 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 479436001862 dimer interface [polypeptide binding]; other site 479436001863 active site 479436001864 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 479436001865 Acetyl-CoA Synthetase and similar proteins; Region: Acetyl-CoA_Synthetase; cl15355 479436001866 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 479436001867 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 479436001868 putative deacylase active site [active] 479436001869 Caulimovirus viroplasmin; Region: Cauli_VI; pfam01693 479436001870 Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Region: RNase_HI_bacteria_HBD; cd09277 479436001871 RNA/DNA hybrid binding site [nucleotide binding]; other site 479436001872 active site 479436001873 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 479436001874 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001875 NAD(P) binding site [chemical binding]; other site 479436001876 active site 479436001877 Protein of unknown function (DUF1294); Region: DUF1294; cl01311 479436001878 glucose-6-phosphate isomerase; Provisional; Region: PRK00973 479436001879 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 479436001880 active site 479436001881 dimer interface [polypeptide binding]; other site 479436001882 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 479436001883 dimer interface [polypeptide binding]; other site 479436001884 active site 479436001885 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 479436001886 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 479436001887 NAD binding site [chemical binding]; other site 479436001888 homodimer interface [polypeptide binding]; other site 479436001889 active site 479436001890 substrate binding site [chemical binding]; other site 479436001891 type III secretion outer membrane pore, YscC/HrcC family; Region: type_III_yscC; TIGR02516 479436001892 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 479436001893 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 479436001894 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 479436001895 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001896 Walker A/P-loop; other site 479436001897 ATP binding site [chemical binding]; other site 479436001898 Q-loop/lid; other site 479436001899 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 479436001900 ABC transporter signature motif; other site 479436001901 Walker B; other site 479436001902 D-loop; other site 479436001903 ABC transporter; Region: ABC_tran_2; pfam12848 479436001904 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 479436001905 ABC transporter; Region: ABC_tran_2; pfam12848 479436001906 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 479436001907 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 479436001908 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 479436001909 TM-ABC transporter signature motif; other site 479436001910 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 479436001911 TM-ABC transporter signature motif; other site 479436001912 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 479436001913 The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E; Region: ABC_Mj1267_LivG_branched; cd03219 479436001914 Walker A/P-loop; other site 479436001915 ATP binding site [chemical binding]; other site 479436001916 Q-loop/lid; other site 479436001917 ABC transporter signature motif; other site 479436001918 Walker B; other site 479436001919 D-loop; other site 479436001920 H-loop/switch region; other site 479436001921 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 479436001922 LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a...; Region: ABC_TM1139_LivF_branched; cd03224 479436001923 Walker A/P-loop; other site 479436001924 ATP binding site [chemical binding]; other site 479436001925 Q-loop/lid; other site 479436001926 ABC transporter signature motif; other site 479436001927 Walker B; other site 479436001928 D-loop; other site 479436001929 H-loop/switch region; other site 479436001930 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 479436001931 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 479436001932 SLBB domain; Region: SLBB; pfam10531 479436001933 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 479436001934 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 479436001935 NAD(P) binding site [chemical binding]; other site 479436001936 homodimer interface [polypeptide binding]; other site 479436001937 substrate binding site [chemical binding]; other site 479436001938 active site 479436001939 Chain length determinant protein; Region: Wzz; cl01623 479436001940 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 479436001941 capsular exopolysaccharide family; Region: eps_fam; TIGR01007 479436001942 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436001943 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 479436001944 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 479436001945 inhibitor-cofactor binding pocket; inhibition site 479436001946 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436001947 catalytic residue [active] 479436001948 Bacterial sugar transferase; Region: Bac_transf; cl00939 479436001949 LicD family; Region: LicD; cl01378 479436001950 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 479436001951 substrate binding site; other site 479436001952 dimer interface; other site 479436001953 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001954 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 479436001955 NAD(P) binding site [chemical binding]; other site 479436001956 active site 479436001957 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 479436001958 This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be...; Region: GT1_amsD_like; cd03820 479436001959 putative ADP-binding pocket [chemical binding]; other site 479436001960 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 479436001961 O-Antigen ligase; Region: Wzy_C; cl04850 479436001962 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 479436001963 putative active site [active] 479436001964 putative metal binding site [ion binding]; other site 479436001965 MatE; Region: MatE; cl10513 479436001966 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 479436001967 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001968 NAD(P) binding site [chemical binding]; other site 479436001969 active site 479436001970 UDP-glucose 6-dehydrogenase; Provisional; Region: PRK15057 479436001971 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001972 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 479436001973 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436001974 VanZ like family; Region: VanZ; cl01971 479436001975 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 479436001976 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 479436001977 ATP cone domain; Region: ATP-cone; pfam03477 479436001978 Class III ribonucleotide reductase; Region: RNR_III; cd01675 479436001979 effector binding site; other site 479436001980 active site 479436001981 Zn binding site [ion binding]; other site 479436001982 glycine loop; other site 479436001983 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; cl15367 479436001984 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG; TIGR02491 479436001985 Putative ClC chloride channel. Clc proteins are putative halogen ion (Cl-, Br- and I-) transporters found in eubacteria. They belong to the ClC superfamily of halogen ion channels, which share a unique double-barreled architecture and voltage-dependent...; Region: ClC_like; cd01033 479436001986 putative ion selectivity filter; other site 479436001987 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 479436001988 putative pore gating glutamate residue; other site 479436001989 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 479436001990 trimer interface [polypeptide binding]; other site 479436001991 putative metal binding site [ion binding]; other site 479436001992 putative enoyl-(acyl-carrier-protein) reductase II; Region: enACPred_II; TIGR03151 479436001993 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 479436001994 FMN binding site [chemical binding]; other site 479436001995 substrate binding site [chemical binding]; other site 479436001996 putative catalytic residue [active] 479436001997 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 479436001998 Rubredoxin; Region: Rubredoxin; pfam00301 479436001999 iron binding site [ion binding]; other site 479436002000 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 479436002001 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 479436002002 fatty acid biosynthesis transcriptional regulator; Provisional; Region: PRK04424 479436002003 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 479436002004 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 479436002005 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 479436002006 dimer interface [polypeptide binding]; other site 479436002007 active site 479436002008 CoA binding pocket [chemical binding]; other site 479436002009 putative enoyl-(acyl-carrier-protein) reductase II; Region: enACPred_II; TIGR03151 479436002010 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 479436002011 FMN binding site [chemical binding]; other site 479436002012 substrate binding site [chemical binding]; other site 479436002013 putative catalytic residue [active] 479436002014 Acyl transferase domain; Region: Acyl_transf_1; cl08282 479436002015 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 479436002016 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 479436002017 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 479436002018 NAD(P) binding site [chemical binding]; other site 479436002019 homotetramer interface [polypeptide binding]; other site 479436002020 homodimer interface [polypeptide binding]; other site 479436002021 active site 479436002022 Phosphopantetheine attachment site; Region: PP-binding; cl09936 479436002023 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 479436002024 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 479436002025 FMN binding site [chemical binding]; other site 479436002026 substrate binding site [chemical binding]; other site 479436002027 putative catalytic residue [active] 479436002028 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 479436002029 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 479436002030 dimer interface [polypeptide binding]; other site 479436002031 active site 479436002032 ribonuclease III; Reviewed; Region: rnc; PRK00102 479436002033 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 479436002034 dimerization interface [polypeptide binding]; other site 479436002035 active site 479436002036 metal binding site [ion binding]; metal-binding site 479436002037 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 479436002038 dsRNA binding site [nucleotide binding]; other site 479436002039 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 479436002040 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 479436002041 FeS/SAM binding site; other site 479436002042 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 479436002043 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 479436002044 Walker A/P-loop; other site 479436002045 ATP binding site [chemical binding]; other site 479436002046 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 479436002047 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 479436002048 Q-loop/lid; other site 479436002049 ABC transporter signature motif; other site 479436002050 Walker B; other site 479436002051 D-loop; other site 479436002052 H-loop/switch region; other site 479436002053 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 479436002054 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 479436002055 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002056 excinuclease ABC subunit B; Provisional; Region: PRK05298 479436002057 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 479436002058 ATP binding site [chemical binding]; other site 479436002059 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 479436002060 nucleotide binding region [chemical binding]; other site 479436002061 ATP-binding site [chemical binding]; other site 479436002062 Ultra-violet resistance protein B; Region: UvrB; pfam12344 479436002063 UvrB/uvrC motif; Region: UVR; pfam02151 479436002064 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 479436002065 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 479436002066 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 479436002067 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 479436002068 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 479436002069 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 479436002070 GIY-YIG motif/motif A; other site 479436002071 active site 479436002072 catalytic site [active] 479436002073 putative DNA binding site [nucleotide binding]; other site 479436002074 metal binding site [ion binding]; metal-binding site 479436002075 UvrB/uvrC motif; Region: UVR; pfam02151 479436002076 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 479436002077 multidrug efflux protein; Reviewed; Region: PRK01766 479436002078 MatE; Region: MatE; cl10513 479436002079 MatE; Region: MatE; cl10513 479436002080 Integral membrane protein TerC family; Region: TerC; cl10468 479436002081 Integral membrane protein TerC family; Region: TerC; cl10468 479436002082 TRAM domain; Region: TRAM; cl01282 479436002083 23S rRNA (uracil-5-)-methyltransferase RumA; Region: rumA; TIGR00479 479436002084 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 479436002085 S-adenosylmethionine binding site [chemical binding]; other site 479436002086 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 479436002087 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 479436002088 N-terminal plug; other site 479436002089 ligand-binding site [chemical binding]; other site 479436002090 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 479436002091 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 479436002092 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 479436002093 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 479436002094 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 479436002095 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 479436002096 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 479436002097 SMI1 / KNR4 family; Region: SMI1_KNR4; cl01747 479436002098 Domain of unknown function (DUF1704); Region: DUF1704; cl06858 479436002099 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cl00022 479436002100 putative deacylase active site [active] 479436002101 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 479436002102 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 479436002103 Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly...; Region: Macro; cl00019 479436002104 ADP-ribose binding site [chemical binding]; other site 479436002105 SIR2 superfamily 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; cl00195 479436002106 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 479436002107 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 479436002108 DNA binding site [nucleotide binding] 479436002109 active site 479436002110 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 479436002111 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 479436002112 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 479436002113 homodimer interface [polypeptide binding]; other site 479436002114 substrate-cofactor binding pocket; other site 479436002115 catalytic residue [active] 479436002116 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 479436002117 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 479436002118 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 479436002119 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 479436002120 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 479436002121 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436002122 homodimer interface [polypeptide binding]; other site 479436002123 catalytic residue [active] 479436002124 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 479436002125 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 479436002126 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; cl15357 479436002127 transmembrane helices; other site 479436002128 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 479436002129 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 479436002130 active site 479436002131 metal binding site [ion binding]; metal-binding site 479436002132 pyruvate carboxylase; Reviewed; Region: PRK12999 479436002133 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 479436002134 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 479436002135 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 479436002136 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 479436002137 active site 479436002138 catalytic residues [active] 479436002139 metal binding site [ion binding]; metal-binding site 479436002140 homodimer binding site [polypeptide binding]; other site 479436002141 Conserved carboxylase domain; Region: PYC_OADA; pfam02436 479436002142 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 479436002143 carboxyltransferase (CT) interaction site; other site 479436002144 biotinylation site [posttranslational modification]; other site 479436002145 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 479436002146 ATP cone domain; Region: ATP-cone; pfam03477 479436002147 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 479436002148 active site 479436002149 dimer interface [polypeptide binding]; other site 479436002150 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 479436002151 dimer interface [polypeptide binding]; other site 479436002152 active site 479436002153 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional; Region: PRK11316 479436002154 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 479436002155 putative ribose interaction site [chemical binding]; other site 479436002156 putative ADP binding site [chemical binding]; other site 479436002157 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436002158 active site 479436002159 HIGH motif; other site 479436002160 nucleotide binding site [chemical binding]; other site 479436002161 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 479436002162 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 479436002163 NADP binding site [chemical binding]; other site 479436002164 homopentamer interface [polypeptide binding]; other site 479436002165 substrate binding site [chemical binding]; other site 479436002166 active site 479436002167 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 479436002168 active site 479436002169 motif I; other site 479436002170 motif II; other site 479436002171 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 479436002172 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 479436002173 putative active site [active] 479436002174 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 479436002175 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 479436002176 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 479436002177 putative active site [active] 479436002178 DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; Region: ERI-1_3'hExo_like; cd06133 479436002179 active site 479436002180 substrate binding site [chemical binding]; other site 479436002181 catalytic site [active] 479436002182 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 479436002183 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 479436002184 oligomer interface [polypeptide binding]; other site 479436002185 putative active site [active] 479436002186 metal binding site [ion binding]; metal-binding site 479436002187 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 479436002188 zinc binding site [ion binding]; other site 479436002189 putative ligand binding site [chemical binding]; other site 479436002190 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 479436002191 zinc binding site [ion binding]; other site 479436002192 putative ligand binding site [chemical binding]; other site 479436002193 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 479436002194 TM-ABC transporter signature motif; other site 479436002195 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 479436002196 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002197 Walker A/P-loop; other site 479436002198 ATP binding site [chemical binding]; other site 479436002199 Q-loop/lid; other site 479436002200 ABC transporter signature motif; other site 479436002201 Walker B; other site 479436002202 D-loop; other site 479436002203 H-loop/switch region; other site 479436002204 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 479436002205 16S/18S rRNA binding site [nucleotide binding]; other site 479436002206 S13e-L30e interaction site [polypeptide binding]; other site 479436002207 25S rRNA binding site [nucleotide binding]; other site 479436002208 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 479436002209 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 479436002210 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 479436002211 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 479436002212 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 479436002213 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 479436002214 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 479436002215 putative nucleic acid binding region [nucleotide binding]; other site 479436002216 G-X-X-G motif; other site 479436002217 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 479436002218 RNA binding site [nucleotide binding]; other site 479436002219 domain interface; other site 479436002220 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 479436002221 trimer interface [polypeptide binding]; other site 479436002222 active site 479436002223 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 479436002224 S-adenosylmethionine binding site [chemical binding]; other site 479436002225 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 479436002226 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 479436002227 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 479436002228 dimer interface [polypeptide binding]; other site 479436002229 ADP-ribose binding site [chemical binding]; other site 479436002230 active site 479436002231 nudix motif; other site 479436002232 metal binding site [ion binding]; metal-binding site 479436002233 Sulfatase; Region: Sulfatase; cl10460 479436002234 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 479436002235 Permease family; Region: Xan_ur_permease; cl00967 479436002236 Adenine deaminase [Nucleotide transport and metabolism]; Region: AdeC; COG1001 479436002237 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 479436002238 Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source...; Region: AdeC; cd01295 479436002239 active site 479436002240 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 479436002241 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002242 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 479436002243 active site 479436002244 metal binding site [ion binding]; metal-binding site 479436002245 RNA ligase; Region: RNA_lig_T4_1; cl09743 479436002246 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 479436002247 DNA polymerase I; Provisional; Region: PRK05755 479436002248 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 479436002249 active site 479436002250 metal binding site 1 [ion binding]; metal-binding site 479436002251 putative 5' ssDNA interaction site; other site 479436002252 metal binding site 3; metal-binding site 479436002253 metal binding site 2 [ion binding]; metal-binding site 479436002254 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 479436002255 putative DNA binding site [nucleotide binding]; other site 479436002256 putative metal binding site [ion binding]; other site 479436002257 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 479436002258 active site 479436002259 DNA binding site [nucleotide binding] 479436002260 catalytic site [active] 479436002261 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 479436002262 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 479436002263 CoA-binding site [chemical binding]; other site 479436002264 ATP-binding [chemical binding]; other site 479436002265 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 479436002266 N-acetyl-D-glucosamine binding site [chemical binding]; other site 479436002267 catalytic residue [active] 479436002268 Uncharacterised BCR, YhbC family COG0779; Region: DUF150; pfam02576 479436002269 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 479436002270 YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix...; Region: YlxS_C; cd01734 479436002271 Sm1 motif; other site 479436002272 predicted subunit interaction site [polypeptide binding]; other site 479436002273 RNA binding pocket [nucleotide binding]; other site 479436002274 Sm2 motif; other site 479436002275 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 479436002276 NusA N-terminal domain; Region: NusA_N; pfam08529 479436002277 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 479436002278 RNA binding site [nucleotide binding]; other site 479436002279 homodimer interface [polypeptide binding]; other site 479436002280 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 479436002281 G-X-X-G motif; other site 479436002282 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 479436002283 putative RNA binding cleft [nucleotide binding]; other site 479436002284 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 479436002285 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 479436002286 translation initiation factor IF-2; Region: IF-2; TIGR00487 479436002287 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 479436002288 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases; Region: IF2_eIF5B; cd01887 479436002289 G1 box; other site 479436002290 putative GEF interaction site [polypeptide binding]; other site 479436002291 GTP/Mg2+ binding site [chemical binding]; other site 479436002292 Switch I region; other site 479436002293 G2 box; other site 479436002294 G3 box; other site 479436002295 Switch II region; other site 479436002296 G4 box; other site 479436002297 G5 box; other site 479436002298 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 479436002299 Translation-initiation factor 2; Region: IF-2; pfam11987 479436002300 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 479436002301 Ribosome-binding factor A; Region: RBFA; cl00542 479436002302 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 479436002303 DHH family; Region: DHH; pfam01368 479436002304 DHHA1 domain; Region: DHHA1; pfam02272 479436002305 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 479436002306 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 479436002307 RNA binding site [nucleotide binding]; other site 479436002308 active site 479436002309 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 479436002310 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 479436002311 active site 479436002312 Riboflavin kinase; Region: Flavokinase; cl03312 479436002313 Chorismate mutase type II; Region: CM_2; cl00693 479436002314 shikimate kinase; Reviewed; Region: aroK; PRK00131 479436002315 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 479436002316 ADP binding site [chemical binding]; other site 479436002317 magnesium binding site [ion binding]; other site 479436002318 putative shikimate binding site; other site 479436002319 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 479436002320 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 479436002321 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436002322 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 479436002323 Zn2+ binding site [ion binding]; other site 479436002324 Mg2+ binding site [ion binding]; other site 479436002325 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 479436002326 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 479436002327 substrate binding pocket [chemical binding]; other site 479436002328 membrane-bound complex binding site; other site 479436002329 hinge residues; other site 479436002330 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 479436002331 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 479436002332 dimer interface [polypeptide binding]; other site 479436002333 conserved gate region; other site 479436002334 putative PBP binding loops; other site 479436002335 ABC-ATPase subunit interface; other site 479436002336 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 479436002337 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 479436002338 Walker A/P-loop; other site 479436002339 ATP binding site [chemical binding]; other site 479436002340 Q-loop/lid; other site 479436002341 ABC transporter signature motif; other site 479436002342 Walker B; other site 479436002343 D-loop; other site 479436002344 H-loop/switch region; other site 479436002345 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 479436002346 DNA-binding site [nucleotide binding]; DNA binding site 479436002347 RNA-binding motif; other site 479436002348 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 479436002349 30S subunit binding site; other site 479436002350 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 479436002351 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002352 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 479436002353 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 479436002354 nucleotide binding region [chemical binding]; other site 479436002355 ATP-binding site [chemical binding]; other site 479436002356 peptide chain release factor 2; Validated; Region: prfB; PRK00578 479436002357 RF-1 domain; Region: RF-1; cl02875 479436002358 RF-1 domain; Region: RF-1; cl02875 479436002359 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; cl09156 479436002360 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 479436002361 TPP-binding site [chemical binding]; other site 479436002362 dimer interface [polypeptide binding]; other site 479436002363 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 479436002364 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 479436002365 PYR/PP interface [polypeptide binding]; other site 479436002366 dimer interface [polypeptide binding]; other site 479436002367 TPP binding site [chemical binding]; other site 479436002368 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 479436002369 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 479436002370 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002371 Walker A/P-loop; other site 479436002372 ATP binding site [chemical binding]; other site 479436002373 Q-loop/lid; other site 479436002374 ABC transporter signature motif; other site 479436002375 Walker B; other site 479436002376 D-loop; other site 479436002377 H-loop/switch region; other site 479436002378 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 479436002379 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3883 479436002380 Peptidase family M23; Region: Peptidase_M23; pfam01551 479436002381 C-terminal peptidase (prc); Region: prc; TIGR00225 479436002382 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 479436002383 protein binding site [polypeptide binding]; other site 479436002384 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 479436002385 Catalytic dyad [active] 479436002386 GTPase CgtA; Reviewed; Region: obgE; PRK12297 479436002387 GTP1/OBG; Region: GTP1_OBG; pfam01018 479436002388 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 479436002389 G1 box; other site 479436002390 GTP/Mg2+ binding site [chemical binding]; other site 479436002391 Switch I region; other site 479436002392 G2 box; other site 479436002393 G3 box; other site 479436002394 Switch II region; other site 479436002395 G4 box; other site 479436002396 G5 box; other site 479436002397 Domain of unknown function (DUF1967); Region: DUF1967; cl07779 479436002398 CRS1 / YhbY (CRM) domain; Region: CRS1_YhbY; cl00663 479436002399 gamma-glutamyl kinase; Provisional; Region: PRK05429 479436002400 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 479436002401 nucleotide binding site [chemical binding]; other site 479436002402 homotetrameric interface [polypeptide binding]; other site 479436002403 putative phosphate binding site [ion binding]; other site 479436002404 putative allosteric binding site; other site 479436002405 PUA domain; Region: PUA; cl00607 479436002406 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 479436002407 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 479436002408 putative catalytic cysteine [active] 479436002409 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 479436002410 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 479436002411 active site 479436002412 (T/H)XGH motif; other site 479436002413 Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]; Region: COG1713 479436002414 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 479436002415 Cell envelope-related transcriptional attenuator domain; Region: LytR_cpsA_psr; cl00581 479436002416 Domain of unknown function DUF143; Region: DUF143; cl00519 479436002417 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 479436002418 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 479436002419 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 479436002420 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002421 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; cl15357 479436002422 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002423 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; cl15357 479436002424 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 479436002425 Cation transport protein; Region: TrkH; cl10514 479436002426 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436002427 Protein of unknown function (DUF523); Region: DUF523; cl00733 479436002428 Sulfatase; Region: Sulfatase; cl10460 479436002429 ScpA/B protein; Region: ScpA_ScpB; cl00598 479436002430 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 479436002431 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 479436002432 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 479436002433 RNA binding surface [nucleotide binding]; other site 479436002434 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 479436002435 active site 479436002436 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002437 flavoprotein, HI0933 family; Region: TIGR00275 479436002438 cytidylate kinase; Provisional; Region: cmk; PRK00023 479436002439 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 479436002440 CMP-binding site; other site 479436002441 The sites determining sugar specificity; other site 479436002442 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 479436002443 putative acyl-acceptor binding pocket; other site 479436002444 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed; Region: PRK00087 479436002445 LytB protein; Region: LYTB; cl00507 479436002446 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 479436002447 RNA binding site [nucleotide binding]; other site 479436002448 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 479436002449 RNA binding site [nucleotide binding]; other site 479436002450 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 479436002451 RNA binding site [nucleotide binding]; other site 479436002452 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 479436002453 RNA binding site [nucleotide binding]; other site 479436002454 domain interface; other site 479436002455 GTP-binding protein Der; Reviewed; Region: PRK00093 479436002456 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA1; cd01894 479436002457 G1 box; other site 479436002458 GTP/Mg2+ binding site [chemical binding]; other site 479436002459 Switch I region; other site 479436002460 G2 box; other site 479436002461 Switch II region; other site 479436002462 G3 box; other site 479436002463 G4 box; other site 479436002464 G5 box; other site 479436002465 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA2; cd01895 479436002466 G1 box; other site 479436002467 GTP/Mg2+ binding site [chemical binding]; other site 479436002468 Switch I region; other site 479436002469 G2 box; other site 479436002470 G3 box; other site 479436002471 Switch II region; other site 479436002472 G4 box; other site 479436002473 G5 box; other site 479436002474 Domain of unknown function (DUF205); Region: DUF205; cl00410 479436002475 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 479436002476 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002477 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 479436002478 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 479436002479 S-adenosylmethionine binding site [chemical binding]; other site 479436002480 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 479436002481 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 479436002482 active site 479436002483 (T/H)XGH motif; other site 479436002484 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 479436002485 Domain of unknown function (DUF814); Region: DUF814; pfam05670 479436002486 hypothetical protein; Provisional; Region: PRK11820 479436002487 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 479436002488 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 479436002489 Domain of unknown function (DUF370); Region: DUF370; cl00898 479436002490 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 479436002491 catalytic site [active] 479436002492 G-X2-G-X-G-K; other site 479436002493 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 479436002494 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 479436002495 Flavoprotein; Region: Flavoprotein; cl08021 479436002496 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 479436002497 putative transporter; Provisional; Region: PRK11660 479436002498 Permease family; Region: Xan_ur_permease; cl00967 479436002499 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 479436002500 S-adenosylmethionine synthetase; Validated; Region: PRK05250 479436002501 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 479436002502 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 479436002503 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 479436002504 primosome assembly protein PriA; Validated; Region: PRK05580 479436002505 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 479436002506 ATP binding site [chemical binding]; other site 479436002507 putative Mg++ binding site [ion binding]; other site 479436002508 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002509 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 479436002510 active site 479436002511 catalytic residues [active] 479436002512 metal binding site [ion binding]; metal-binding site 479436002513 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 479436002514 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 479436002515 putative active site [active] 479436002516 substrate binding site [chemical binding]; other site 479436002517 putative cosubstrate binding site; other site 479436002518 catalytic site [active] 479436002519 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 479436002520 substrate binding site [chemical binding]; other site 479436002521 Protein of unknown function DUF116; Region: DUF116; cl00800 479436002522 16S rRNA methyltransferase B; Provisional; Region: PRK14902 479436002523 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 479436002524 putative RNA binding site [nucleotide binding]; other site 479436002525 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436002526 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 479436002527 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 479436002528 FeS/SAM binding site; other site 479436002529 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 479436002530 Protein phosphatase 2C; Region: PP2C; pfam00481 479436002531 active site 479436002532 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 479436002533 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 479436002534 active site 479436002535 ATP binding site [chemical binding]; other site 479436002536 substrate binding site [chemical binding]; other site 479436002537 activation loop (A-loop); other site 479436002538 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 479436002539 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 479436002540 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 479436002541 GTPase RsgA; Reviewed; Region: PRK00098 479436002542 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs...; Region: YjeQ_engC; cd01854 479436002543 GTPase/OB domain interface [polypeptide binding]; other site 479436002544 GTPase/Zn-binding domain interface [polypeptide binding]; other site 479436002545 GTP/Mg2+ binding site [chemical binding]; other site 479436002546 G4 box; other site 479436002547 G5 box; other site 479436002548 G1 box; other site 479436002549 Switch I region; other site 479436002550 G2 box; other site 479436002551 G3 box; other site 479436002552 Switch II region; other site 479436002553 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 479436002554 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 479436002555 substrate binding site [chemical binding]; other site 479436002556 hexamer interface [polypeptide binding]; other site 479436002557 metal binding site [ion binding]; metal-binding site 479436002558 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 479436002559 rRNA interaction site [nucleotide binding]; other site 479436002560 S8 interaction site; other site 479436002561 putative laminin-1 binding site; other site 479436002562 elongation factor Ts; Reviewed; Region: tsf; PRK12332 479436002563 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 479436002564 Elongation factor TS; Region: EF_TS; pfam00889 479436002565 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 479436002566 putative nucleotide binding site [chemical binding]; other site 479436002567 uridine monophosphate binding site [chemical binding]; other site 479436002568 homohexameric interface [polypeptide binding]; other site 479436002569 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 479436002570 hinge region; other site 479436002571 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 479436002572 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 479436002573 catalytic residue [active] 479436002574 putative FPP diphosphate binding site; other site 479436002575 putative FPP binding hydrophobic cleft; other site 479436002576 dimer interface [polypeptide binding]; other site 479436002577 putative IPP diphosphate binding site; other site 479436002578 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 479436002579 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 479436002580 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 479436002581 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 479436002582 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 479436002583 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 479436002584 active site 479436002585 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 479436002586 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 479436002587 putative substrate binding region [chemical binding]; other site 479436002588 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 479436002589 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694; cl15446 479436002590 prolyl-tRNA synthetase; Provisional; Region: PRK09194 479436002591 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 479436002592 dimer interface [polypeptide binding]; other site 479436002593 motif 1; other site 479436002594 active site 479436002595 motif 2; other site 479436002596 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 479436002597 putative deacylase active site [active] 479436002598 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 attaches...; Region: class_II_aaRS-like_core; cl00268 479436002599 active site 479436002600 motif 3; other site 479436002601 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 479436002602 anticodon binding site; other site 479436002603 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 479436002604 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 479436002605 Protein of unknown function (DUF322); Region: DUF322; cl00574 479436002606 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14328 479436002607 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 479436002608 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 479436002609 FeS/SAM binding site; other site 479436002610 TRAM domain; Region: TRAM; cl01282 479436002611 Leucine carboxyl methyltransferase; Region: LCM; cl01306 479436002612 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 479436002613 MutS domain I; Region: MutS_I; pfam01624 479436002614 MutS domain II; Region: MutS_II; pfam05188 479436002615 MutS family domain IV; Region: MutS_IV; pfam05190 479436002616 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 479436002617 Walker A/P-loop; other site 479436002618 ATP binding site [chemical binding]; other site 479436002619 Q-loop/lid; other site 479436002620 ABC transporter signature motif; other site 479436002621 Walker B; other site 479436002622 D-loop; other site 479436002623 H-loop/switch region; other site 479436002624 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 479436002625 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 479436002626 ATP binding site [chemical binding]; other site 479436002627 Mg2+ binding site [ion binding]; other site 479436002628 G-X-G motif; other site 479436002629 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 479436002630 ATP binding site [chemical binding]; other site 479436002631 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 479436002632 Brix domain; Region: Brix; cl00935 479436002633 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436002634 IPP transferase; Region: IPPT; cl00403 479436002635 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 479436002636 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 479436002637 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 479436002638 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 479436002639 catalytic residue [active] 479436002640 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 479436002641 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 479436002642 Ligand Binding Site [chemical binding]; other site 479436002643 GTP-binding protein LepA; Provisional; Region: PRK05433 479436002644 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 479436002645 G1 box; other site 479436002646 putative GEF interaction site [polypeptide binding]; other site 479436002647 GTP/Mg2+ binding site [chemical binding]; other site 479436002648 Switch I region; other site 479436002649 G2 box; other site 479436002650 G3 box; other site 479436002651 Switch II region; other site 479436002652 G4 box; other site 479436002653 G5 box; other site 479436002654 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 479436002655 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 479436002656 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 479436002657 coproporphyrinogen III oxidase; Provisional; Region: PRK08599 479436002658 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 479436002659 FeS/SAM binding site; other site 479436002660 HemN C-terminal region; Region: HemN_C; pfam06969 479436002661 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 479436002662 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 479436002663 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 479436002664 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436002665 HrcA protein C terminal domain; Region: HrcA; pfam01628 479436002666 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 479436002667 dimer interface [polypeptide binding]; other site 479436002668 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 479436002669 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 479436002670 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 479436002671 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 479436002672 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 479436002673 HSP70 interaction site [polypeptide binding]; other site 479436002674 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 479436002675 substrate binding site [polypeptide binding]; other site 479436002676 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 479436002677 Zn binding sites [ion binding]; other site 479436002678 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 479436002679 dimer interface [polypeptide binding]; other site 479436002680 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 479436002681 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 479436002682 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 479436002683 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 479436002684 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 479436002685 FeS/SAM binding site; other site 479436002686 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 479436002687 nucleotide binding site/active site [active] 479436002688 HIT family signature motif; other site 479436002689 catalytic residue [active] 479436002690 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 479436002691 GatB domain; Region: GatB_Yqey; cl11497 479436002692 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 479436002693 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 479436002694 Phosphate-starvation-inducible E; Region: PsiE; cl01264 479436002695 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 479436002696 dimer interface [polypeptide binding]; other site 479436002697 catalytic triad [active] 479436002698 peroxidatic and resolving cysteines [active] 479436002699 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 479436002700 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 479436002701 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002702 Walker A/P-loop; other site 479436002703 ATP binding site [chemical binding]; other site 479436002704 Q-loop/lid; other site 479436002705 ABC transporter signature motif; other site 479436002706 Walker B; other site 479436002707 D-loop; other site 479436002708 H-loop/switch region; other site 479436002709 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 479436002710 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 479436002711 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002712 Walker A/P-loop; other site 479436002713 ATP binding site [chemical binding]; other site 479436002714 Q-loop/lid; other site 479436002715 ABC transporter signature motif; other site 479436002716 Walker B; other site 479436002717 D-loop; other site 479436002718 H-loop/switch region; other site 479436002719 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 479436002720 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 479436002721 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 479436002722 YdjC-like protein; Region: YdjC; cl01344 479436002723 Predicted integral membrane protein [Function unknown]; Region: COG0392 479436002724 Uncharacterised protein family (UPF0104); Region: UPF0104; cl04219 479436002725 hypothetical protein; Provisional; Region: PRK04435 479436002726 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 479436002727 homoserine dehydrogenase; Provisional; Region: PRK06349 479436002728 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002729 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 479436002730 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 479436002731 homoserine kinase; Provisional; Region: PRK01212 479436002732 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 479436002733 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 479436002734 Peptidase family M48; Region: Peptidase_M48; cl12018 479436002735 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 479436002736 active site 479436002737 multimer interface [polypeptide binding]; other site 479436002738 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; cl00920 479436002739 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 479436002740 homotrimer interface [polypeptide binding]; other site 479436002741 Walker A motif; other site 479436002742 GTP binding site [chemical binding]; other site 479436002743 Walker B motif; other site 479436002744 cobyric acid synthase; Provisional; Region: PRK00784 479436002745 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002746 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 479436002747 catalytic triad [active] 479436002748 CobD/Cbib protein; Region: CobD_Cbib; cl00561 479436002749 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 479436002750 Protein involved in propanediol utilization, and related proteins (includes coumermycin biosynthetic protein), possible kinase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PduX; COG4542 479436002751 GHMP kinases N terminal domain; Region: GHMP_kinases_N; cl08256 479436002752 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 479436002753 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 479436002754 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436002755 homodimer interface [polypeptide binding]; other site 479436002756 catalytic residue [active] 479436002757 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 479436002758 catalytic core [active] 479436002759 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 479436002760 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 479436002761 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 479436002762 active site 479436002763 uracil binding [chemical binding]; other site 479436002764 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 479436002765 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 479436002766 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 479436002767 active site 479436002768 elongation factor P; Validated; Region: PRK00529 479436002769 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 479436002770 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 479436002771 RNA binding site [nucleotide binding]; other site 479436002772 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 479436002773 RNA binding site [nucleotide binding]; other site 479436002774 Protein of unknown function (DUF322); Region: DUF322; cl00574 479436002775 Protein of unknown function (DUF322); Region: DUF322; cl00574 479436002776 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 479436002777 putative RNA binding site [nucleotide binding]; other site 479436002778 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 479436002779 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 479436002780 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 479436002781 generic binding surface II; other site 479436002782 generic binding surface I; other site 479436002783 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 479436002784 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 479436002785 substrate binding pocket [chemical binding]; other site 479436002786 chain length determination region; other site 479436002787 substrate-Mg2+ binding site; other site 479436002788 catalytic residues [active] 479436002789 aspartate-rich region 1; other site 479436002790 active site lid residues [active] 479436002791 aspartate-rich region 2; other site 479436002792 Divergent PAP2 family; Region: DUF212; cl00855 479436002793 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 479436002794 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 479436002795 RNA binding surface [nucleotide binding]; other site 479436002796 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436002797 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 479436002798 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436002799 arginine repressor; Provisional; Region: PRK04280 479436002800 Arginine repressor, DNA binding domain; Region: Arg_repressor; pfam01316 479436002801 Arginine repressor, C-terminal domain; Region: Arg_repressor_C; pfam02863 479436002802 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 479436002803 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 479436002804 Walker A/P-loop; other site 479436002805 ATP binding site [chemical binding]; other site 479436002806 Q-loop/lid; other site 479436002807 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 479436002808 Q-loop/lid; other site 479436002809 ABC transporter signature motif; other site 479436002810 Walker B; other site 479436002811 D-loop; other site 479436002812 H-loop/switch region; other site 479436002813 dihydrodipicolinate reductase; Provisional; Region: PRK00048 479436002814 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002815 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 479436002816 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 479436002817 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002818 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 479436002819 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 479436002820 dihydrodipicolinate synthase; Region: dapA; TIGR00674 479436002821 dimer interface [polypeptide binding]; other site 479436002822 active site 479436002823 catalytic residue [active] 479436002824 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 479436002825 tetramerization interface [polypeptide binding]; other site 479436002826 active site 479436002827 pantoate--beta-alanine ligase; Reviewed; Region: panC; PRK00380 479436002828 Pantoate-beta-alanine ligase; Region: PanC; cd00560 479436002829 active site 479436002830 ATP-binding site [chemical binding]; other site 479436002831 pantoate-binding site; other site 479436002832 HXXH motif; other site 479436002833 Membrane transport protein; Region: Mem_trans; cl09117 479436002834 bile acid transporter; Region: bass; TIGR00841 479436002835 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436002836 LexA repressor; Validated; Region: PRK00215 479436002837 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 479436002838 Catalytic site [active] 479436002839 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 479436002840 putative peptidoglycan binding site; other site 479436002841 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 479436002842 DNA binding site [nucleotide binding] 479436002843 dimer interface [polypeptide binding]; other site 479436002844 Phage integrase family; Region: Phage_integrase; pfam00589 479436002845 Int/Topo IB signature motif; other site 479436002846 active site 479436002847 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 479436002848 VanW like protein; Region: VanW; pfam04294 479436002849 G5 domain; Region: G5; pfam07501 479436002850 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 479436002851 active site 479436002852 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436002853 Domain of unknown function (DUF1848); Region: DUF1848; pfam08902 479436002854 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 479436002855 S-adenosylmethionine binding site [chemical binding]; other site 479436002856 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 479436002857 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 479436002858 active site 479436002859 putative substrate binding pocket [chemical binding]; other site 479436002860 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 479436002861 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436002862 oligomerization interface [polypeptide binding]; other site 479436002863 active site 479436002864 NAD+ binding site [chemical binding]; other site 479436002865 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 479436002866 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 479436002867 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 479436002868 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 479436002869 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 479436002870 dimerization interface [polypeptide binding]; other site 479436002871 domain crossover interface; other site 479436002872 redox-dependent activation switch; other site 479436002873 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 479436002874 homopentamer interface [polypeptide binding]; other site 479436002875 active site 479436002876 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 479436002877 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 479436002878 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 479436002879 dimerization interface [polypeptide binding]; other site 479436002880 active site 479436002881 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 479436002882 Lumazine binding domain; Region: Lum_binding; pfam00677 479436002883 Lumazine binding domain; Region: Lum_binding; pfam00677 479436002884 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 479436002885 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 479436002886 catalytic motif [active] 479436002887 Zn binding site [ion binding]; other site 479436002888 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 479436002889 pyruvate dehydrogenase; Provisional; Region: PRK09124 479436002890 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 479436002891 PYR/PP interface [polypeptide binding]; other site 479436002892 tetramer interface [polypeptide binding]; other site 479436002893 dimer interface [polypeptide binding]; other site 479436002894 TPP binding site [chemical binding]; other site 479436002895 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 479436002896 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 479436002897 TPP-binding site [chemical binding]; other site 479436002898 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 479436002899 generic binding surface II; other site 479436002900 generic binding surface I; other site 479436002901 PHP domain; Region: PHP; pfam02811 479436002902 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 479436002903 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 479436002904 DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]; Region: DnaE; COG0587 479436002905 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 479436002906 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 479436002907 Competence protein; Region: Competence; cl00471 479436002908 SLBB domain; Region: SLBB; pfam10531 479436002909 comEA protein; Region: comE; TIGR01259 479436002910 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 479436002911 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 479436002912 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 479436002913 catalytic motif [active] 479436002914 Zn binding site [ion binding]; other site 479436002915 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 479436002916 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 479436002917 HIGH motif; other site 479436002918 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 479436002919 active site 479436002920 KMSKS motif; other site 479436002921 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 479436002922 tRNA binding surface [nucleotide binding]; other site 479436002923 Predicted glycosyl hydrolase [General function prediction only]; Region: COG3858 479436002924 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 479436002925 active site 479436002926 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 479436002927 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 479436002928 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335; cl15440 479436002929 DNA topoisomerase I; Validated; Region: PRK05582 479436002930 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 479436002931 active site 479436002932 interdomain interaction site; other site 479436002933 putative metal-binding site [ion binding]; other site 479436002934 nucleotide binding site [chemical binding]; other site 479436002935 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 479436002936 domain I; other site 479436002937 DNA binding groove [nucleotide binding] 479436002938 phosphate binding site [ion binding]; other site 479436002939 domain II; other site 479436002940 domain III; other site 479436002941 nucleotide binding site [chemical binding]; other site 479436002942 catalytic site [active] 479436002943 domain IV; other site 479436002944 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 479436002945 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 479436002946 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 479436002947 Mg chelatase-related protein; Region: TIGR00368 479436002948 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436002949 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 479436002950 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 479436002951 RNA/DNA hybrid binding site [nucleotide binding]; other site 479436002952 active site 479436002953 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 479436002954 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The...; Region: YlqF; cd01856 479436002955 GTP/Mg2+ binding site [chemical binding]; other site 479436002956 G4 box; other site 479436002957 G5 box; other site 479436002958 G1 box; other site 479436002959 Switch I region; other site 479436002960 G2 box; other site 479436002961 G3 box; other site 479436002962 Switch II region; other site 479436002963 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 479436002964 Transcriptional regulators [Transcription]; Region: MarR; COG1846 479436002965 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436002966 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 479436002967 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 479436002968 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 479436002969 dimer interface [polypeptide binding]; other site 479436002970 motif 1; other site 479436002971 active site 479436002972 motif 2; other site 479436002973 motif 3; other site 479436002974 haemagglutination activity domain; Region: Haemagg_act; cl05436 479436002975 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 479436002976 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 479436002977 Surface antigen; Region: Bac_surface_Ag; cl03097 479436002978 M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family; Region: M20_Acy1L2_like_2; cd09849 479436002979 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 479436002980 metal binding site [ion binding]; metal-binding site 479436002981 Protein of unknown function (DUF3100); Region: DUF3100; pfam11299 479436002982 Domain of unknown function (DUF2088); Region: DUF2088; cl15406 479436002983 Protein of unknown function DUF111; Region: DUF111; cl03398 479436002984 AIR carboxylase; Region: AIRC; cl00310 479436002985 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]; Region: COG1606 479436002986 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 479436002987 Ligand Binding Site [chemical binding]; other site 479436002988 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecO; COG1381 479436002989 Recombination protein O C terminal; Region: RecO_C; pfam02565 479436002990 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 479436002991 Domain of unknown function DUF21; Region: DUF21; pfam01595 479436002992 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 479436002993 Transporter associated domain; Region: CorC_HlyC; cl08393 479436002994 GTPase Era; Reviewed; Region: era; PRK00089 479436002995 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly...; Region: Era; cd04163 479436002996 G1 box; other site 479436002997 GTP/Mg2+ binding site [chemical binding]; other site 479436002998 Switch I region; other site 479436002999 G2 box; other site 479436003000 Switch II region; other site 479436003001 G3 box; other site 479436003002 G4 box; other site 479436003003 G5 box; other site 479436003004 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 479436003005 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 479436003006 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 479436003007 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003008 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 479436003009 Fe-S oxidoreductase [Energy production and conversion]; Region: COG1032 479436003010 B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the...; Region: radical_SAM_B12_BD; cd02068 479436003011 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 479436003012 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 479436003013 GatB domain; Region: GatB_Yqey; cl11497 479436003014 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 479436003015 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 479436003016 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 479436003017 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 479436003018 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 479436003019 nucleotide binding pocket [chemical binding]; other site 479436003020 K-X-D-G motif; other site 479436003021 catalytic site [active] 479436003022 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 479436003023 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 479436003024 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 479436003025 Dimer interface [polypeptide binding]; other site 479436003026 BRCT sequence motif; other site 479436003027 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 479436003028 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003029 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003030 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK05427 479436003031 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 479436003032 DHHA2 domain; Region: DHHA2; pfam02833 479436003033 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 479436003034 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 479436003035 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 479436003036 conserved cys residue [active] 479436003037 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 479436003038 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 479436003039 substrate-cofactor binding pocket; other site 479436003040 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436003041 catalytic residue [active] 479436003042 6-carboxyhexanoate--CoA ligase; Region: BioW; cl00625 479436003043 Pimeloyl-CoA synthetase [Coenzyme metabolism]; Region: BioW; COG1424 479436003044 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 479436003045 SmpB-tmRNA interface; other site 479436003046 ribonuclease R; Region: RNase_R; TIGR02063 479436003047 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 479436003048 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 479436003049 RNB domain; Region: RNB; pfam00773 479436003050 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 479436003051 RNA binding site [nucleotide binding]; other site 479436003052 Preprotein translocase SecG subunit; Region: SecG; cl09123 479436003053 RNA polymerase factor sigma-70; Validated; Region: PRK08295 479436003054 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 479436003055 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; cl15358 479436003056 YacP-like NYN domain; Region: NYN_YacP; cl01491 479436003057 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 479436003058 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 479436003059 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 479436003060 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; cl00258 479436003061 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 479436003062 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 479436003063 active site 479436003064 HIGH motif; other site 479436003065 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 479436003066 KMSKS motif; other site 479436003067 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 479436003068 tRNA binding surface [nucleotide binding]; other site 479436003069 anticodon binding site; other site 479436003070 Membrane transport protein; Region: Mem_trans; cl09117 479436003071 bile acid transporter; Region: bass; TIGR00841 479436003072 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 479436003073 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 479436003074 active site 479436003075 HIGH motif; other site 479436003076 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 479436003077 active site 479436003078 KMSKS motif; other site 479436003079 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 479436003080 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 479436003081 substrate binding site; other site 479436003082 dimer interface; other site 479436003083 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 479436003084 homotrimer interaction site [polypeptide binding]; other site 479436003085 zinc binding site [ion binding]; other site 479436003086 CDP-binding sites; other site 479436003087 Integral membrane protein (PIN domain superfamily) [General function prediction only]; Region: COG4956 479436003088 PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; Region: PIN_YacL; cd09877 479436003089 putative active site [active] 479436003090 DNA repair protein RadA; Provisional; Region: PRK11823 479436003091 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 479436003092 Walker A motif/ATP binding site; other site 479436003093 ATP binding site [chemical binding]; other site 479436003094 Walker B motif; other site 479436003095 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 479436003096 Clp protease ATP binding subunit; Region: clpC; CHL00095 479436003097 Clp amino terminal domain; Region: Clp_N; pfam02861 479436003098 Clp amino terminal domain; Region: Clp_N; pfam02861 479436003099 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 479436003100 Walker A motif; other site 479436003101 ATP binding site [chemical binding]; other site 479436003102 Walker B motif; other site 479436003103 arginine finger; other site 479436003104 UvrB/uvrC motif; Region: UVR; pfam02151 479436003105 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 479436003106 Walker A motif; other site 479436003107 ATP binding site [chemical binding]; other site 479436003108 Walker B motif; other site 479436003109 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 479436003110 ATP:guanido phosphotransferase; Provisional; Region: PRK01059 479436003111 Phosphagen (guanidino) kinases found in bacteria; Region: bacterial_phosphagen_kinase; cd07930 479436003112 ADP binding site [chemical binding]; other site 479436003113 phosphagen binding site; other site 479436003114 substrate specificity loop; other site 479436003115 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]; Region: COG3880 479436003116 UvrB/uvrC motif; Region: UVR; pfam02151 479436003117 Firmicute transcriptional repressor of class III stress genes (CtsR); Region: CtsR; cl01850 479436003118 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 479436003119 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 479436003120 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436003121 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 479436003122 motif II; other site 479436003123 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436003124 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 479436003125 trimerization site [polypeptide binding]; other site 479436003126 active site 479436003127 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 479436003128 Aminotransferase class-V; Region: Aminotran_5; pfam00266 479436003129 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 479436003130 catalytic residue [active] 479436003131 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 479436003132 FeS assembly protein SufB; Region: sufB; TIGR01980 479436003133 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 479436003134 FeS assembly ATPase SufC; Region: sufC; TIGR01978 479436003135 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 479436003136 Walker A/P-loop; other site 479436003137 ATP binding site [chemical binding]; other site 479436003138 Q-loop/lid; other site 479436003139 ABC transporter signature motif; other site 479436003140 Walker B; other site 479436003141 D-loop; other site 479436003142 H-loop/switch region; other site 479436003143 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 479436003144 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 479436003145 active site 479436003146 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 479436003147 substrate binding site [chemical binding]; other site 479436003148 catalytic residues [active] 479436003149 dimer interface [polypeptide binding]; other site 479436003150 DoxX; Region: DoxX; cl00976 479436003151 DoxX; Region: DoxX; cl00976 479436003152 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 479436003153 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 479436003154 ring oligomerisation interface [polypeptide binding]; other site 479436003155 ATP/Mg binding site [chemical binding]; other site 479436003156 stacking interactions; other site 479436003157 hinge regions; other site 479436003158 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 479436003159 oligomerisation interface [polypeptide binding]; other site 479436003160 mobile loop; other site 479436003161 roof hairpin; other site 479436003162 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 479436003163 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 479436003164 active site 479436003165 phosphorylation site [posttranslational modification] 479436003166 intermolecular recognition site; other site 479436003167 dimerization interface [polypeptide binding]; other site 479436003168 ANTAR domain; Region: ANTAR; cl04297 479436003169 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 479436003170 Histidine kinase; Region: HisKA_2; cl06527 479436003171 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 479436003172 ATP binding site [chemical binding]; other site 479436003173 Mg2+ binding site [ion binding]; other site 479436003174 G-X-G motif; other site 479436003175 UGMP family protein; Validated; Region: PRK09604 479436003176 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 479436003177 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 479436003178 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 479436003179 Coenzyme A binding pocket [chemical binding]; other site 479436003180 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 479436003181 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 479436003182 thiamine monophosphate kinase; Provisional; Region: PRK05731 479436003183 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 479436003184 ATP binding site [chemical binding]; other site 479436003185 dimerization interface [polypeptide binding]; other site 479436003186 Sporulation and spore germination; Region: Germane; cl11253 479436003187 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 479436003188 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 479436003189 active site 479436003190 metal binding site [ion binding]; metal-binding site 479436003191 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436003192 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 479436003193 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 479436003194 putative substrate binding site [chemical binding]; other site 479436003195 putative ATP binding site [chemical binding]; other site 479436003196 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 479436003197 Survival protein SurE; Region: SurE; cl00448 479436003198 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 479436003199 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 479436003200 DXD motif; other site 479436003201 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 479436003202 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 479436003203 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 479436003204 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 479436003205 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 479436003206 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 479436003207 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 479436003208 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 479436003209 active site 479436003210 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 479436003211 active site 1 [active] 479436003212 dimer interface [polypeptide binding]; other site 479436003213 hexamer interface [polypeptide binding]; other site 479436003214 active site 2 [active] 479436003215 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 479436003216 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 479436003217 ssDNA binding site; other site 479436003218 generic binding surface II; other site 479436003219 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 479436003220 ATP binding site [chemical binding]; other site 479436003221 putative Mg++ binding site [ion binding]; other site 479436003222 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 479436003223 nucleotide binding region [chemical binding]; other site 479436003224 ATP-binding site [chemical binding]; other site 479436003225 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 479436003226 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 479436003227 Domain of unknown function (DUF299); Region: DUF299; cl00780 479436003228 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436003229 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 479436003230 phosphoenolpyruvate synthase; Validated; Region: PRK06464 479436003231 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 479436003232 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 479436003233 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 479436003234 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 479436003235 putative active site [active] 479436003236 putative CoA binding site [chemical binding]; other site 479436003237 nudix motif; other site 479436003238 metal binding site [ion binding]; metal-binding site 479436003239 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 479436003240 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 479436003241 active site 479436003242 HIGH motif; other site 479436003243 dimer interface [polypeptide binding]; other site 479436003244 KMSKS motif; other site 479436003245 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 479436003246 Transglycosylase; Region: Transgly; cl07896 479436003247 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 479436003248 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 479436003249 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 479436003250 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also...; Region: ABC_MutS2; cd03280 479436003251 Walker A/P-loop; other site 479436003252 ATP binding site [chemical binding]; other site 479436003253 Q-loop/lid; other site 479436003254 ABC transporter signature motif; other site 479436003255 Walker B; other site 479436003256 D-loop; other site 479436003257 H-loop/switch region; other site 479436003258 Smr domain; Region: Smr; cl02619 479436003259 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 479436003260 Peptidase family U32; Region: Peptidase_U32; cl03113 479436003261 Collagenase; Region: DUF3656; pfam12392 479436003262 Peptidase family U32; Region: Peptidase_U32; cl03113 479436003263 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 479436003264 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 479436003265 putative tRNA-binding site [nucleotide binding]; other site 479436003266 B3/4 domain; Region: B3_4; cl11458 479436003267 tRNA synthetase B5 domain; Region: B5; cl08394 479436003268 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 479436003269 dimer interface [polypeptide binding]; other site 479436003270 motif 1; other site 479436003271 motif 3; other site 479436003272 motif 2; other site 479436003273 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 479436003274 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 479436003275 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 479436003276 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 479436003277 dimer interface [polypeptide binding]; other site 479436003278 motif 1; other site 479436003279 active site 479436003280 motif 2; other site 479436003281 motif 3; other site 479436003282 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 479436003283 CoenzymeA binding site [chemical binding]; other site 479436003284 subunit interaction site [polypeptide binding]; other site 479436003285 PHB binding site; other site 479436003286 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 479436003287 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 479436003288 FtsX-like permease family; Region: FtsX; pfam02687 479436003289 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 479436003290 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 479436003291 Walker A/P-loop; other site 479436003292 ATP binding site [chemical binding]; other site 479436003293 Q-loop/lid; other site 479436003294 ABC transporter signature motif; other site 479436003295 Walker B; other site 479436003296 D-loop; other site 479436003297 H-loop/switch region; other site 479436003298 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 479436003299 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 479436003300 6-phosphofructokinase; Provisional; Region: PRK03202 479436003301 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 479436003302 active site 479436003303 ADP/pyrophosphate binding site [chemical binding]; other site 479436003304 dimerization interface [polypeptide binding]; other site 479436003305 allosteric effector site; other site 479436003306 fructose-1,6-bisphosphate binding site; other site 479436003307 shikimate kinase; Reviewed; Region: aroK; PRK00131 479436003308 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 479436003309 ADP binding site [chemical binding]; other site 479436003310 magnesium binding site [ion binding]; other site 479436003311 putative shikimate binding site; other site 479436003312 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 479436003313 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 479436003314 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 479436003315 Bacterial type II secretion system protein F domain; Region: GSPII_F; cl00906 479436003316 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 479436003317 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003318 Walker A motif; other site 479436003319 ATP binding site [chemical binding]; other site 479436003320 Walker B motif; other site 479436003321 Type II/IV secretion system protein; Region: GSPII_E; pfam00437 479436003322 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003323 Walker A motif; other site 479436003324 ATP binding site [chemical binding]; other site 479436003325 Walker B motif; other site 479436003326 enolase; Provisional; Region: eno; PRK00077 479436003327 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 479436003328 dimer interface [polypeptide binding]; other site 479436003329 metal binding site [ion binding]; metal-binding site 479436003330 substrate binding pocket [chemical binding]; other site 479436003331 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 479436003332 Sulfatase; Region: Sulfatase; cl10460 479436003333 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 479436003334 substrate binding site [chemical binding]; other site 479436003335 dimer interface [polypeptide binding]; other site 479436003336 catalytic triad [active] 479436003337 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 479436003338 substrate binding site [chemical binding]; other site 479436003339 hinge regions; other site 479436003340 ADP binding site [chemical binding]; other site 479436003341 catalytic site [active] 479436003342 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 479436003343 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 479436003344 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 479436003345 Predicted transcriptional regulator [Transcription]; Region: COG3388 479436003346 Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]; Region: DeoR; COG2390 479436003347 Putative sugar-binding domain; Region: Sugar-bind; pfam04198 479436003348 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436003349 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 479436003350 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 479436003351 dimer interface [polypeptide binding]; other site 479436003352 glycine-pyridoxal phosphate binding site [chemical binding]; other site 479436003353 active site 479436003354 folate binding site [chemical binding]; other site 479436003355 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 479436003356 Low molecular weight phosphatase family; Region: LMWPc; cd00115 479436003357 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 479436003358 active site 479436003359 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 479436003360 SUA5 domain; Region: SUA5; pfam03481 479436003361 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 479436003362 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 479436003363 S-adenosylmethionine binding site [chemical binding]; other site 479436003364 peptide chain release factor 1; Validated; Region: prfA; PRK00591 479436003365 RF-1 domain; Region: RF-1; cl02875 479436003366 RF-1 domain; Region: RF-1; cl02875 479436003367 Protein of unknown function (DUF1385); Region: DUF1385; cl01595 479436003368 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 479436003369 Uncharacterized protein conserved in bacteria (DUF2128); Region: DUF2128; cl01839 479436003370 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 479436003371 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 479436003372 minor groove reading motif; other site 479436003373 helix-hairpin-helix signature motif; other site 479436003374 substrate binding pocket [chemical binding]; other site 479436003375 active site 479436003376 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 479436003377 Bacterial protein of unknown function (DUF896); Region: DUF896; cl01722 479436003378 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 479436003379 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 479436003380 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436003381 homodimer interface [polypeptide binding]; other site 479436003382 catalytic residue [active] 479436003383 Fimbrial protein; Region: Fimbrial; cl01416 479436003384 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 479436003385 nucleotide binding site [chemical binding]; other site 479436003386 SulA interaction site; other site 479436003387 Protein of unknown function (DUF1290); Region: DUF1290; cl01587 479436003388 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3879 479436003389 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 479436003390 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 479436003391 Cell division protein FtsQ; Region: FtsQ; pfam03799 479436003392 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 479436003393 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 479436003394 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 479436003395 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 479436003396 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 479436003397 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 479436003398 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 479436003399 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 479436003400 active site 479436003401 homodimer interface [polypeptide binding]; other site 479436003402 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK14106 479436003403 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436003404 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 479436003405 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 479436003406 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 479436003407 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 479436003408 Mg++ binding site [ion binding]; other site 479436003409 putative catalytic motif [active] 479436003410 putative substrate binding site [chemical binding]; other site 479436003411 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 479436003412 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 479436003413 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 479436003414 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 479436003415 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 479436003416 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 479436003417 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 479436003418 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 479436003419 Septum formation initiator; Region: DivIC; cl11433 479436003420 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 479436003421 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436003422 cell division protein MraZ; Reviewed; Region: PRK00326 479436003423 MraZ protein; Region: MraZ; pfam02381 479436003424 MraZ protein; Region: MraZ; pfam02381 479436003425 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 479436003426 catalytic residues [active] 479436003427 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436003428 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436003429 active site 479436003430 HIGH motif; other site 479436003431 nucleotide binding site [chemical binding]; other site 479436003432 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436003433 active site 479436003434 KMSKS motif; other site 479436003435 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]; Region: COG1026 479436003436 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 479436003437 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 479436003438 Peptidase M16C associated; Region: M16C_assoc; pfam08367 479436003439 aspartate kinase; Reviewed; Region: PRK06635 479436003440 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 479436003441 putative nucleotide binding site [chemical binding]; other site 479436003442 putative catalytic residues [active] 479436003443 putative Mg ion binding site [ion binding]; other site 479436003444 putative aspartate binding site [chemical binding]; other site 479436003445 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 479436003446 putative allosteric regulatory site; other site 479436003447 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AK-LysC-DapG-like_2; cd04923 479436003448 Superoxide reductase-like (SORL) domain, class II; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals...; Region: SORL_classII; cd03172 479436003449 non-heme iron binding site [ion binding]; other site 479436003450 tetramer interface [polypeptide binding]; other site 479436003451 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 479436003452 homodimer interface [polypeptide binding]; other site 479436003453 Walker A motif; other site 479436003454 ATP binding site [chemical binding]; other site 479436003455 hydroxycobalamin binding site [chemical binding]; other site 479436003456 Walker B motif; other site 479436003457 cobyrinic acid a,c-diamide synthase; Validated; Region: PRK01077 479436003458 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003459 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase; Region: GATase1_CobB; cd03130 479436003460 catalytic triad [active] 479436003461 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 479436003462 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 479436003463 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 479436003464 active site 479436003465 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 479436003466 active site 479436003467 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 479436003468 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 479436003469 active site 479436003470 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 479436003471 active site 479436003472 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436003473 Cobalt chelatase (CbiK); Region: CbiK; pfam06180 479436003474 Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the...; Region: Chelatase_Class_II; cl02784 479436003475 active site 479436003476 Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the...; Region: CbiK_C; cd03413 479436003477 active site 479436003478 N-terminal domain interface [polypeptide binding]; other site 479436003479 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 479436003480 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 479436003481 intersubunit interface [polypeptide binding]; other site 479436003482 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436003483 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 479436003484 Walker A/P-loop; other site 479436003485 ATP binding site [chemical binding]; other site 479436003486 Q-loop/lid; other site 479436003487 ABC transporter signature motif; other site 479436003488 Walker B; other site 479436003489 D-loop; other site 479436003490 H-loop/switch region; other site 479436003491 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 479436003492 ABC-ATPase subunit interface; other site 479436003493 dimer interface [polypeptide binding]; other site 479436003494 putative PBP binding regions; other site 479436003495 Precorrin isomerase [Coenzyme metabolism]; Region: CobH; cl00913 479436003496 Precorrin-8X methylmutase; Region: CbiC; pfam02570 479436003497 Precorrin-6x reductase CbiJ/CobK; Region: CbiJ; cl00922 479436003498 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 479436003499 cobalamin biosynthesis protein CbiG; Validated; Region: PRK05788 479436003500 Cobalamin synthesis G N-terminal; Region: CbiG_N; pfam11760 479436003501 Cobalamin biosynthesis central region; Region: CbiG_mid; pfam11761 479436003502 Cobalamin synthesis G C-terminus; Region: CbiG_C; cl12133 479436003503 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 479436003504 Precorrin-6B methylase 2 [Coenzyme metabolism]; Region: CobL; COG2242 479436003505 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 479436003506 S-adenosylmethionine binding site [chemical binding]; other site 479436003507 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 479436003508 CbiD; Region: CbiD; cl00828 479436003509 Protein of unknown function (DUF520); Region: DUF520; cl00723 479436003510 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 479436003511 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 479436003512 active site 479436003513 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 479436003514 hypothetical protein; Provisional; Region: PRK08185 479436003515 intersubunit interface [polypeptide binding]; other site 479436003516 active site 479436003517 zinc binding site [ion binding]; other site 479436003518 Na+ binding site [ion binding]; other site 479436003519 stage V sporulation protein B; Region: spore_V_B; TIGR02900 479436003520 MatE; Region: MatE; cl10513 479436003521 MatE; Region: MatE; cl10513 479436003522 Membrane transport protein; Region: Mem_trans; cl09117 479436003523 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 479436003524 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 479436003525 catalytic triad [active] 479436003526 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 479436003527 Amino acid permease; Region: AA_permease; cl00524 479436003528 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 479436003529 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 479436003530 motif II; other site 479436003531 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 479436003532 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003533 Walker A motif; other site 479436003534 ATP binding site [chemical binding]; other site 479436003535 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 479436003536 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 479436003537 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 479436003538 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 479436003539 Walker A motif; other site 479436003540 ATP binding site [chemical binding]; other site 479436003541 Walker B motif; other site 479436003542 Uncharacterized conserved protein [Function unknown]; Region: COG3410 479436003543 Bacterial protein of unknown function (DUF898); Region: DUF898; cl01738 479436003544 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 479436003545 23S rRNA binding site [nucleotide binding]; other site 479436003546 L21 binding site [polypeptide binding]; other site 479436003547 L13 binding site [polypeptide binding]; other site 479436003548 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 479436003549 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 479436003550 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 479436003551 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 479436003552 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 479436003553 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; cl15357 479436003554 transmembrane helices; other site 479436003555 benzoate transport; Region: 2A0115; TIGR00895 479436003556 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 479436003557 putative substrate translocation pore; other site 479436003558 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 479436003559 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 479436003560 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 479436003561 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 479436003562 active site 479436003563 dimer interface [polypeptide binding]; other site 479436003564 motif 1; other site 479436003565 motif 2; other site 479436003566 motif 3; other site 479436003567 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 479436003568 anticodon binding site; other site 479436003569 putative protease; Provisional; Region: PRK15452 479436003570 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl07974 479436003571 Peptidase family U32; Region: Peptidase_U32; cl03113 479436003572 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 479436003573 S-adenosylmethionine binding site [chemical binding]; other site 479436003574 YceG-like family; Region: YceG; pfam02618 479436003575 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 479436003576 dimerization interface [polypeptide binding]; other site 479436003577 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 479436003578 Bacterial protein of unknown function (DUF965); Region: DUF965; cl01857 479436003579 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 479436003580 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 479436003581 motif 1; other site 479436003582 active site 479436003583 motif 2; other site 479436003584 motif 3; other site 479436003585 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 479436003586 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 479436003587 DHHA1 domain; Region: DHHA1; pfam02272 479436003588 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 479436003589 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 479436003590 NlpC/P60 family; Region: NLPC_P60; cl11438 479436003591 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 479436003592 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 479436003593 Ligand binding site; other site 479436003594 Putative Catalytic site; other site 479436003595 DXD motif; other site 479436003596 HupH hydrogenase expression protein, C-terminal conserved region; Region: HupH_C; pfam04809 479436003597 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 479436003598 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 479436003599 putative substrate-binding site; other site 479436003600 nickel binding site [ion binding]; other site 479436003601 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 479436003602 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 479436003603 Ni,Fe-hydrogenase I small subunit [Energy production and conversion]; Region: HyaA; COG1740 479436003604 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 479436003605 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 479436003606 catalytic residues [active] 479436003607 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 479436003608 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 479436003609 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 479436003610 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl12011 479436003611 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 479436003612 active site 479436003613 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Region: rSAM_QueE_Clost; TIGR03963 479436003614 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 479436003615 FeS/SAM binding site; other site 479436003616 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 479436003617 active site 479436003618 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 479436003619 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 479436003620 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 479436003621 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 479436003622 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 479436003623 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 479436003624 DNA binding residues [nucleotide binding] 479436003625 DNA primase; Validated; Region: dnaG; PRK05667 479436003626 CHC2 zinc finger; Region: zf-CHC2; cl15369 479436003627 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 479436003628 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 479436003629 active site 479436003630 metal binding site [ion binding]; metal-binding site 479436003631 interdomain interaction site; other site 479436003632 phosphodiesterase; Provisional; Region: PRK12704 479436003633 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 479436003634 RecX family; Region: RecX; cl00936 479436003635 recombinase A; Provisional; Region: recA; PRK09354 479436003636 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 479436003637 hexamer interface [polypeptide binding]; other site 479436003638 Walker A motif; other site 479436003639 ATP binding site [chemical binding]; other site 479436003640 Walker B motif; other site 479436003641 competence damage-inducible protein A; Provisional; Region: PRK00549 479436003642 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 479436003643 putative MPT binding site; other site 479436003644 Competence-damaged protein; Region: CinA; cl00666 479436003645 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 479436003646 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 479436003647 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 479436003648 FeS/SAM binding site; other site 479436003649 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 479436003650 uncharacterized radical SAM protein YgiQ; Region: SAM_YgiQ; TIGR03904 479436003651 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 479436003652 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 479436003653 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 479436003654 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003655 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 479436003656 recombination factor protein RarA; Reviewed; Region: PRK13342 479436003657 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 479436003658 Walker A motif; other site 479436003659 ATP binding site [chemical binding]; other site 479436003660 Walker B motif; other site 479436003661 arginine finger; other site 479436003662 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 479436003663 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 479436003664 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 479436003665 dimer interface [polypeptide binding]; other site 479436003666 anticodon binding site; other site 479436003667 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 479436003668 homodimer interface [polypeptide binding]; other site 479436003669 motif 1; other site 479436003670 active site 479436003671 motif 2; other site 479436003672 GAD domain; Region: GAD; pfam02938 479436003673 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 479436003674 motif 3; other site 479436003675 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 479436003676 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 479436003677 dimer interface [polypeptide binding]; other site 479436003678 motif 1; other site 479436003679 active site 479436003680 motif 2; other site 479436003681 motif 3; other site 479436003682 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 479436003683 anticodon binding site; other site 479436003684 coproporphyrinogen III oxidase; Provisional; Region: PRK08207 479436003685 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 479436003686 FeS/SAM binding site; other site 479436003687 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 479436003688 metal binding site 2 [ion binding]; metal-binding site 479436003689 putative DNA binding helix; other site 479436003690 metal binding site 1 [ion binding]; metal-binding site 479436003691 dimer interface [polypeptide binding]; other site 479436003692 structural Zn2+ binding site [ion binding]; other site 479436003693 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436003694 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 479436003695 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 479436003696 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 479436003697 synthetase active site [active] 479436003698 NTP binding site [chemical binding]; other site 479436003699 metal binding site [ion binding]; metal-binding site 479436003700 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 479436003701 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 479436003702 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 479436003703 DHH family; Region: DHH; pfam01368 479436003704 DHHA1 domain; Region: DHHA1; pfam02272 479436003705 iron-only hydrogenase maturation rSAM protein HydG; Region: rSAM_HydG; TIGR03955 479436003706 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 479436003707 FeS/SAM binding site; other site 479436003708 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 479436003709 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 479436003710 Protein of unknown function (DUF464); Region: DUF464; cl01080 479436003711 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 479436003712 Domain of unknown function DUF; Region: DUF204; pfam02659 479436003713 Domain of unknown function DUF; Region: DUF204; pfam02659 479436003714 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 479436003715 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 479436003716 homodimer interface [polypeptide binding]; other site 479436003717 oligonucleotide binding site [chemical binding]; other site 479436003718 radical SAM-linked protein; Region: sam_1_link_chp; TIGR03936 479436003719 Uncharacterized protein conserved in bacteria (DUF2344); Region: DUF2344; cl02090 479436003720 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 479436003721 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 479436003722 FeS/SAM binding site; other site 479436003723 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 479436003724 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003725 CobQ/CobB/MinD/ParA nucleotide binding domain; Region: CbiA; pfam01656 479436003726 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 479436003727 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 479436003728 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 479436003729 rod shape-determining protein MreD; Region: MreD; cl01087 479436003730 rod shape-determining protein MreC; Provisional; Region: PRK13922 479436003731 rod shape-determining protein MreC; Region: MreC; pfam04085 479436003732 rod shape-determining protein MreB; Provisional; Region: PRK13930 479436003733 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 479436003734 ATP binding site [chemical binding]; other site 479436003735 profilin binding site; other site 479436003736 gelsolin binding site; other site 479436003737 hypothetical protein; Reviewed; Region: PRK00024 479436003738 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 479436003739 MPN+ (JAMM) motif; other site 479436003740 Zinc-binding site [ion binding]; other site 479436003741 Maf-like protein; Region: Maf; pfam02545 479436003742 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 479436003743 active site 479436003744 dimer interface [polypeptide binding]; other site 479436003745 Acetokinase family; Region: Acetate_kinase; cl01029 479436003746 hypothetical protein; Provisional; Region: PRK13670 479436003747 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436003748 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 479436003749 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 479436003750 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 479436003751 active site 479436003752 lipoprotein signal peptidase; Provisional; Region: PRK14787 479436003753 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 479436003754 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 479436003755 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 479436003756 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 479436003757 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 479436003758 transmembrane helices; other site 479436003759 subunit; Region: OAD_beta; cl00816 479436003760 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 479436003761 carboxyltransferase (CT) interaction site; other site 479436003762 biotinylation site [posttranslational modification]; other site 479436003763 Oxaloacetate decarboxylase, gamma chain; Region: OAD_gamma; cl01458 479436003764 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 479436003765 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 479436003766 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 479436003767 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 479436003768 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 479436003769 dimer interface [polypeptide binding]; other site 479436003770 substrate binding site [chemical binding]; other site 479436003771 metal binding site [ion binding]; metal-binding site 479436003772 Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]; Region: ArgK; COG1703 479436003773 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003774 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 479436003775 Walker A; other site 479436003776 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 479436003777 B12 binding site [chemical binding]; other site 479436003778 cobalt ligand [ion binding]; other site 479436003779 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM...; Region: MM_CoA_mutase_ICM_like; cd03680 479436003780 Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid metabolism]; Region: Sbm; COG1884 479436003781 succinate CoA transferases; Region: YgfH_subfam; TIGR03458 479436003782 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 479436003783 O-Antigen ligase; Region: Wzy_C; cl04850 479436003784 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 479436003785 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 479436003786 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 479436003787 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 479436003788 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 479436003789 HIGH motif; other site 479436003790 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 479436003791 active site 479436003792 KMSKS motif; other site 479436003793 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 479436003794 tRNA binding surface [nucleotide binding]; other site 479436003795 anticodon binding site; other site 479436003796 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 479436003797 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 479436003798 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 479436003799 substrate binding pocket [chemical binding]; other site 479436003800 chain length determination region; other site 479436003801 substrate-Mg2+ binding site; other site 479436003802 catalytic residues [active] 479436003803 aspartate-rich region 1; other site 479436003804 active site lid residues [active] 479436003805 aspartate-rich region 2; other site 479436003806 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 479436003807 G1 box; other site 479436003808 GTP/Mg2+ binding site [chemical binding]; other site 479436003809 Switch I region; other site 479436003810 G2 box; other site 479436003811 G3 box; other site 479436003812 Switch II region; other site 479436003813 G4 box; other site 479436003814 G5 box; other site 479436003815 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 479436003816 Found in ATP-dependent protease La (LON); Region: LON; smart00464 479436003817 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 479436003818 Walker A motif; other site 479436003819 ATP binding site [chemical binding]; other site 479436003820 Walker B motif; other site 479436003821 arginine finger; other site 479436003822 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 479436003823 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 479436003824 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 479436003825 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003826 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 479436003827 Walker A motif; other site 479436003828 ATP binding site [chemical binding]; other site 479436003829 Walker B motif; other site 479436003830 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 479436003831 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 479436003832 oligomer interface [polypeptide binding]; other site 479436003833 active site residues [active] 479436003834 trigger factor; Provisional; Region: tig; PRK01490 479436003835 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 479436003836 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 479436003837 FOG: CBS domain [General function prediction only]; Region: COG0517 479436003838 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection...; Region: CBS_pair_BON_assoc; cd04586 479436003839 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 479436003840 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436003841 Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP; Region: RLP_RrRLP; cd08210 479436003842 dimer interface [polypeptide binding]; other site 479436003843 active site 479436003844 catalytic residue [active] 479436003845 metal binding site [ion binding]; metal-binding site 479436003846 Permease family; Region: Xan_ur_permease; cl00967 479436003847 selenium-dependent molybdenum hydroxylase 1; Region: Se_dep_Molyb_1; TIGR03311 479436003848 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 479436003849 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; cl03161 479436003850 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 479436003851 phenylhydantoinase; Validated; Region: PRK08323 479436003852 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine...; Region: D-HYD; cd01314 479436003853 tetramer interface [polypeptide binding]; other site 479436003854 active site 479436003855 putative selenate reductase subunit YgfK; Provisional; Region: PRK09853 479436003856 putative selenate reductase, YgfK subunit; Region: Se_ygfK; TIGR03315 479436003857 putative chlorohydrolase/aminohydrolase; Validated; Region: PRK07203 479436003858 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 479436003859 active site 479436003860 putative substrate binding pocket [chemical binding]; other site 479436003861 carbamate kinase; Reviewed; Region: PRK12686 479436003862 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 479436003863 putative substrate binding site [chemical binding]; other site 479436003864 nucleotide binding site [chemical binding]; other site 479436003865 nucleotide binding site [chemical binding]; other site 479436003866 homodimer interface [polypeptide binding]; other site 479436003867 aspartate/ornithine carbamoyltransferase family protein; Validated; Region: PRK07200 479436003868 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 479436003869 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436003870 peptidase; Reviewed; Region: PRK13004 479436003871 M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases; Region: M20_ArgE_DapE_like4; cd05649 479436003872 putative metal binding site [ion binding]; other site 479436003873 putative dimer interface [polypeptide binding]; other site 479436003874 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 479436003875 catalytic residue [active] 479436003876 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 479436003877 YheO-like PAS domain; Region: PAS_6; pfam08348 479436003878 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 479436003879 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 479436003880 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 479436003881 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436003882 active site 479436003883 HIGH motif; other site 479436003884 nucleotide binding site [chemical binding]; other site 479436003885 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 479436003886 KMSKS motif; other site 479436003887 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 479436003888 glyoxylate reductase; Reviewed; Region: PRK13243 479436003889 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436003890 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 479436003891 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]; Region: COG3593 479436003892 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003893 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 479436003894 putative active site [active] 479436003895 putative metal-binding site [ion binding]; other site 479436003896 Predicted permeases [General function prediction only]; Region: RarD; COG2962 479436003897 EamA-like transporter family; Region: EamA; cl01037 479436003898 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 479436003899 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, cyanobacteria; Region: Thr-synth_2; cd01560 479436003900 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436003901 catalytic residue [active] 479436003902 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 479436003903 molybdenum cofactor biosynthesis protein A, bacterial; Region: moaA; TIGR02666 479436003904 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 479436003905 FeS/SAM binding site; other site 479436003906 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 479436003907 MOSC domain; Region: MOSC; pfam03473 479436003908 Permease family; Region: Xan_ur_permease; cl00967 479436003909 Formiminotransferase-cyclodeaminase; Region: FTCD_C; cl01350 479436003910 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 479436003911 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 479436003912 Potassium binding sites [ion binding]; other site 479436003913 Cesium cation binding sites [ion binding]; other site 479436003914 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 479436003915 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 479436003916 transmembrane helices; other site 479436003917 Fumarase C-terminus; Region: Fumerase_C; cl00795 479436003918 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 479436003919 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 479436003920 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 479436003921 Cupin domain; Region: Cupin_2; cl09118 479436003922 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 479436003923 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 479436003924 Cupin domain; Region: Cupin_2; cl09118 479436003925 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 479436003926 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 479436003927 dimer interface [polypeptide binding]; other site 479436003928 putative functional site; other site 479436003929 putative MPT binding site; other site 479436003930 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 479436003931 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 479436003932 GTP binding site; other site 479436003933 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436003934 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 479436003935 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 479436003936 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 479436003937 active site 479436003938 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 479436003939 Major Facilitator Superfamily; Region: MFS_1; pfam07690 479436003940 putative substrate translocation pore; other site 479436003941 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 479436003942 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_subfamily5; cd08019 479436003943 metal binding site [ion binding]; metal-binding site 479436003944 putative dimer interface [polypeptide binding]; other site 479436003945 acetylornithine aminotransferase; Provisional; Region: PRK02627 479436003946 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 479436003947 inhibitor-cofactor binding pocket; inhibition site 479436003948 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436003949 catalytic residue [active] 479436003950 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 479436003951 feedback inhibition sensing region; other site 479436003952 homohexameric interface [polypeptide binding]; other site 479436003953 nucleotide binding site [chemical binding]; other site 479436003954 N-acetyl-L-glutamate binding site [chemical binding]; other site 479436003955 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 479436003956 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436003957 ornithine carbamoyltransferase; Validated; Region: PRK02102 479436003958 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 479436003959 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436003960 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 479436003961 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 479436003962 metal binding site [ion binding]; metal-binding site 479436003963 dimer interface [polypeptide binding]; other site 479436003964 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 479436003965 active site 479436003966 metal binding site [ion binding]; metal-binding site 479436003967 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 479436003968 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 479436003969 active site 479436003970 metal binding site [ion binding]; metal-binding site 479436003971 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeD; cd03379 479436003972 active site clefts [active] 479436003973 zinc binding site [ion binding]; other site 479436003974 dimer interface [polypeptide binding]; other site 479436003975 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 479436003976 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 479436003977 putative valine binding site [chemical binding]; other site 479436003978 dimer interface [polypeptide binding]; other site 479436003979 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 479436003980 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 479436003981 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 479436003982 PYR/PP interface [polypeptide binding]; other site 479436003983 dimer interface [polypeptide binding]; other site 479436003984 TPP binding site [chemical binding]; other site 479436003985 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 479436003986 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 479436003987 TPP-binding site [chemical binding]; other site 479436003988 dimer interface [polypeptide binding]; other site 479436003989 Nitrous oxide-stimulated promoter; Region: YgbA_NO; cl08119 479436003990 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 479436003991 S-adenosylmethionine binding site [chemical binding]; other site 479436003992 LemA family; Region: LemA; cl00742 479436003993 Low molecular weight phosphatase family; Region: LMWPc; cd00115 479436003994 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 479436003995 active site 479436003996 Autotransporter beta-domain; Region: Autotransporter; cl02365 479436003997 ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CbiK; COG5266 479436003998 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 479436003999 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 479436004000 G1 box; other site 479436004001 putative GEF interaction site [polypeptide binding]; other site 479436004002 GTP/Mg2+ binding site [chemical binding]; other site 479436004003 Switch I region; other site 479436004004 G2 box; other site 479436004005 G3 box; other site 479436004006 Switch II region; other site 479436004007 G4 box; other site 479436004008 G5 box; other site 479436004009 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 479436004010 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 479436004011 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 479436004012 FAD binding domain; Region: FAD_binding_4; pfam01565 479436004013 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 479436004014 Protein of unknown function (DUF964); Region: DUF964; cl01483 479436004015 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 479436004016 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 479436004017 trimer interface [polypeptide binding]; other site 479436004018 dimer interface [polypeptide binding]; other site 479436004019 putative active site [active] 479436004020 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436004021 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 479436004022 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 479436004023 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 479436004024 Walker A motif; other site 479436004025 ATP binding site [chemical binding]; other site 479436004026 Walker B motif; other site 479436004027 arginine finger; other site 479436004028 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 479436004029 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436004030 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; cl15357 479436004031 Cation transport protein; Region: TrkH; cl10514 479436004032 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 479436004033 Cation transport protein; Region: TrkH; cl10514 479436004034 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 479436004035 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 479436004036 substrate binding site [chemical binding]; other site 479436004037 ATP binding site [chemical binding]; other site 479436004038 coproporphyrinogen III oxidase; Provisional; Region: PRK09058 479436004039 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 479436004040 FeS/SAM binding site; other site 479436004041 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 479436004042 Gram-negative bacterial tonB protein; Region: TonB; cl10048 479436004043 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 479436004044 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 479436004045 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; cl00284 479436004046 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; cl00284 479436004047 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; cl00284 479436004048 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; cl00284 479436004049 transcriptional regulator EutR; Provisional; Region: PRK10130 479436004050 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 479436004051 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 479436004052 Protein of unknown function (DUF454); Region: DUF454; cl01063 479436004053 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 479436004054 PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a...; Region: PTS_IIB_ascorbate; cd05563 479436004055 P-loop; other site 479436004056 active site 479436004057 phosphorylation site [posttranslational modification] 479436004058 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 479436004059 active site 479436004060 phosphorylation site [posttranslational modification] 479436004061 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 479436004062 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 479436004063 ABC-ATPase subunit interface; other site 479436004064 dimer interface [polypeptide binding]; other site 479436004065 putative PBP binding regions; other site 479436004066 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436004067 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 479436004068 Walker A/P-loop; other site 479436004069 ATP binding site [chemical binding]; other site 479436004070 Q-loop/lid; other site 479436004071 ABC transporter signature motif; other site 479436004072 Walker B; other site 479436004073 D-loop; other site 479436004074 H-loop/switch region; other site 479436004075 proposed F420-0 ABC transporter, periplasmic F420-0 binding protein; Region: F420-O_ABCperi; TIGR03868 479436004076 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 479436004077 intersubunit interface [polypeptide binding]; other site 479436004078 Phosphate transporter family; Region: PHO4; cl00396 479436004079 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 479436004080 hydrogenase, Fe-only; Region: Fe_only_hydrog; TIGR02512 479436004081 4Fe-4S binding domain; Region: Fer4; cl02805 479436004082 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 479436004083 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; cl03503 479436004084 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 479436004085 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 479436004086 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436004087 Walker A/P-loop; other site 479436004088 ATP binding site [chemical binding]; other site 479436004089 Q-loop/lid; other site 479436004090 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 479436004091 ABC transporter signature motif; other site 479436004092 Walker B; other site 479436004093 D-loop; other site 479436004094 ABC transporter; Region: ABC_tran_2; pfam12848 479436004095 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 479436004096 diacylglycerol glucosyltransferase; Provisional; Region: PRK13609 479436004097 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 479436004098 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 479436004099 IHF - DNA interface [nucleotide binding]; other site 479436004100 IHF dimer interface [polypeptide binding]; other site 479436004101 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 479436004102 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 479436004103 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 479436004104 stage V sporulation protein B; Region: spore_V_B; TIGR02900 479436004105 MatE; Region: MatE; cl10513 479436004106 MatE; Region: MatE; cl10513 479436004107 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 479436004108 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 479436004109 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 479436004110 ATP binding site [chemical binding]; other site 479436004111 putative Mg++ binding site [ion binding]; other site 479436004112 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 479436004113 nucleotide binding region [chemical binding]; other site 479436004114 ATP-binding site [chemical binding]; other site 479436004115 TRCF domain; Region: TRCF; cl04088 479436004116 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 479436004117 ABC-2 type transporter; Region: ABC2_membrane; cl11417 479436004118 type VII secretion protein EsaA, N-terminal domain; Region: T7_esaA_Nterm; TIGR03929 479436004119 ABC-2 type transporter; Region: ABC2_membrane; cl11417 479436004120 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 479436004121 The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency; Region: ABC_subfamily_A; cd03263 479436004122 Walker A/P-loop; other site 479436004123 ATP binding site [chemical binding]; other site 479436004124 Q-loop/lid; other site 479436004125 ABC transporter signature motif; other site 479436004126 Walker B; other site 479436004127 D-loop; other site 479436004128 H-loop/switch region; other site 479436004129 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 479436004130 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436004131 Walker A/P-loop; other site 479436004132 ATP binding site [chemical binding]; other site 479436004133 Q-loop/lid; other site 479436004134 ABC transporter signature motif; other site 479436004135 Walker B; other site 479436004136 D-loop; other site 479436004137 H-loop/switch region; other site 479436004138 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 479436004139 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 479436004140 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 479436004141 non-specific DNA binding site [nucleotide binding]; other site 479436004142 salt bridge; other site 479436004143 sequence-specific DNA binding site [nucleotide binding]; other site 479436004144 spermidine synthase; Provisional; Region: PRK00811 479436004145 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 479436004146 S-adenosylmethionine binding site [chemical binding]; other site 479436004147 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 479436004148 active site 479436004149 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 479436004150 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 479436004151 putative ATP binding site [chemical binding]; other site 479436004152 putative substrate interface [chemical binding]; other site 479436004153 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 479436004154 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 479436004155 dimer interface [polypeptide binding]; other site 479436004156 active site 479436004157 metal binding site [ion binding]; metal-binding site 479436004158 glutathione binding site [chemical binding]; other site 479436004159 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 479436004160 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 479436004161 Walker A/P-loop; other site 479436004162 ATP binding site [chemical binding]; other site 479436004163 Q-loop/lid; other site 479436004164 SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini; Region: ABC_sbcCD; cd03279 479436004165 ABC transporter signature motif; other site 479436004166 Walker B; other site 479436004167 D-loop; other site 479436004168 H-loop/switch region; other site 479436004169 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 479436004170 active site 479436004171 metal binding site [ion binding]; metal-binding site 479436004172 DNA binding site [nucleotide binding] 479436004173 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 479436004174 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 479436004175 endonuclease IV; Provisional; Region: PRK01060 479436004176 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 479436004177 AP (apurinic/apyrimidinic) site pocket; other site 479436004178 DNA interaction; other site 479436004179 Metal-binding active site; metal-binding site 479436004180 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 479436004181 metal binding site 2 [ion binding]; metal-binding site 479436004182 putative DNA binding helix; other site 479436004183 metal binding site 1 [ion binding]; metal-binding site 479436004184 dimer interface [polypeptide binding]; other site 479436004185 structural Zn2+ binding site [ion binding]; other site 479436004186 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 479436004187 DEAD-like helicases superfamily; Region: DEXDc; smart00487 479436004188 ATP binding site [chemical binding]; other site 479436004189 Mg++ binding site [ion binding]; other site 479436004190 motif III; other site 479436004191 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 479436004192 nucleotide binding region [chemical binding]; other site 479436004193 ATP-binding site [chemical binding]; other site 479436004194 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 479436004195 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 479436004196 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 479436004197 NAD(P) binding site [chemical binding]; other site 479436004198 catalytic residues [active] 479436004199 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 479436004200 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 479436004201 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 479436004202 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 479436004203 RNA binding site [nucleotide binding]; other site 479436004204 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 479436004205 folate binding site [chemical binding]; other site 479436004206 NADP+ binding site [chemical binding]; other site 479436004207 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 479436004208 dimerization interface [polypeptide binding]; other site 479436004209 active site 479436004210 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 479436004211 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 479436004212 ATP binding site [chemical binding]; other site 479436004213 putative Mg++ binding site [ion binding]; other site 479436004214 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 479436004215 nucleotide binding region [chemical binding]; other site 479436004216 ATP-binding site [chemical binding]; other site 479436004217 RQC domain; Region: RQC; cl09632 479436004218 HRDC domain; Region: HRDC; cl02578 479436004219 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 479436004220 Sodium:solute symporter family; Region: SSF; cl00456 479436004221 Predicted transcriptional regulator [Transcription]; Region: COG2378 479436004222 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 479436004223 S-adenosylmethionine binding site [chemical binding]; other site 479436004224 Predicted methyltransferase regulatory domain; Region: MethyTransf_Reg; pfam10119 479436004225 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 479436004226 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 479436004227 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 479436004228 dimer interface [polypeptide binding]; other site 479436004229 PYR/PP interface [polypeptide binding]; other site 479436004230 TPP binding site [chemical binding]; other site 479436004231 substrate binding site [chemical binding]; other site 479436004232 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 479436004233 Domain of unknown function; Region: EKR; cl11037 479436004234 4Fe-4S binding domain; Region: Fer4; cl02805 479436004235 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 479436004236 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 479436004237 TPP-binding site [chemical binding]; other site 479436004238 dimer interface [polypeptide binding]; other site 479436004239 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436004240 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004241 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 479436004242 putative dimerization interface [polypeptide binding]; other site 479436004243 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 479436004244 D-galactonate transporter; Region: 2A0114; TIGR00893 479436004245 putative substrate translocation pore; other site 479436004246 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 479436004247 Cupin domain; Region: Cupin_2; cl09118 479436004248 NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]; Region: NuoG; COG1034 479436004249 citrate lyase, alpha subunit; Region: citF; TIGR01584 479436004250 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 479436004251 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 479436004252 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 479436004253 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; cl15357 479436004254 transmembrane helices; other site 479436004255 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436004256 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004257 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 479436004258 dimerization interface [polypeptide binding]; other site 479436004259 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 479436004260 pyruvate kinase; Provisional; Region: PRK06354 479436004261 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 479436004262 domain interfaces; other site 479436004263 active site 479436004264 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 479436004265 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06826 479436004266 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 479436004267 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 479436004268 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 479436004269 generic binding surface II; other site 479436004270 generic binding surface I; other site 479436004271 Protein of unknown function DUF45; Region: DUF45; cl00636 479436004272 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 479436004273 haemagglutination activity domain; Region: Haemagg_act; cl05436 479436004274 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 479436004275 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 479436004276 Surface antigen; Region: Bac_surface_Ag; cl03097 479436004277 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 479436004278 non-specific DNA binding site [nucleotide binding]; other site 479436004279 transcriptional repressor DicA; Reviewed; Region: PRK09706 479436004280 salt bridge; other site 479436004281 sequence-specific DNA binding site [nucleotide binding]; other site 479436004282 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 479436004283 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 479436004284 inhibitor-cofactor binding pocket; inhibition site 479436004285 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436004286 catalytic residue [active] 479436004287 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 479436004288 dimer interface [polypeptide binding]; other site 479436004289 active site 479436004290 Schiff base residues; other site 479436004291 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 479436004292 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 479436004293 active site 479436004294 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 479436004295 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 479436004296 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 479436004297 domain interfaces; other site 479436004298 active site 479436004299 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 479436004300 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 479436004301 tRNA; other site 479436004302 putative tRNA binding site [nucleotide binding]; other site 479436004303 putative NADP binding site [chemical binding]; other site 479436004304 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 479436004305 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436004306 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 479436004307 Uncharacterized conserved protein, contains S4-like domain [Function unknown]; Region: COG2302 479436004308 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 479436004309 RNA binding surface [nucleotide binding]; other site 479436004310 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436004311 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 479436004312 Protein of unknown function (DUF552); Region: DUF552; cl00775 479436004313 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 479436004314 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 479436004315 catalytic residue [active] 479436004316 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 479436004317 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 479436004318 radical SAM family uncharacterized protein; Region: rSAM_fuse_unch; TIGR03960 479436004319 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 479436004320 B12 binding site [chemical binding]; other site 479436004321 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 479436004322 FeS/SAM binding site; other site 479436004323 Protein of unknown function (DUF421); Region: DUF421; cl00990 479436004324 Protein of unknown function (DUF3290); Region: DUF3290; pfam11694 479436004325 ketol-acid reductoisomerase; Provisional; Region: PRK05479 479436004326 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436004327 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 479436004328 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436004329 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 479436004330 Walker A/P-loop; other site 479436004331 ATP binding site [chemical binding]; other site 479436004332 Q-loop/lid; other site 479436004333 ABC transporter signature motif; other site 479436004334 Walker B; other site 479436004335 D-loop; other site 479436004336 H-loop/switch region; other site 479436004337 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 479436004338 putative valine binding site [chemical binding]; other site 479436004339 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 479436004340 dimer interface [polypeptide binding]; other site 479436004341 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 479436004342 acetolactate synthase 3 catalytic subunit; Reviewed; Region: PRK06048 479436004343 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 479436004344 PYR/PP interface [polypeptide binding]; other site 479436004345 dimer interface [polypeptide binding]; other site 479436004346 TPP binding site [chemical binding]; other site 479436004347 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 479436004348 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 479436004349 TPP-binding site [chemical binding]; other site 479436004350 dimer interface [polypeptide binding]; other site 479436004351 threonine dehydratase; Provisional; Region: PRK08198 479436004352 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 479436004353 tetramer interface [polypeptide binding]; other site 479436004354 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436004355 catalytic residue [active] 479436004356 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 479436004357 Dehydratase family; Region: ILVD_EDD; cl00340 479436004358 6-phosphogluconate dehydratase; Region: edd; TIGR01196 479436004359 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 479436004360 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; cl15357 479436004361 transmembrane helices; other site 479436004362 Cupin domain; Region: Cupin_2; cl09118 479436004363 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 479436004364 metal-binding site [ion binding] 479436004365 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 479436004366 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 479436004367 putative active site [active] 479436004368 enoyl-CoA hydratase; Provisional; Region: PRK07260 479436004369 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 479436004370 substrate binding site [chemical binding]; other site 479436004371 oxyanion hole (OAH) forming residues; other site 479436004372 trimer interface [polypeptide binding]; other site 479436004373 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 479436004374 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 479436004375 23S rRNA interface [nucleotide binding]; other site 479436004376 L3 interface [polypeptide binding]; other site 479436004377 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 479436004378 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 479436004379 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 479436004380 RNA binding surface [nucleotide binding]; other site 479436004381 Transcriptional regulator [Transcription]; Region: LysR; COG0583 479436004382 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004383 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 479436004384 dimerization interface [polypeptide binding]; other site 479436004385 Uncharacterised BCR, YnfA/UPF0060 family; Region: UPF0060; cl00757 479436004386 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 479436004387 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 479436004388 putative dimer interface [polypeptide binding]; other site 479436004389 active site pocket [active] 479436004390 putative cataytic base [active] 479436004391 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 479436004392 putative dimer interface [polypeptide binding]; other site 479436004393 active site pocket [active] 479436004394 putative cataytic base [active] 479436004395 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 479436004396 MatE; Region: MatE; cl10513 479436004397 MatE; Region: MatE; cl10513 479436004398 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 479436004399 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 479436004400 TPP-binding site [chemical binding]; other site 479436004401 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 479436004402 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 479436004403 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 479436004404 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 479436004405 dimer interface [polypeptide binding]; other site 479436004406 PYR/PP interface [polypeptide binding]; other site 479436004407 TPP binding site [chemical binding]; other site 479436004408 substrate binding site [chemical binding]; other site 479436004409 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 479436004410 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 479436004411 dimerization interface 3.5A [polypeptide binding]; other site 479436004412 active site 479436004413 Cobalt transport protein; Region: CbiQ; cl00463 479436004414 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13637 479436004415 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 479436004416 Walker A/P-loop; other site 479436004417 ATP binding site [chemical binding]; other site 479436004418 Q-loop/lid; other site 479436004419 ABC transporter signature motif; other site 479436004420 Walker B; other site 479436004421 D-loop; other site 479436004422 H-loop/switch region; other site 479436004423 Cobalt ATP-binding cassette C terminal; Region: CoABC_C; pfam12370 479436004424 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13633 479436004425 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 479436004426 Walker A/P-loop; other site 479436004427 ATP binding site [chemical binding]; other site 479436004428 Q-loop/lid; other site 479436004429 ABC transporter signature motif; other site 479436004430 Walker B; other site 479436004431 D-loop; other site 479436004432 H-loop/switch region; other site 479436004433 Cobalt ATP-binding cassette C terminal; Region: CoABC_C; pfam12370 479436004434 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 479436004435 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 479436004436 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 479436004437 alphaNTD - beta interaction site [polypeptide binding]; other site 479436004438 alphaNTD homodimer interface [polypeptide binding]; other site 479436004439 alphaNTD - beta' interaction site [polypeptide binding]; other site 479436004440 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 479436004441 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 479436004442 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 479436004443 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 479436004444 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 479436004445 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 479436004446 rRNA binding site [nucleotide binding]; other site 479436004447 predicted 30S ribosome binding site; other site 479436004448 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 479436004449 active site 479436004450 adenylate kinase; Reviewed; Region: adk; PRK00279 479436004451 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 479436004452 AMP-binding site [chemical binding]; other site 479436004453 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 479436004454 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 479436004455 SecY translocase; Region: SecY; pfam00344 479436004456 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 479436004457 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 479436004458 23S rRNA binding site [nucleotide binding]; other site 479436004459 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 479436004460 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 479436004461 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 479436004462 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 479436004463 23S rRNA interface [nucleotide binding]; other site 479436004464 L21e interface [polypeptide binding]; other site 479436004465 5S rRNA interface [nucleotide binding]; other site 479436004466 L27 interface [polypeptide binding]; other site 479436004467 L5 interface [polypeptide binding]; other site 479436004468 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 479436004469 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 479436004470 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 479436004471 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 479436004472 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 479436004473 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 479436004474 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 479436004475 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 479436004476 KOW motif; Region: KOW; cl00354 479436004477 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 479436004478 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 479436004479 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 479436004480 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 479436004481 23S rRNA interface [nucleotide binding]; other site 479436004482 putative translocon interaction site; other site 479436004483 signal recognition particle (SRP54) interaction site; other site 479436004484 L23 interface [polypeptide binding]; other site 479436004485 trigger factor interaction site; other site 479436004486 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 479436004487 23S rRNA interface [nucleotide binding]; other site 479436004488 5S rRNA interface [nucleotide binding]; other site 479436004489 putative antibiotic binding site [chemical binding]; other site 479436004490 L25 interface [polypeptide binding]; other site 479436004491 L27 interface [polypeptide binding]; other site 479436004492 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 479436004493 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 479436004494 G-X-X-G motif; other site 479436004495 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 479436004496 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 479436004497 putative translocon binding site; other site 479436004498 protein-rRNA interface [nucleotide binding]; other site 479436004499 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 479436004500 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 479436004501 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 479436004502 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 479436004503 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 479436004504 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 479436004505 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 479436004506 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 479436004507 elongation factor Tu; Reviewed; Region: PRK00049 479436004508 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 479436004509 G1 box; other site 479436004510 GEF interaction site [polypeptide binding]; other site 479436004511 GTP/Mg2+ binding site [chemical binding]; other site 479436004512 Switch I region; other site 479436004513 G2 box; other site 479436004514 G3 box; other site 479436004515 Switch II region; other site 479436004516 G4 box; other site 479436004517 G5 box; other site 479436004518 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 479436004519 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 479436004520 Antibiotic Binding Site [chemical binding]; other site 479436004521 elongation factor G; Reviewed; Region: PRK00007 479436004522 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so...; Region: EF-G; cd01886 479436004523 G1 box; other site 479436004524 putative GEF interaction site [polypeptide binding]; other site 479436004525 GTP/Mg2+ binding site [chemical binding]; other site 479436004526 Switch I region; other site 479436004527 G2 box; other site 479436004528 G3 box; other site 479436004529 Switch II region; other site 479436004530 G4 box; other site 479436004531 G5 box; other site 479436004532 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 479436004533 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 479436004534 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 479436004535 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 479436004536 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 479436004537 S17 interaction site [polypeptide binding]; other site 479436004538 S8 interaction site; other site 479436004539 16S rRNA interaction site [nucleotide binding]; other site 479436004540 streptomycin interaction site [chemical binding]; other site 479436004541 23S rRNA interaction site [nucleotide binding]; other site 479436004542 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 479436004543 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 479436004544 BCCT family transporter; Region: BCCT; cl00569 479436004545 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 479436004546 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 479436004547 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 479436004548 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 479436004549 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 479436004550 RNA polymerase beta'' subunit; Reviewed; Region: rpoC2; CHL00117 479436004551 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 479436004552 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 479436004553 G-loop; other site 479436004554 Apocytochrome F, C-terminal; Region: Apocytochr_F_C; cl03168 479436004555 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 479436004556 DNA binding site [nucleotide binding] 479436004557 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 479436004558 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 479436004559 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 479436004560 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 479436004561 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 479436004562 RNA polymerase beta subunit external 1 domain; Region: RNA_pol_Rpb2_45; pfam10385 479436004563 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 479436004564 RPB10 interaction site [polypeptide binding]; other site 479436004565 RPB11 interaction site [polypeptide binding]; other site 479436004566 RPB3 interaction site [polypeptide binding]; other site 479436004567 RPB12 interaction site [polypeptide binding]; other site 479436004568 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 479436004569 RPB1 interaction site [polypeptide binding]; other site 479436004570 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 479436004571 Aspartase; Region: Aspartase; cd01357 479436004572 active sites [active] 479436004573 tetramer interface [polypeptide binding]; other site 479436004574 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 479436004575 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl15364 479436004576 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 479436004577 core dimer interface [polypeptide binding]; other site 479436004578 peripheral dimer interface [polypeptide binding]; other site 479436004579 L10 interface [polypeptide binding]; other site 479436004580 L11 interface [polypeptide binding]; other site 479436004581 putative EF-Tu interaction site [polypeptide binding]; other site 479436004582 putative EF-G interaction site [polypeptide binding]; other site 479436004583 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 479436004584 23S rRNA interface [nucleotide binding]; other site 479436004585 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 479436004586 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 479436004587 mRNA/rRNA interface [nucleotide binding]; other site 479436004588 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 479436004589 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 479436004590 23S rRNA interface [nucleotide binding]; other site 479436004591 L7/L12 interface [polypeptide binding]; other site 479436004592 putative thiostrepton binding site; other site 479436004593 L25 interface [polypeptide binding]; other site 479436004594 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 479436004595 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 479436004596 putative homodimer interface [polypeptide binding]; other site 479436004597 KOW motif; Region: KOW; cl00354 479436004598 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 479436004599 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 479436004600 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 479436004601 elongation factor Tu; Reviewed; Region: PRK00049 479436004602 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 479436004603 G1 box; other site 479436004604 GEF interaction site [polypeptide binding]; other site 479436004605 GTP/Mg2+ binding site [chemical binding]; other site 479436004606 Switch I region; other site 479436004607 G2 box; other site 479436004608 G3 box; other site 479436004609 Switch II region; other site 479436004610 G4 box; other site 479436004611 G5 box; other site 479436004612 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 479436004613 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 479436004614 Antibiotic Binding Site [chemical binding]; other site 479436004615 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436004616 active site 479436004617 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436004618 Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]; Region: HybF; cl00418 479436004619 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 479436004620 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 479436004621 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 479436004622 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 479436004623 homodimer interface [polypeptide binding]; other site 479436004624 NADP binding site [chemical binding]; other site 479436004625 substrate binding site [chemical binding]; other site 479436004626 stage V sporulation protein D; Region: spoVD_pbp; TIGR02214 479436004627 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 479436004628 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 479436004629 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 479436004630 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 479436004631 active site 479436004632 NTP binding site [chemical binding]; other site 479436004633 metal binding triad [ion binding]; metal-binding site 479436004634 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 479436004635 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 479436004636 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 479436004637 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 479436004638 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 479436004639 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 479436004640 C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; Region: ACT_LSD; cd04903 479436004641 putative L-serine binding site [chemical binding]; other site 479436004642 hybrid cluster protein; Provisional; Region: PRK05290 479436004643 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 479436004644 CODH interaction site; other site 479436004645 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 479436004646 ACS interaction site; other site 479436004647 CODH interaction site; other site 479436004648 metal cluster binding site [ion binding]; other site 479436004649 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 479436004650 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 479436004651 ligand binding site [chemical binding]; other site 479436004652 flexible hinge region; other site 479436004653 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004654 Protein of unknown function (DUF436); Region: DUF436; cl01860 479436004655 Fumarase C-terminus; Region: Fumerase_C; cl00795 479436004656 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 479436004657 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 479436004658 ATP synthase, Delta/Epsilon chain, long alpha-helix domain; Region: ATP-synt_DE; pfam00401 479436004659 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 479436004660 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 479436004661 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 479436004662 alpha subunit interaction interface [polypeptide binding]; other site 479436004663 Walker A motif; other site 479436004664 ATP binding site [chemical binding]; other site 479436004665 Walker B motif; other site 479436004666 inhibitor binding site; inhibition site 479436004667 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 479436004668 ATP synthase; Region: ATP-synt; cl00365 479436004669 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 479436004670 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 479436004671 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 479436004672 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 479436004673 beta subunit interaction interface [polypeptide binding]; other site 479436004674 Walker A motif; other site 479436004675 ATP binding site [chemical binding]; other site 479436004676 Walker B motif; other site 479436004677 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 479436004678 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl15360 479436004679 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 479436004680 Plant ATP synthase F0; Region: YMF19; cl07975 479436004681 ATP synthase B/B' CF(0); Region: ATP-synt_B; pfam00430 479436004682 ATP synthase subunit C; Region: ATP-synt_C; cl00466 479436004683 ATP synthase A chain; Region: ATP-synt_A; cl00413 479436004684 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 479436004685 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 479436004686 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 479436004687 active site 479436004688 homodimer interface [polypeptide binding]; other site 479436004689 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 479436004690 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 479436004691 Mg++ binding site [ion binding]; other site 479436004692 putative catalytic motif [active] 479436004693 substrate binding site [chemical binding]; other site 479436004694 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 479436004695 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 479436004696 phosphoglucomutase; Validated; Region: PRK07564 479436004697 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 479436004698 active site 479436004699 substrate binding site [chemical binding]; other site 479436004700 metal binding site [ion binding]; metal-binding site 479436004701 Uncharacterized conserved protein [Function unknown]; Region: COG1284 479436004702 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 479436004703 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 479436004704 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; cl10498 479436004705 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate synthase [Lipid metabolism]; Region: IspE; COG1947 479436004706 Transcriptional regulators [Transcription]; Region: GntR; COG1802 479436004707 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 479436004708 DNA-binding site [nucleotide binding]; DNA binding site 479436004709 FCD domain; Region: FCD; cl11656 479436004710 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 479436004711 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 479436004712 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 479436004713 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 479436004714 NAD(P) binding site [chemical binding]; other site 479436004715 QueT transporter; Region: QueT; cl01932 479436004716 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 479436004717 Ligand Binding Site [chemical binding]; other site 479436004718 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 479436004719 active site 479436004720 DNA binding site [nucleotide binding] 479436004721 putative phosphate binding site [ion binding]; other site 479436004722 putative catalytic site [active] 479436004723 metal binding site A [ion binding]; metal-binding site 479436004724 AP binding site [nucleotide binding]; other site 479436004725 metal binding site B [ion binding]; metal-binding site 479436004726 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 479436004727 3-mercaptopyruvate sulfurtransferase; Provisional; Region: sseA; PRK11493 479436004728 active site residue [active] 479436004729 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 479436004730 active site residue [active] 479436004731 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 479436004732 active site 479436004733 8-oxo-dGMP binding site [chemical binding]; other site 479436004734 nudix motif; other site 479436004735 metal binding site [ion binding]; metal-binding site 479436004736 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_b2; cd09204 479436004737 putative homodimer interface [polypeptide binding]; other site 479436004738 putative active site [active] 479436004739 catalytic site [active] 479436004740 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 479436004741 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 479436004742 ATP binding site [chemical binding]; other site 479436004743 putative Mg++ binding site [ion binding]; other site 479436004744 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 479436004745 nucleotide binding region [chemical binding]; other site 479436004746 ATP-binding site [chemical binding]; other site 479436004747 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 479436004748 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_3; cd08490 479436004749 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 479436004750 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 479436004751 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 479436004752 Walker A/P-loop; other site 479436004753 ATP binding site [chemical binding]; other site 479436004754 Q-loop/lid; other site 479436004755 ABC transporter signature motif; other site 479436004756 Walker B; other site 479436004757 D-loop; other site 479436004758 H-loop/switch region; other site 479436004759 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 479436004760 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 479436004761 Walker A/P-loop; other site 479436004762 ATP binding site [chemical binding]; other site 479436004763 Q-loop/lid; other site 479436004764 ABC transporter signature motif; other site 479436004765 Walker B; other site 479436004766 D-loop; other site 479436004767 H-loop/switch region; other site 479436004768 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_3; cd08490 479436004769 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 479436004770 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 479436004771 nickel transporter permease NikC; Provisional; Region: nikC; PRK10417 479436004772 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 479436004773 dimer interface [polypeptide binding]; other site 479436004774 conserved gate region; other site 479436004775 putative PBP binding loops; other site 479436004776 ABC-ATPase subunit interface; other site 479436004777 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 479436004778 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 479436004779 dimer interface [polypeptide binding]; other site 479436004780 conserved gate region; other site 479436004781 putative PBP binding loops; other site 479436004782 ABC-ATPase subunit interface; other site 479436004783 Amino acid permease; Region: AA_permease; cl00524 479436004784 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 479436004785 argininosuccinate lyase; Provisional; Region: PRK00855 479436004786 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 479436004787 active sites [active] 479436004788 tetramer interface [polypeptide binding]; other site 479436004789 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 479436004790 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 479436004791 ANP binding site [chemical binding]; other site 479436004792 Substrate Binding Site II [chemical binding]; other site 479436004793 Substrate Binding Site I [chemical binding]; other site 479436004794 Transglycosylase; Region: Transgly; cl07896 479436004795 Uncharacterized family 3; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Region: CsoR-like_DUF156_3; cd10160 479436004796 putative homotetramer interface [polypeptide binding]; other site 479436004797 putative homodimer interface [polypeptide binding]; other site 479436004798 putative metal binding site [ion binding]; other site 479436004799 putative homodimer-homodimer interface [polypeptide binding]; other site 479436004800 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 479436004801 dimerization domain swap beta strand [polypeptide binding]; other site 479436004802 regulatory protein interface [polypeptide binding]; other site 479436004803 active site 479436004804 regulatory phosphorylation site [posttranslational modification]; other site 479436004805 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 479436004806 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 479436004807 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 479436004808 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 479436004809 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 479436004810 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 479436004811 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 479436004812 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 479436004813 Na+/H+ antiporter family; Region: Na_H_antiporter; cl15356 479436004814 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 479436004815 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 479436004816 putative substrate binding site [chemical binding]; other site 479436004817 putative ATP binding site [chemical binding]; other site 479436004818 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional; Region: PRK09765 479436004819 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 479436004820 active site 479436004821 phosphorylation site [posttranslational modification] 479436004822 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 479436004823 P-loop; other site 479436004824 active site 479436004825 phosphorylation site [posttranslational modification] 479436004826 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]; Region: PtsG; cl00557 479436004827 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 479436004828 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 479436004829 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 479436004830 dimer interface [polypeptide binding]; other site 479436004831 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436004832 catalytic residue [active] 479436004833 Predicted transcriptional regulator [Transcription]; Region: COG1959 479436004834 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004835 peroxiredoxin; Region: AhpC; TIGR03137 479436004836 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 479436004837 dimer interface [polypeptide binding]; other site 479436004838 decamer (pentamer of dimers) interface [polypeptide binding]; other site 479436004839 catalytic triad [active] 479436004840 peroxidatic and resolving cysteines [active] 479436004841 CTP synthetase; Validated; Region: pyrG; PRK05380 479436004842 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 479436004843 Catalytic site [active] 479436004844 active site 479436004845 UTP binding site [chemical binding]; other site 479436004846 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 479436004847 active site 479436004848 putative oxyanion hole; other site 479436004849 catalytic triad [active] 479436004850 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 479436004851 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 479436004852 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 479436004853 active site 479436004854 HIGH motif; other site 479436004855 nucleotide binding site [chemical binding]; other site 479436004856 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 479436004857 KMSK motif region; other site 479436004858 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 479436004859 tRNA binding surface [nucleotide binding]; other site 479436004860 anticodon binding site; other site 479436004861 Domain of unknown function (DUF1934); Region: DUF1934; cl01870 479436004862 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 479436004863 GIY-YIG motif/motif A; other site 479436004864 putative active site [active] 479436004865 putative metal binding site [ion binding]; other site 479436004866 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 479436004867 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 479436004868 active site 479436004869 Tht1-like nuclear fusion protein; Region: Tht1; pfam04163 479436004870 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 479436004871 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 479436004872 active site 479436004873 motif I; other site 479436004874 motif II; other site 479436004875 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436004876 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 479436004877 Glycerol dehydrogenase-like; Region: GlyDH-like2; cd08171 479436004878 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 479436004879 putative active site [active] 479436004880 metal binding site [ion binding]; metal-binding site 479436004881 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 479436004882 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 479436004883 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 479436004884 putative [4Fe-4S] binding site [ion binding]; other site 479436004885 putative molybdopterin cofactor binding site [chemical binding]; other site 479436004886 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 479436004887 molybdopterin cofactor binding site; other site 479436004888 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 479436004889 glycolate transporter; Provisional; Region: PRK09695 479436004890 L-lactate permease; Region: Lactate_perm; cl00701 479436004891 Peptidase propeptide and YPEB domain; Region: PepSY; cl15480 479436004892 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 479436004893 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 479436004894 putative substrate translocation pore; other site 479436004895 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 479436004896 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 479436004897 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 479436004898 CoA enzyme activase uncharacterised domain (DUF2229); Region: DUF2229; cl12083 479436004899 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 479436004900 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 479436004901 Domain of unknown function (DUF389); Region: DUF389; cl00781 479436004902 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 479436004903 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 479436004904 active site pocket [active] 479436004905 putative dimer interface [polypeptide binding]; other site 479436004906 putative cataytic base [active] 479436004907 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 479436004908 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 479436004909 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 479436004910 active site 479436004911 NAD binding site [chemical binding]; other site 479436004912 metal binding site [ion binding]; metal-binding site 479436004913 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07088 479436004914 ATP cone domain; Region: ATP-cone; pfam03477 479436004915 Class I ribonucleotide reductase; Region: RNR_I; cd01679 479436004916 active site 479436004917 dimer interface [polypeptide binding]; other site 479436004918 catalytic residues [active] 479436004919 effector binding site; other site 479436004920 R2 peptide binding site; other site 479436004921 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 479436004922 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 479436004923 dimer interface [polypeptide binding]; other site 479436004924 putative radical transfer pathway; other site 479436004925 diiron center [ion binding]; other site 479436004926 tyrosyl radical; other site 479436004927 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 479436004928 Coenzyme A binding pocket [chemical binding]; other site 479436004929 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 479436004930 NeuB family; Region: NeuB; cl00496 479436004931 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 479436004932 active site 479436004933 dimer interface [polypeptide binding]; other site 479436004934 metal binding site [ion binding]; metal-binding site 479436004935 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 479436004936 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 479436004937 hinge; other site 479436004938 active site 479436004939 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 479436004940 Tetramer interface [polypeptide binding]; other site 479436004941 active site 479436004942 FMN-binding site [chemical binding]; other site 479436004943 Chorismate mutase type II; Region: CM_2; cl00693 479436004944 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 479436004945 Prephenate dehydratase; Region: PDT; pfam00800 479436004946 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 479436004947 putative L-Phe binding site [chemical binding]; other site 479436004948 Shikimate 5-dehydrogenase [Amino acid transport and metabolism]; Region: AroE; COG0169 479436004949 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 479436004950 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 479436004951 shikimate binding site; other site 479436004952 NAD(P) binding site [chemical binding]; other site 479436004953 shikimate kinase; Reviewed; Region: aroK; PRK00131 479436004954 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 479436004955 ADP binding site [chemical binding]; other site 479436004956 magnesium binding site [ion binding]; other site 479436004957 putative shikimate binding site; other site 479436004958 RelB antitoxin; Region: RelB; cl01171 479436004959 RelB antitoxin; Region: RelB; cl01171 479436004960 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 479436004961 3-dehydroquinate dehydratase, type I; Region: aroD; TIGR01093 479436004962 active site 479436004963 catalytic residue [active] 479436004964 dimer interface [polypeptide binding]; other site 479436004965 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 479436004966 Major Facilitator Superfamily; Region: MFS_1; pfam07690 479436004967 putative substrate translocation pore; other site 479436004968 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004969 Rrf2 family protein; Region: rrf2_super; TIGR00738 479436004970 Permease family; Region: Xan_ur_permease; cl00967 479436004971 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 479436004972 transcriptional regulator SlyA; Provisional; Region: PRK03573 479436004973 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436004974 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 479436004975 hydrophobic ligand binding site; other site 479436004976 Amino acid permease; Region: AA_permease; cl00524 479436004977 Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; Region: AnsP; COG1113 479436004978 Protein of unknown function, DUF600; Region: DUF600; cl04640 479436004979 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 479436004980 Cation efflux family; Region: Cation_efflux; cl00316 479436004981 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 479436004982 active site 479436004983 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436004984 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 479436004985 active site 479436004986 substrate binding site [chemical binding]; other site 479436004987 catalytic site [active] 479436004988 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 479436004989 recombination protein RecR; Reviewed; Region: recR; PRK00076 479436004990 RecR protein; Region: RecR; pfam02132 479436004991 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 479436004992 putative active site [active] 479436004993 putative metal-binding site [ion binding]; other site 479436004994 tetramer interface [polypeptide binding]; other site 479436004995 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 479436004996 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 479436004997 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 479436004998 Walker A motif; other site 479436004999 ATP binding site [chemical binding]; other site 479436005000 Walker B motif; other site 479436005001 arginine finger; other site 479436005002 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 479436005003 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 479436005004 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 479436005005 active site 479436005006 dimer interface [polypeptide binding]; other site 479436005007 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 479436005008 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 479436005009 active site 479436005010 FMN binding site [chemical binding]; other site 479436005011 substrate binding site [chemical binding]; other site 479436005012 3Fe-4S cluster binding site [ion binding]; other site 479436005013 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 479436005014 domain interface; other site 479436005015 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 479436005016 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 479436005017 active site 479436005018 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 479436005019 Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]; Region: Eis; COG4552 479436005020 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 479436005021 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 479436005022 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 479436005023 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 479436005024 active site 479436005025 catalytic tetrad [active] 479436005026 Branched-chain amino acid transport protein (AzlD); Region: AzlD; cl00735 479436005027 AzlC protein; Region: AzlC; cl00570 479436005028 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 479436005029 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 479436005030 dimer interface [polypeptide binding]; other site 479436005031 active site 479436005032 metal binding site [ion binding]; metal-binding site 479436005033 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 479436005034 4Fe-4S binding domain; Region: Fer4; cl02805 479436005035 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 479436005036 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 479436005037 FMN binding site [chemical binding]; other site 479436005038 dimer interface [polypeptide binding]; other site 479436005039 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 479436005040 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 479436005041 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 479436005042 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 479436005043 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 479436005044 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 479436005045 4Fe-4S binding domain; Region: Fer4; cl02805 479436005046 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 479436005047 Cysteine-rich domain; Region: CCG; pfam02754 479436005048 Cysteine-rich domain; Region: CCG; pfam02754 479436005049 S-layer homology domain; Region: SLH; pfam00395 479436005050 S-layer homology domain; Region: SLH; pfam00395 479436005051 S-layer homology domain; Region: SLH; pfam00395 479436005052 S-layer homology domain; Region: SLH; pfam00395 479436005053 S-layer homology domain; Region: SLH; pfam00395 479436005054 S-layer homology domain; Region: SLH; pfam00395 479436005055 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 479436005056 OPT oligopeptide transporter protein; Region: OPT; cl14607 479436005057 fumarate hydratase; Reviewed; Region: fumC; PRK00485 479436005058 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 479436005059 tetramer interface [polypeptide binding]; other site 479436005060 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 479436005061 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 479436005062 putative active site [active] 479436005063 putative metal binding site [ion binding]; other site 479436005064 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 479436005065 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 479436005066 minor groove reading motif; other site 479436005067 helix-hairpin-helix signature motif; other site 479436005068 substrate binding pocket [chemical binding]; other site 479436005069 active site 479436005070 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 479436005071 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 479436005072 DNA binding and oxoG recognition site [nucleotide binding] 479436005073 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 479436005074 putative active site [active] 479436005075 nucleotide binding site [chemical binding]; other site 479436005076 nudix motif; other site 479436005077 putative metal binding site [ion binding]; other site 479436005078 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 479436005079 nucleotide binding site/active site [active] 479436005080 HIT family signature motif; other site 479436005081 catalytic residue [active] 479436005082 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 479436005083 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 479436005084 active site 479436005085 metal binding site [ion binding]; metal-binding site 479436005086 Hep_Hag; Region: Hep_Hag; pfam05658 479436005087 Hep_Hag; Region: Hep_Hag; pfam05658 479436005088 Haemagglutinin; Region: HIM; pfam05662 479436005089 S-layer homology domain; Region: SLH; pfam00395 479436005090 MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is...; Region: MoeA_like; cd03522 479436005091 putative MPT binding site; other site 479436005092 CrcB-like protein; Region: CRCB; cl09114 479436005093 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 479436005094 non-specific DNA binding site [nucleotide binding]; other site 479436005095 salt bridge; other site 479436005096 sequence-specific DNA binding site [nucleotide binding]; other site 479436005097 Transcriptional regulators [Transcription]; Region: GntR; COG1802 479436005098 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 479436005099 DNA-binding site [nucleotide binding]; DNA binding site 479436005100 FCD domain; Region: FCD; cl11656 479436005101 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 479436005102 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 479436005103 helicase-exonuclease AddAB, AddA subunit; Region: addA_Gpos; TIGR02785 479436005104 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436005105 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436005106 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 479436005107 helicase-exonuclease AddAB, AddB subunit; Region: addB_Gpos; TIGR02773 479436005108 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 479436005109 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 479436005110 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 479436005111 active site 479436005112 catalytic triad [active] 479436005113 oxyanion hole [active] 479436005114 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 479436005115 D-galactonate transporter; Region: 2A0114; TIGR00893 479436005116 putative substrate translocation pore; other site 479436005117 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 479436005118 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 479436005119 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 479436005120 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 479436005121 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 479436005122 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436005123 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 479436005124 dimer interface [polypeptide binding]; other site 479436005125 conserved gate region; other site 479436005126 putative PBP binding loops; other site 479436005127 ABC-ATPase subunit interface; other site 479436005128 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 479436005129 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 479436005130 YolD-like protein; Region: YolD; pfam08863 479436005131 DNA polymerase IV; Reviewed; Region: PRK03103 479436005132 Y-family of DNA polymerases; Region: PolY; cl12025 479436005133 active site 479436005134 DNA binding site [nucleotide binding] 479436005135 replicative DNA helicase; Region: DnaB; TIGR00665 479436005136 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 479436005137 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 479436005138 Walker A motif; other site 479436005139 ATP binding site [chemical binding]; other site 479436005140 Walker B motif; other site 479436005141 DNA binding loops [nucleotide binding] 479436005142 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 479436005143 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 479436005144 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 479436005145 DHH family; Region: DHH; pfam01368 479436005146 DHHA1 domain; Region: DHHA1; pfam02272 479436005147 Predicted membrane protein (DUF2232); Region: DUF2232; cl01728 479436005148 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 479436005149 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436005150 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 479436005151 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436005152 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_3; cd10035 479436005153 putative uracil binding site [chemical binding]; other site 479436005154 putative active site [active] 479436005155 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 479436005156 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 479436005157 Walker A/P-loop; other site 479436005158 ATP binding site [chemical binding]; other site 479436005159 Q-loop/lid; other site 479436005160 ABC transporter signature motif; other site 479436005161 Walker B; other site 479436005162 D-loop; other site 479436005163 H-loop/switch region; other site 479436005164 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 479436005165 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 479436005166 dimer interface [polypeptide binding]; other site 479436005167 conserved gate region; other site 479436005168 putative PBP binding loops; other site 479436005169 ABC-ATPase subunit interface; other site 479436005170 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 479436005171 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 479436005172 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT; cl15364 479436005173 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 479436005174 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 479436005175 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 479436005176 Walker A/P-loop; other site 479436005177 ATP binding site [chemical binding]; other site 479436005178 Q-loop/lid; other site 479436005179 ABC transporter signature motif; other site 479436005180 Walker B; other site 479436005181 D-loop; other site 479436005182 H-loop/switch region; other site 479436005183 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 479436005184 ABC-ATPase subunit interface; other site 479436005185 dimer interface [polypeptide binding]; other site 479436005186 putative PBP binding regions; other site 479436005187 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 479436005188 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 479436005189 intersubunit interface [polypeptide binding]; other site 479436005190 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 479436005191 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 479436005192 N-terminal plug; other site 479436005193 ligand-binding site [chemical binding]; other site 479436005194 Gram-negative bacterial tonB protein; Region: TonB; cl10048 479436005195 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 479436005196 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 479436005197 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 479436005198 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 479436005199 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 479436005200 Cysteine-rich domain; Region: CCG; pfam02754 479436005201 Cysteine-rich domain; Region: CCG; pfam02754 479436005202 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 479436005203 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436005204 succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup; Region: sdhA_frdA_Gneg; TIGR01812 479436005205 domain; Region: Succ_DH_flav_C; pfam02910 479436005206 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 479436005207 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 479436005208 active site 479436005209 phosphorylation site [posttranslational modification] 479436005210 intermolecular recognition site; other site 479436005211 dimerization interface [polypeptide binding]; other site 479436005212 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 479436005213 DNA binding site [nucleotide binding] 479436005214 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 479436005215 dimerization interface [polypeptide binding]; other site 479436005216 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 479436005217 dimer interface [polypeptide binding]; other site 479436005218 phosphorylation site [posttranslational modification] 479436005219 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 479436005220 ATP binding site [chemical binding]; other site 479436005221 Mg2+ binding site [ion binding]; other site 479436005222 G-X-G motif; other site 479436005223 Protein of unknown function (DUF445); Region: DUF445; pfam04286 479436005224 Protein of unknown function (DUF445); Region: DUF445; pfam04286 479436005225 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 479436005226 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 479436005227 putative DNA binding site [nucleotide binding]; other site 479436005228 dimerization interface [polypeptide binding]; other site 479436005229 putative Zn2+ binding site [ion binding]; other site 479436005230 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 479436005231 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 479436005232 putative active site [active] 479436005233 metal binding site [ion binding]; metal-binding site 479436005234 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 479436005235 catalytic residues [active] 479436005236 dimer interface [polypeptide binding]; other site 479436005237 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 479436005238 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 479436005239 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 479436005240 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 479436005241 Uncharacterised ACR, YkgG family COG1556; Region: DUF162; cl00674 479436005242 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 479436005243 non-specific DNA binding site [nucleotide binding]; other site 479436005244 salt bridge; other site 479436005245 sequence-specific DNA binding site [nucleotide binding]; other site 479436005246 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 479436005247 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436005248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 479436005249 Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]; Region: MalY; COG1168 479436005250 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 479436005251 pyridoxal 5'-phosphate binding site [chemical binding]; other site 479436005252 homodimer interface [polypeptide binding]; other site 479436005253 catalytic residue [active] 479436005254 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 479436005255 Uncharacterized conserved protein [Function unknown]; Region: COG2461 479436005256 Family of unknown function (DUF438); Region: DUF438; pfam04282 479436005257 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 479436005258 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 479436005259 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 479436005260 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 479436005261 Isochorismatase family; Region: Isochorismatase; pfam00857 479436005262 catalytic triad [active] 479436005263 conserved cis-peptide bond; other site 479436005264 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 479436005265 tetramer interfaces [polypeptide binding]; other site 479436005266 binuclear metal-binding site [ion binding]; other site 479436005267 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 479436005268 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 479436005269 PhnA protein; Region: PhnA; pfam03831 479436005270 Uncharacterised protein family (UPF0150); Region: UPF0150; cl00691 479436005271 YcfA-like protein; Region: YcfA; cl00752 479436005272 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 479436005273 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 479436005274 DNA binding residues [nucleotide binding] 479436005275 putative dimer interface [polypeptide binding]; other site 479436005276 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 479436005277 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 479436005278 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 479436005279 Protein of unknown function (DUF2695); Region: DUF2695; pfam10905 479436005280 Domain of unknown function (DUF1877); Region: DUF1877; pfam08974 479436005281 Uncharacterized protein conserved in bacteria (DUF2262); Region: DUF2262; cl01757 479436005282 McrBC 5-methylcytosine restriction system component; Region: McrBC; cl01737 479436005283 Uncharacterized conserved protein [Function unknown]; Region: COG4127 479436005284 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 479436005285 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 479436005286 Walker A motif; other site 479436005287 ATP binding site [chemical binding]; other site 479436005288 Walker B motif; other site 479436005289 arginine finger; other site 479436005290 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 479436005291 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436005292 ABC transporter signature motif; other site 479436005293 Walker B; other site 479436005294 D-loop; other site 479436005295 H-loop/switch region; other site 479436005296 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 479436005297 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 479436005298 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 479436005299 tetramer interface [polypeptide binding]; other site 479436005300 heme binding pocket [chemical binding]; other site 479436005301 NADPH binding site [chemical binding]; other site 479436005302 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 479436005303 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 479436005304 active site 479436005305 DNA binding site [nucleotide binding] 479436005306 DNA polymerase IV; Reviewed; Region: PRK03103 479436005307 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 479436005308 dimerization interface [polypeptide binding]; other site 479436005309 putative DNA binding site [nucleotide binding]; other site 479436005310 putative Zn2+ binding site [ion binding]; other site 479436005311 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 479436005312 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 479436005313 GDP-binding site [chemical binding]; other site 479436005314 ACT binding site; other site 479436005315 IMP binding site; other site 479436005316 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 479436005317 non-specific DNA binding site [nucleotide binding]; other site 479436005318 salt bridge; other site 479436005319 sequence-specific DNA binding site [nucleotide binding]; other site 479436005320 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 479436005321 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 479436005322 Major Facilitator Superfamily; Region: MFS_1; pfam07690 479436005323 putative substrate translocation pore; other site 479436005324 adenylosuccinate lyase; Provisional; Region: PRK07492 479436005325 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 479436005326 tetramer interface [polypeptide binding]; other site 479436005327 active site 479436005328 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 479436005329 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 479436005330 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 479436005331 membrane ATPase/protein kinase; Provisional; Region: PRK09435 479436005332 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 479436005333 Walker A; other site 479436005334 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436005335 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 479436005336 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain...; Region: MM_CoA_mutase_alpha_like; cd03679 479436005337 active site 479436005338 substrate binding site [chemical binding]; other site 479436005339 coenzyme B12 binding site [chemical binding]; other site 479436005340 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 479436005341 B12 binding site [chemical binding]; other site 479436005342 cobalt ligand [ion binding]; other site 479436005343 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta...; Region: MM_CoA_mutase_beta; cd03677 479436005344 heterodimer interface [polypeptide binding]; other site 479436005345 Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid metabolism]; Region: Sbm; COG1884 479436005346 substrate interaction site [chemical binding]; other site 479436005347 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 479436005348 Predicted permeases [General function prediction only]; Region: RarD; COG2962 479436005349 Uncharacterised protein family (UPF0150); Region: UPF0150; cl00691 479436005350 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 479436005351 binding surface 479436005352 TPR motif; other site 479436005353 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 479436005354 FAD binding domain; Region: FAD_binding_4; pfam01565 479436005355 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 479436005356 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 479436005357 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 479436005358 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 479436005359 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 479436005360 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 479436005361 Cl- selectivity filter; other site 479436005362 Cl- binding residues [ion binding]; other site 479436005363 pore gating glutamate residue; other site 479436005364 dimer interface [polypeptide binding]; other site 479436005365 H+/Cl- coupling transport residue; other site 479436005366 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; cl15357 479436005367 lactaldehyde reductase; Region: lactal_redase; TIGR02638 479436005368 Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria; Region: LPO; cd08176 479436005369 dimer interface [polypeptide binding]; other site 479436005370 active site 479436005371 metal binding site [ion binding]; metal-binding site 479436005372 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 479436005373 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 479436005374 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 479436005375 active site 479436005376 putative substrate binding region [chemical binding]; other site 479436005377 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 479436005378 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 479436005379 Transcriptional regulators [Transcription]; Region: MarR; COG1846 479436005380 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl00088 479436005381 NAD(P)H:flavin oxidoreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes; Region: NADPH_oxidoreductase_1; cd02150 479436005382 putative FMN binding site [chemical binding]; other site 479436005383 sn-glycerol-3-phosphate transporter; Provisional; Region: glpT; PRK11273 479436005384 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 479436005385 putative substrate translocation pore; other site 479436005386 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 479436005387 Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX)...; Region: ArsC_like; cd03036 479436005388 ArsC family; Region: ArsC; pfam03960 479436005389 putative ArsC-like catalytic residues; other site 479436005390 putative TRX-like catalytic residues [active] 479436005391 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 479436005392 non-specific DNA binding site [nucleotide binding]; other site 479436005393 salt bridge; other site 479436005394 sequence-specific DNA binding site [nucleotide binding]; other site 479436005395 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 479436005396 Protein of unknown function (DUF554); Region: DUF554; cl00784 479436005397 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 479436005398 Flavin Reductases; Region: FlaRed; cl00801 479436005399 Sodium:solute symporter family; Region: SSF; cl00456 479436005400 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 479436005401 Sodium:solute symporter family; Region: SSF; cl00456 479436005402 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 479436005403 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 479436005404 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 479436005405 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 479436005406 CRISPR/Cas system-associated protein Csm2; Region: Csm2_III-A; cl00622 479436005407 CRISPR/Cas system-associated protein Cas10; Region: Cas10_III; cd09680 479436005408 CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE; Region: cas_TM1811_Csm1; TIGR02578 479436005409 ribonucleotide-diphosphate reductase subunit alpha; Provisional; Region: PRK12365 479436005410 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 479436005411 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 479436005412 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 479436005413 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cl00592 479436005414 CRISPR-associated protein, TIGR03984 family; Region: TIGR03984 479436005415 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cd09726 479436005416 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cd09726 479436005417 potential frameshift: common BLAST hit: gi|222528183|ref|YP_002572065.1| protein of unknown function DUF324 479436005418 CRISPR/Cas system-associated RAMP superfamily protein; Region: RAMP_I_III; cd09726 479436005419 CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE; Region: cas_TM1811_Csm1; TIGR02578 479436005420 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cd09634 479436005421 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 479436005422 Protein of unknown function (DUF805); Region: DUF805; cl01224 479436005423 CRISPR/Cas system-associated protein Csx1; Region: Csx1_III-U; cl14784 479436005424 CRISPR/Cas system-associated protein Csx1; Region: Csx1_III-U; cl14784 479436005425 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 479436005426 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 479436005427 DNA binding residues [nucleotide binding] 479436005428 Archaeal ATPase; Region: Arch_ATPase; pfam01637 479436005429 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 479436005430 hydrogenase, Fe-only; Region: Fe_only_hydrog; TIGR02512 479436005431 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 479436005432 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 479436005433 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; cl03503 479436005434 DNA gyrase subunit A; Validated; Region: PRK05560 479436005435 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 479436005436 CAP-like domain; other site 479436005437 active site 479436005438 primary dimer interface [polypeptide binding]; other site 479436005439 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 479436005440 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 479436005441 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 479436005442 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 479436005443 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 479436005444 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 479436005445 Sugar fermentation stimulation protein; Region: SfsA; cl00647 479436005446 GIY-YIG domain of hypothetical proteins from archaea and their bacterial homologs; Region: GIY-YIG_COG1833; cd10441 479436005447 GIY-YIG motif/motif A; other site 479436005448 putative active site [active] 479436005449 putative metal binding site [ion binding]; other site 479436005450 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 479436005451 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 479436005452 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 479436005453 Nitroreductase-like family 3. 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_3; cd02139 479436005454 putative FMN binding site [chemical binding]; other site 479436005455 Sporulation protein YtfJ (Spore_YtfJ); Region: Spore_YtfJ; cl01596 479436005456 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436005457 Walker A motif; other site 479436005458 ATP binding site [chemical binding]; other site 479436005459 Walker B motif; other site 479436005460 Peptidase family M23; Region: Peptidase_M23; pfam01551 479436005461 hydrogenase maturation GTPase HydF; Region: GTP_HydF; TIGR03918 479436005462 Era (E. coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs); Region: Era_like; cd00880 479436005463 G1 box; other site 479436005464 GTP/Mg2+ binding site [chemical binding]; other site 479436005465 Switch I region; other site 479436005466 G2 box; other site 479436005467 Switch II region; other site 479436005468 G3 box; other site 479436005469 G4 box; other site 479436005470 G5 box; other site 479436005471 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 479436005472 ParB-like nuclease domain; Region: ParBc; cl02129 479436005473 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 479436005474 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 479436005475 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 479436005476 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 479436005477 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 479436005478 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 479436005479 Pterin binding enzyme; Region: Pterin_bind; pfam00809 479436005480 substrate binding pocket [chemical binding]; other site 479436005481 dimer interface [polypeptide binding]; other site 479436005482 inhibitor binding site; inhibition site 479436005483 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 479436005484 methyltransferase cognate corrinoid proteins, Methanosarcina family; Region: pyl_corrinoid; TIGR02370 479436005485 B12 binding site [chemical binding]; other site 479436005486 cobalt ligand [ion binding]; other site 479436005487 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 479436005488 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 479436005489 FAD binding site [chemical binding]; other site 479436005490 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 479436005491 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 479436005492 S-adenosylmethionine binding site [chemical binding]; other site 479436005493 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 479436005494 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335; cl15440 479436005495 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335; cl15440 479436005496 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 479436005497 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 479436005498 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 479436005499 G1 box; other site 479436005500 GTP/Mg2+ binding site [chemical binding]; other site 479436005501 Switch I region; other site 479436005502 G2 box; other site 479436005503 Switch II region; other site 479436005504 G3 box; other site 479436005505 G4 box; other site 479436005506 G5 box; other site 479436005507 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 479436005508 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 479436005509 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 479436005510 G-X-X-G motif; other site 479436005511 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 479436005512 RxxxH motif; other site 479436005513 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 479436005514 Domain of unknown function DUF37; Region: DUF37; cl00506 479436005515 Ribonuclease P; Region: Ribonuclease_P; cl00457 479436005516 Ribosomal protein L34; Region: Ribosomal_L34; cl00370