-- dump date 20140619_115655 -- class Genbank::misc_feature -- table misc_feature_note -- id note 228405000001 Kinase/pyrophosphorylase; Region: Kinase-PPPase; pfam03618 228405000002 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 228405000003 active site 228405000004 dimer interface [polypeptide binding]; other site 228405000005 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 228405000006 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 228405000007 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 228405000008 shikimate binding site; other site 228405000009 NAD(P) binding site [chemical binding]; other site 228405000010 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 228405000011 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 228405000012 CoA-binding site [chemical binding]; other site 228405000013 ATP-binding [chemical binding]; other site 228405000014 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 228405000015 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 228405000016 active site 228405000017 catalytic site [active] 228405000018 substrate binding site [chemical binding]; other site 228405000019 preprotein translocase subunit SecB; Validated; Region: PRK05751 228405000020 SecA binding site; other site 228405000021 Preprotein binding site; other site 228405000022 Tim44-like domain; Region: Tim44; pfam04280 228405000023 MltA specific insert domain; Region: MltA; smart00925 228405000024 3D domain; Region: 3D; pfam06725 228405000025 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 228405000026 Smr domain; Region: Smr; pfam01713 228405000027 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 228405000028 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 228405000029 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 228405000030 NAD(P) binding site [chemical binding]; other site 228405000031 Protein of unknown function (DUF1192); Region: DUF1192; pfam06698 228405000032 Protein of unknown function (DUF1465); Region: DUF1465; pfam07323 228405000033 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405000034 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405000035 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 228405000036 active site clefts [active] 228405000037 zinc binding site [ion binding]; other site 228405000038 dimer interface [polypeptide binding]; other site 228405000039 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 228405000040 dimer interface [polypeptide binding]; other site 228405000041 substrate binding site [chemical binding]; other site 228405000042 metal binding sites [ion binding]; metal-binding site 228405000043 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405000044 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405000045 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 228405000046 putative effector binding pocket; other site 228405000047 putative dimerization interface [polypeptide binding]; other site 228405000048 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 228405000049 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405000050 NAD(P) binding site [chemical binding]; other site 228405000051 active site 228405000052 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 228405000053 Agrobacterium tumefaciens protein Atu4866; Region: Atu4866; pfam11512 228405000054 conserved hypothetical protein; Region: TIGR02466 228405000055 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_3; cd08896 228405000056 putative hydrophobic ligand binding site [chemical binding]; other site 228405000057 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_2; cd08895 228405000058 putative hydrophobic ligand binding site [chemical binding]; other site 228405000059 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405000060 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405000061 Predicted methyltransferase [General function prediction only]; Region: COG4798 228405000062 Methyltransferase domain; Region: Methyltransf_23; pfam13489 228405000063 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 228405000064 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 228405000065 putative dimer interface [polypeptide binding]; other site 228405000066 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405000067 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 228405000068 sugar transferase, PEP-CTERM/EpsH1 system associated; Region: stp2; TIGR03088 228405000069 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 228405000070 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 228405000071 catalytic motif [active] 228405000072 Zn binding site [ion binding]; other site 228405000073 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 228405000074 catalytic core [active] 228405000075 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 228405000076 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 228405000077 dimerization interface [polypeptide binding]; other site 228405000078 putative active cleft [active] 228405000079 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 228405000080 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405000081 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 228405000082 signal recognition particle protein; Provisional; Region: PRK10867 228405000083 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 228405000084 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 228405000085 P loop; other site 228405000086 GTP binding site [chemical binding]; other site 228405000087 Signal peptide binding domain; Region: SRP_SPB; pfam02978 228405000088 chorismate mutase; Provisional; Region: PRK09239 228405000089 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 228405000090 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405000091 Beta/Gamma crystallin; Region: Crystall; pfam00030 228405000092 Beta/Gamma crystallin; Region: Crystall; pfam00030 228405000093 RimM N-terminal domain; Region: RimM; pfam01782 228405000094 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK13828 228405000095 PRC-barrel domain; Region: PRC; pfam05239 228405000096 Beta/Gamma crystallin; Region: Crystall; pfam00030 228405000097 dolichyl-phosphate beta-D-mannosyltransferase; Region: PLN02726 228405000098 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 228405000099 Ligand binding site; other site 228405000100 Putative Catalytic site; other site 228405000101 DXD motif; other site 228405000102 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 228405000103 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 228405000104 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 228405000105 TrkA-N domain; Region: TrkA_N; pfam02254 228405000106 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 228405000107 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 228405000108 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 228405000109 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 228405000110 substrate binding site [chemical binding]; other site 228405000111 ligand binding site [chemical binding]; other site 228405000112 biotin synthase; Region: bioB; TIGR00433 228405000113 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 228405000114 FeS/SAM binding site; other site 228405000115 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 228405000116 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 228405000117 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 228405000118 dimer interface [polypeptide binding]; other site 228405000119 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405000120 catalytic residue [active] 228405000121 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405000122 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 228405000123 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405000124 dimer interface [polypeptide binding]; other site 228405000125 N-terminal domain interface [polypeptide binding]; other site 228405000126 substrate binding pocket (H-site) [chemical binding]; other site 228405000127 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 228405000128 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405000129 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 228405000130 active site 228405000131 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 228405000132 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 228405000133 substrate binding site [chemical binding]; other site 228405000134 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 228405000135 tartrate dehydrogenase; Region: TTC; TIGR02089 228405000136 Amidohydrolase; Region: Amidohydro_2; pfam04909 228405000137 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 228405000138 dimerization interface [polypeptide binding]; other site 228405000139 putative DNA binding site [nucleotide binding]; other site 228405000140 putative Zn2+ binding site [ion binding]; other site 228405000141 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_6; cd08899 228405000142 putative hydrophobic ligand binding site [chemical binding]; other site 228405000143 SnoaL-like domain; Region: SnoaL_2; pfam12680 228405000144 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 228405000145 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 228405000146 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 228405000147 putative deacylase active site [active] 228405000148 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 228405000149 metal binding site [ion binding]; metal-binding site 228405000150 enoyl-CoA hydratase; Provisional; Region: PRK07509 228405000151 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 228405000152 substrate binding site [chemical binding]; other site 228405000153 oxyanion hole (OAH) forming residues; other site 228405000154 trimer interface [polypeptide binding]; other site 228405000155 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 228405000156 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 228405000157 substrate binding site [chemical binding]; other site 228405000158 glutamase interaction surface [polypeptide binding]; other site 228405000159 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405000160 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405000161 metal binding site [ion binding]; metal-binding site 228405000162 active site 228405000163 I-site; other site 228405000164 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 228405000165 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 228405000166 catalytic residues [active] 228405000167 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 228405000168 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 228405000169 putative active site [active] 228405000170 oxyanion strand; other site 228405000171 catalytic triad [active] 228405000172 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 228405000173 Domain of unknown function DUF21; Region: DUF21; pfam01595 228405000174 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 228405000175 Transporter associated domain; Region: CorC_HlyC; smart01091 228405000176 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 228405000177 putative active site pocket [active] 228405000178 4-fold oligomerization interface [polypeptide binding]; other site 228405000179 metal binding residues [ion binding]; metal-binding site 228405000180 3-fold/trimer interface [polypeptide binding]; other site 228405000181 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405000182 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405000183 metal binding site [ion binding]; metal-binding site 228405000184 active site 228405000185 I-site; other site 228405000186 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405000187 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 228405000188 SnoaL-like domain; Region: SnoaL_2; pfam12680 228405000189 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 228405000190 Proteolipid membrane potential modulator; Region: Pmp3; pfam01679 228405000191 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 228405000192 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 228405000193 active site 228405000194 DNA binding site [nucleotide binding] 228405000195 Int/Topo IB signature motif; other site 228405000196 shikimate kinase; Provisional; Region: PRK13946 228405000197 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 228405000198 ADP binding site [chemical binding]; other site 228405000199 magnesium binding site [ion binding]; other site 228405000200 putative shikimate binding site; other site 228405000201 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 228405000202 active site 228405000203 dimer interface [polypeptide binding]; other site 228405000204 metal binding site [ion binding]; metal-binding site 228405000205 Domain of unknown function DUF21; Region: DUF21; pfam01595 228405000206 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 228405000207 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 228405000208 Transporter associated domain; Region: CorC_HlyC; smart01091 228405000209 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 228405000210 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 228405000211 HSP70 interaction site [polypeptide binding]; other site 228405000212 Spore Coat Protein U domain; Region: SCPU; pfam05229 228405000213 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 228405000214 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 228405000215 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 228405000216 Spore Coat Protein U domain; Region: SCPU; pfam05229 228405000217 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 228405000218 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 228405000219 putative NAD(P) binding site [chemical binding]; other site 228405000220 active site 228405000221 Bacitracin resistance protein BacA; Region: BacA; pfam02673 228405000222 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 228405000223 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405000224 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 228405000225 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 228405000226 active site 228405000227 dimer interface [polypeptide binding]; other site 228405000228 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 228405000229 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 228405000230 active site 228405000231 FMN binding site [chemical binding]; other site 228405000232 substrate binding site [chemical binding]; other site 228405000233 3Fe-4S cluster binding site [ion binding]; other site 228405000234 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 228405000235 domain interface; other site 228405000236 Domain of unknown function (DUF4349); Region: DUF4349; pfam14257 228405000237 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 228405000238 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 228405000239 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405000240 homodimer interface [polypeptide binding]; other site 228405000241 catalytic residue [active] 228405000242 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 228405000243 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 228405000244 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 228405000245 SCP-2 sterol transfer family; Region: SCP2; pfam02036 228405000246 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 228405000247 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405000248 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405000249 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 228405000250 acyl-activating enzyme (AAE) consensus motif; other site 228405000251 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 228405000252 putative AMP binding site [chemical binding]; other site 228405000253 putative active site [active] 228405000254 acyl-activating enzyme (AAE) consensus motif; other site 228405000255 putative CoA binding site [chemical binding]; other site 228405000256 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR7; cd08276 228405000257 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 228405000258 putative NAD(P) binding site [chemical binding]; other site 228405000259 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 228405000260 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 228405000261 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 228405000262 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 228405000263 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 228405000264 FeS/SAM binding site; other site 228405000265 TRAM domain; Region: TRAM; pfam01938 228405000266 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 228405000267 PhoH-like protein; Region: PhoH; pfam02562 228405000268 Uncharacterized protein family UPF0054; Region: UPF0054; pfam02130 228405000269 FOG: CBS domain [General function prediction only]; Region: COG0517 228405000270 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 228405000271 Transporter associated domain; Region: CorC_HlyC; smart01091 228405000272 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 228405000273 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 228405000274 putative active site [active] 228405000275 catalytic triad [active] 228405000276 putative dimer interface [polypeptide binding]; other site 228405000277 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405000278 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 228405000279 non-specific DNA binding site [nucleotide binding]; other site 228405000280 salt bridge; other site 228405000281 sequence-specific DNA binding site [nucleotide binding]; other site 228405000282 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 228405000283 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 228405000284 DNA-binding site [nucleotide binding]; DNA binding site 228405000285 RNA-binding motif; other site 228405000286 ribosome maturation protein RimP; Reviewed; Region: PRK00092 228405000287 Sm and related proteins; Region: Sm_like; cl00259 228405000288 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 228405000289 putative oligomer interface [polypeptide binding]; other site 228405000290 putative RNA binding site [nucleotide binding]; other site 228405000291 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 228405000292 NusA N-terminal domain; Region: NusA_N; pfam08529 228405000293 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 228405000294 RNA binding site [nucleotide binding]; other site 228405000295 homodimer interface [polypeptide binding]; other site 228405000296 NusA-like KH domain; Region: KH_5; pfam13184 228405000297 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 228405000298 G-X-X-G motif; other site 228405000299 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 228405000300 hypothetical protein; Provisional; Region: PRK09190 228405000301 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 228405000302 putative RNA binding cleft [nucleotide binding]; other site 228405000303 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 228405000304 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 228405000305 translation initiation factor IF-2; Region: IF-2; TIGR00487 228405000306 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 228405000307 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 228405000308 G1 box; other site 228405000309 putative GEF interaction site [polypeptide binding]; other site 228405000310 GTP/Mg2+ binding site [chemical binding]; other site 228405000311 Switch I region; other site 228405000312 G2 box; other site 228405000313 G3 box; other site 228405000314 Switch II region; other site 228405000315 G4 box; other site 228405000316 G5 box; other site 228405000317 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 228405000318 Translation-initiation factor 2; Region: IF-2; pfam11987 228405000319 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 228405000320 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 228405000321 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 228405000322 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 228405000323 RNA binding site [nucleotide binding]; other site 228405000324 active site 228405000325 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 228405000326 SelR domain; Region: SelR; pfam01641 228405000327 Heavy-metal-associated domain; Region: HMA; pfam00403 228405000328 metal-binding site [ion binding] 228405000329 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 228405000330 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405000331 NAD(P) binding site [chemical binding]; other site 228405000332 active site 228405000333 Predicted membrane protein [Function unknown]; Region: COG3766 228405000334 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 228405000335 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 228405000336 active site 228405000337 dimer interface [polypeptide binding]; other site 228405000338 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 228405000339 PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II); Region: PQQ_ADH_II; cd10279 228405000340 Trp docking motif [polypeptide binding]; other site 228405000341 cytochrome domain interface [polypeptide binding]; other site 228405000342 active site 228405000343 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 228405000344 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 228405000345 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 228405000346 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 228405000347 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405000348 putative C-terminal domain interface [polypeptide binding]; other site 228405000349 putative GSH binding site (G-site) [chemical binding]; other site 228405000350 putative dimer interface [polypeptide binding]; other site 228405000351 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 228405000352 putative N-terminal domain interface [polypeptide binding]; other site 228405000353 putative dimer interface [polypeptide binding]; other site 228405000354 putative substrate binding pocket (H-site) [chemical binding]; other site 228405000355 YCII-related domain; Region: YCII; cl00999 228405000356 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405000357 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405000358 UGMP family protein; Validated; Region: PRK09604 228405000359 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 228405000360 Uncharacterized conserved protein [Function unknown]; Region: COG2353 228405000361 MAPEG family; Region: MAPEG; pfam01124 228405000362 GTP-binding protein LepA; Provisional; Region: PRK05433 228405000363 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 228405000364 G1 box; other site 228405000365 putative GEF interaction site [polypeptide binding]; other site 228405000366 GTP/Mg2+ binding site [chemical binding]; other site 228405000367 Switch I region; other site 228405000368 G2 box; other site 228405000369 G3 box; other site 228405000370 Switch II region; other site 228405000371 G4 box; other site 228405000372 G5 box; other site 228405000373 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 228405000374 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 228405000375 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 228405000376 Chagasin family peptidase inhibitor I42; Region: Inhibitor_I42; pfam09394 228405000377 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 228405000378 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 228405000379 [2Fe-2S] cluster binding site [ion binding]; other site 228405000380 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 228405000381 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 228405000382 Fasciclin domain; Region: Fasciclin; pfam02469 228405000383 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 228405000384 active site 228405000385 putative DNA-binding cleft [nucleotide binding]; other site 228405000386 dimer interface [polypeptide binding]; other site 228405000387 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 228405000388 RuvA N terminal domain; Region: RuvA_N; pfam01330 228405000389 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 228405000390 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 228405000391 Walker A motif; other site 228405000392 ATP binding site [chemical binding]; other site 228405000393 Walker B motif; other site 228405000394 arginine finger; other site 228405000395 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 228405000396 Protein of unknown function (DUF983); Region: DUF983; cl02211 228405000397 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 228405000398 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 228405000399 active site 228405000400 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 228405000401 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 228405000402 TolR protein; Region: tolR; TIGR02801 228405000403 translocation protein TolB; Provisional; Region: tolB; PRK05137 228405000404 TolB amino-terminal domain; Region: TolB_N; pfam04052 228405000405 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 228405000406 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 228405000407 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 228405000408 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 228405000409 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405000410 ligand binding site [chemical binding]; other site 228405000411 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 228405000412 Tetratricopeptide repeat; Region: TPR_6; pfam13174 228405000413 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 228405000414 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 228405000415 Ligand Binding Site [chemical binding]; other site 228405000416 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 228405000417 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 228405000418 Walker A motif; other site 228405000419 ATP binding site [chemical binding]; other site 228405000420 Walker B motif; other site 228405000421 arginine finger; other site 228405000422 Peptidase family M41; Region: Peptidase_M41; pfam01434 228405000423 hypothetical protein; Validated; Region: PRK00110 228405000424 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405000425 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405000426 hypothetical protein; Validated; Region: PRK00029 228405000427 Uncharacterized conserved protein [Function unknown]; Region: COG0397 228405000428 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405000429 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405000430 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405000431 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405000432 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405000433 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 228405000434 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 228405000435 acyl-CoA synthetase; Provisional; Region: PRK12582 228405000436 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 228405000437 acyl-activating enzyme (AAE) consensus motif; other site 228405000438 putative AMP binding site [chemical binding]; other site 228405000439 putative active site [active] 228405000440 putative CoA binding site [chemical binding]; other site 228405000441 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 228405000442 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 228405000443 active site 228405000444 substrate binding site [chemical binding]; other site 228405000445 metal binding site [ion binding]; metal-binding site 228405000446 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 228405000447 active site 228405000448 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 228405000449 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 228405000450 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 228405000451 threonine dehydratase; Provisional; Region: PRK07334 228405000452 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 228405000453 tetramer interface [polypeptide binding]; other site 228405000454 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405000455 catalytic residue [active] 228405000456 C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains; Region: ACT_ThrD-II-like; cd04886 228405000457 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 228405000458 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 228405000459 Walker A/P-loop; other site 228405000460 ATP binding site [chemical binding]; other site 228405000461 Q-loop/lid; other site 228405000462 ABC transporter signature motif; other site 228405000463 Walker B; other site 228405000464 D-loop; other site 228405000465 H-loop/switch region; other site 228405000466 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 228405000467 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 228405000468 Walker A/P-loop; other site 228405000469 ATP binding site [chemical binding]; other site 228405000470 Q-loop/lid; other site 228405000471 ABC transporter signature motif; other site 228405000472 Walker B; other site 228405000473 D-loop; other site 228405000474 H-loop/switch region; other site 228405000475 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 228405000476 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 228405000477 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 228405000478 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 228405000479 putative active site [active] 228405000480 metal binding site [ion binding]; metal-binding site 228405000481 Methyladenine glycosylase; Region: Adenine_glyco; cl01059 228405000482 Phytase; Region: Phytase; cl17685 228405000483 The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family; Region: CHAD; smart00880 228405000484 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 228405000485 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 228405000486 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 228405000487 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 228405000488 dimer interface [polypeptide binding]; other site 228405000489 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405000490 catalytic residue [active] 228405000491 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 228405000492 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 228405000493 putative DNA binding site [nucleotide binding]; other site 228405000494 putative Zn2+ binding site [ion binding]; other site 228405000495 AsnC family; Region: AsnC_trans_reg; pfam01037 228405000496 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 228405000497 Protein of unknown function (DUF2796); Region: DUF2796; pfam10986 228405000498 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 228405000499 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 228405000500 Walker A/P-loop; other site 228405000501 ATP binding site [chemical binding]; other site 228405000502 Q-loop/lid; other site 228405000503 ABC transporter signature motif; other site 228405000504 Walker B; other site 228405000505 D-loop; other site 228405000506 H-loop/switch region; other site 228405000507 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 228405000508 FtsX-like permease family; Region: FtsX; pfam02687 228405000509 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 228405000510 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 228405000511 ?-D-glucose-1-phosphatase; Provisional; Region: PRK09456 228405000512 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 228405000513 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 228405000514 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 228405000515 IHF dimer interface [polypeptide binding]; other site 228405000516 IHF - DNA interface [nucleotide binding]; other site 228405000517 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 228405000518 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 228405000519 RNA binding site [nucleotide binding]; other site 228405000520 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 228405000521 RNA binding site [nucleotide binding]; other site 228405000522 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 228405000523 RNA binding site [nucleotide binding]; other site 228405000524 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 228405000525 RNA binding site [nucleotide binding]; other site 228405000526 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 228405000527 RNA binding site [nucleotide binding]; other site 228405000528 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 228405000529 RNA binding site [nucleotide binding]; other site 228405000530 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 228405000531 Uncharacterized conserved protein [Function unknown]; Region: COG3743 228405000532 cytidylate kinase; Provisional; Region: cmk; PRK00023 228405000533 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 228405000534 CMP-binding site; other site 228405000535 The sites determining sugar specificity; other site 228405000536 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN_family; cd02803 228405000537 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 228405000538 active site 228405000539 FMN binding site [chemical binding]; other site 228405000540 substrate binding site [chemical binding]; other site 228405000541 putative catalytic residue [active] 228405000542 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 228405000543 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 228405000544 hinge; other site 228405000545 active site 228405000546 Protein of unknown function (FYDLN_acid); Region: FYDLN_acid; pfam09538 228405000547 TIGR02300 family protein; Region: FYDLN_acid 228405000548 Protein of unknown function (DUF1150); Region: DUF1150; pfam06620 228405000549 parallel beta-helix repeat-containing protein; Region: beta_helix_1; TIGR03805 228405000550 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 228405000551 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 228405000552 conserved hypothetical protein, HNE_0200 family; Region: chp_HNE_0200; TIGR03806 228405000553 Planctomycete cytochrome C; Region: PSCyt1; pfam07635 228405000554 Uncharacterized BCR, YaiI/YqxD family COG1671; Region: DUF188; cl00727 228405000555 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 228405000556 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 228405000557 catalytic site [active] 228405000558 putative active site [active] 228405000559 putative substrate binding site [chemical binding]; other site 228405000560 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 228405000561 OstA-like protein; Region: OstA; pfam03968 228405000562 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 228405000563 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 228405000564 Walker A/P-loop; other site 228405000565 ATP binding site [chemical binding]; other site 228405000566 Q-loop/lid; other site 228405000567 ABC transporter signature motif; other site 228405000568 Walker B; other site 228405000569 D-loop; other site 228405000570 H-loop/switch region; other site 228405000571 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 228405000572 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 228405000573 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 228405000574 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 228405000575 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 228405000576 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 228405000577 substrate binding site [chemical binding]; other site 228405000578 dimer interface [polypeptide binding]; other site 228405000579 ATP binding site [chemical binding]; other site 228405000580 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 228405000581 active site 228405000582 tetramer interface [polypeptide binding]; other site 228405000583 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 228405000584 active site 228405000585 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 228405000586 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 228405000587 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405000588 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 228405000589 potassium/proton antiporter; Reviewed; Region: PRK05326 228405000590 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 228405000591 Transporter associated domain; Region: CorC_HlyC; smart01091 228405000592 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 228405000593 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 228405000594 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405000595 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405000596 Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain; Region: MPP_ACP5; cd07378 228405000597 active site 228405000598 metal binding site [ion binding]; metal-binding site 228405000599 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 228405000600 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405000601 NAD(P) binding site [chemical binding]; other site 228405000602 active site 228405000603 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 228405000604 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405000605 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 228405000606 DNA binding residues [nucleotide binding] 228405000607 Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]; Region: FecR; COG3712 228405000608 FecR protein; Region: FecR; pfam04773 228405000609 Secretin and TonB N terminus short domain; Region: STN; smart00965 228405000610 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405000611 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 228405000612 N-terminal plug; other site 228405000613 ligand-binding site [chemical binding]; other site 228405000614 Penicillin amidase; Region: Penicil_amidase; pfam01804 228405000615 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 228405000616 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 228405000617 active site 228405000618 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 228405000619 Family description; Region: VCBS; pfam13517 228405000620 Family description; Region: VCBS; pfam13517 228405000621 Family description; Region: VCBS; pfam13517 228405000622 Family description; Region: VCBS; pfam13517 228405000623 Family description; Region: VCBS; pfam13517 228405000624 Family description; Region: VCBS; pfam13517 228405000625 ASPIC and UnbV; Region: UnbV_ASPIC; pfam07593 228405000626 TraB family; Region: TraB; pfam01963 228405000627 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates; Region: Bacterial_IMPase_like_1; cd01641 228405000628 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 228405000629 active site 228405000630 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405000631 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 228405000632 sequence-specific DNA binding site [nucleotide binding]; other site 228405000633 salt bridge; other site 228405000634 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 228405000635 Response regulator receiver domain; Region: Response_reg; pfam00072 228405000636 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 228405000637 active site 228405000638 phosphorylation site [posttranslational modification] 228405000639 intermolecular recognition site; other site 228405000640 dimerization interface [polypeptide binding]; other site 228405000641 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405000642 Protoporphyrinogen oxidase [Coenzyme metabolism]; Region: HemY; COG1232 228405000643 Predicted transcriptional regulator [Transcription]; Region: COG1959 228405000644 Transcriptional regulator; Region: Rrf2; pfam02082 228405000645 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 228405000646 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405000647 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405000648 active site 228405000649 Uncharacterized protein conserved in bacteria (DUF2236); Region: DUF2236; cl01472 228405000650 Uncharacterized conserved protein [Function unknown]; Region: COG3334 228405000651 Flagellar basal body-associated protein FliL; Region: FliL; pfam03748 228405000652 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 228405000653 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 228405000654 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 228405000655 flagellar assembly protein H; Validated; Region: fliH; PRK06032 228405000656 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 228405000657 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 228405000658 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 228405000659 FliG C-terminal domain; Region: FliG_C; pfam01706 228405000660 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 228405000661 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 228405000662 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK06008 228405000663 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 228405000664 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07521 228405000665 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 228405000666 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 228405000667 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 228405000668 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 228405000669 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 228405000670 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 228405000671 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 228405000672 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405000673 ligand binding site [chemical binding]; other site 228405000674 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 228405000675 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 228405000676 flagellar motor protein MotA; Validated; Region: PRK09110 228405000677 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12690 228405000678 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 228405000679 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 228405000680 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 228405000681 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 228405000682 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 228405000683 SAF-like; Region: SAF_2; pfam13144 228405000684 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 228405000685 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 228405000686 Flagellar L-ring protein; Region: FlgH; cl17277 228405000687 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 228405000688 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 228405000689 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 228405000690 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 228405000691 Flagellin and related hook-associated proteins [Cell motility and secretion]; Region: FlgL; COG1344 228405000692 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 228405000693 Flagellar protein FlaF; Region: FlaF; pfam07309 228405000694 flagellar biosynthesis repressor FlbT; Reviewed; Region: flbT; PRK00794 228405000695 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 228405000696 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 228405000697 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 228405000698 Walker A motif; other site 228405000699 ATP binding site [chemical binding]; other site 228405000700 Walker B motif; other site 228405000701 flagellar basal body rod protein FlgB; Provisional; Region: flgB; PRK12627 228405000702 flagellar basal body rod protein FlgC; Provisional; Region: flgC; PRK12632 228405000703 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 228405000704 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 228405000705 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 228405000706 Bacterial export proteins, family 3; Region: Bac_export_3; pfam01313 228405000707 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 228405000708 FHIPEP family; Region: FHIPEP; pfam00771 228405000709 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 228405000710 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 228405000711 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 228405000712 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405000713 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405000714 active site 228405000715 PAS fold; Region: PAS_4; pfam08448 228405000716 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405000717 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405000718 metal binding site [ion binding]; metal-binding site 228405000719 active site 228405000720 I-site; other site 228405000721 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405000722 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 228405000723 GAF domain; Region: GAF; pfam01590 228405000724 RNA polymerase sigma factor; Provisional; Region: PRK12547 228405000725 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405000726 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 228405000727 DNA binding residues [nucleotide binding] 228405000728 Restriction endonuclease; Region: Mrr_cat; pfam04471 228405000729 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 228405000730 AAA domain; Region: AAA_14; pfam13173 228405000731 AAA domain; Region: AAA_13; pfam13166 228405000732 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405000733 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 228405000734 non-specific DNA binding site [nucleotide binding]; other site 228405000735 salt bridge; other site 228405000736 sequence-specific DNA binding site [nucleotide binding]; other site 228405000737 Domain of unknown function (DUF955); Region: DUF955; cl01076 228405000738 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 228405000739 Protein of unknown function (DUF3644); Region: DUF3644; pfam12358 228405000740 integrase; Provisional; Region: int; PHA02601 228405000741 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 228405000742 active site 228405000743 DNA binding site [nucleotide binding] 228405000744 Int/Topo IB signature motif; other site 228405000745 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 228405000746 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 228405000747 FMN binding site [chemical binding]; other site 228405000748 active site 228405000749 catalytic residues [active] 228405000750 substrate binding site [chemical binding]; other site 228405000751 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 228405000752 dimer interface [polypeptide binding]; other site 228405000753 phosphorylation site [posttranslational modification] 228405000754 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 228405000755 ATP binding site [chemical binding]; other site 228405000756 Mg2+ binding site [ion binding]; other site 228405000757 G-X-G motif; other site 228405000758 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 228405000759 active site 228405000760 phosphorylation site [posttranslational modification] 228405000761 intermolecular recognition site; other site 228405000762 muropeptide transporter; Validated; Region: ampG; cl17669 228405000763 muropeptide transporter; Validated; Region: ampG; cl17669 228405000764 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 228405000765 Malic enzyme, N-terminal domain; Region: malic; pfam00390 228405000766 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 228405000767 putative NAD(P) binding site [chemical binding]; other site 228405000768 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 228405000769 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 228405000770 MutS domain I; Region: MutS_I; pfam01624 228405000771 MutS domain II; Region: MutS_II; pfam05188 228405000772 MutS domain III; Region: MutS_III; pfam05192 228405000773 MutS domain V; Region: MutS_V; pfam00488 228405000774 Walker A/P-loop; other site 228405000775 ATP binding site [chemical binding]; other site 228405000776 Q-loop/lid; other site 228405000777 ABC transporter signature motif; other site 228405000778 Walker B; other site 228405000779 D-loop; other site 228405000780 H-loop/switch region; other site 228405000781 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 228405000782 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405000783 active site 228405000784 metal binding site [ion binding]; metal-binding site 228405000785 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405000786 glutathione synthetase; Provisional; Region: PRK05246 228405000787 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 228405000788 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 228405000789 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 228405000790 BON domain; Region: BON; pfam04972 228405000791 BON domain; Region: BON; pfam04972 228405000792 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 228405000793 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 228405000794 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 228405000795 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 228405000796 LytTr DNA-binding domain; Region: LytTR; smart00850 228405000797 Predicted membrane protein (DUF2306); Region: DUF2306; cl02232 228405000798 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 228405000799 putative active site [active] 228405000800 putative metal binding site [ion binding]; other site 228405000801 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 228405000802 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405000803 putative substrate translocation pore; other site 228405000804 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 228405000805 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 228405000806 CoA-ligase; Region: Ligase_CoA; pfam00549 228405000807 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 228405000808 CoA binding domain; Region: CoA_binding; smart00881 228405000809 CoA-ligase; Region: Ligase_CoA; pfam00549 228405000810 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 228405000811 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 228405000812 TPP-binding site [chemical binding]; other site 228405000813 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 228405000814 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 228405000815 E3 interaction surface; other site 228405000816 lipoyl attachment site [posttranslational modification]; other site 228405000817 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 228405000818 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 228405000819 E3 interaction surface; other site 228405000820 lipoyl attachment site [posttranslational modification]; other site 228405000821 e3 binding domain; Region: E3_binding; pfam02817 228405000822 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 228405000823 Methyltransferase domain; Region: Methyltransf_31; pfam13847 228405000824 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 228405000825 S-adenosylmethionine binding site [chemical binding]; other site 228405000826 putative S-transferase; Provisional; Region: PRK11752 228405000827 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 228405000828 C-terminal domain interface [polypeptide binding]; other site 228405000829 GSH binding site (G-site) [chemical binding]; other site 228405000830 dimer interface [polypeptide binding]; other site 228405000831 C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YghU_like; cd10292 228405000832 dimer interface [polypeptide binding]; other site 228405000833 N-terminal domain interface [polypeptide binding]; other site 228405000834 active site 228405000835 Chorismate mutase type II; Region: CM_2; smart00830 228405000836 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 228405000837 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405000838 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 228405000839 dimerization interface [polypeptide binding]; other site 228405000840 substrate binding pocket [chemical binding]; other site 228405000841 siroheme synthase; Provisional; Region: cysG; PRK10637 228405000842 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 228405000843 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 228405000844 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 228405000845 active site 228405000846 SAM binding site [chemical binding]; other site 228405000847 homodimer interface [polypeptide binding]; other site 228405000848 Protein of unknown function (DUF2849); Region: DUF2849; pfam11011 228405000849 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405000850 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_4; cd03056 228405000851 putative C-terminal domain interface [polypeptide binding]; other site 228405000852 putative GSH binding site (G-site) [chemical binding]; other site 228405000853 putative dimer interface [polypeptide binding]; other site 228405000854 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405000855 N-terminal domain interface [polypeptide binding]; other site 228405000856 dimer interface [polypeptide binding]; other site 228405000857 substrate binding pocket (H-site) [chemical binding]; other site 228405000858 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 228405000859 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 228405000860 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 228405000861 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 228405000862 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 228405000863 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 228405000864 Active Sites [active] 228405000865 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 228405000866 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 228405000867 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 228405000868 Domain of unknown function (DUF3315); Region: DUF3315; pfam11776 228405000869 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 228405000870 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 228405000871 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405000872 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 228405000873 DNA binding residues [nucleotide binding] 228405000874 Predicted ATPase [General function prediction only]; Region: COG1485 228405000875 Rhomboid family; Region: Rhomboid; pfam01694 228405000876 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 228405000877 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 228405000878 putative acyl-acceptor binding pocket; other site 228405000879 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405000880 Coenzyme A binding pocket [chemical binding]; other site 228405000881 muropeptide transporter; Validated; Region: ampG; cl17669 228405000882 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 228405000883 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 228405000884 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 228405000885 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 228405000886 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 228405000887 Protein of unknown function DUF58; Region: DUF58; pfam01882 228405000888 MoxR-like ATPases [General function prediction only]; Region: COG0714 228405000889 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 228405000890 ATP binding site [chemical binding]; other site 228405000891 Walker B motif; other site 228405000892 arginine finger; other site 228405000893 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 228405000894 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 228405000895 putative active site [active] 228405000896 putative CoA binding site [chemical binding]; other site 228405000897 nudix motif; other site 228405000898 metal binding site [ion binding]; metal-binding site 228405000899 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 228405000900 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 228405000901 active site 228405000902 NTP binding site [chemical binding]; other site 228405000903 metal binding triad [ion binding]; metal-binding site 228405000904 putative addiction module antidote; Region: doc_partner; TIGR02609 228405000905 Prophage maintenance system killer protein [General function prediction only]; Region: Doc; COG3654 228405000906 Coproporphyrinogen III oxidase [Coenzyme metabolism]; Region: HemF; COG0408 228405000907 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl17752 228405000908 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 228405000909 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 228405000910 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 228405000911 [2Fe-2S] cluster binding site [ion binding]; other site 228405000912 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 228405000913 cytochrome b; Provisional; Region: CYTB; MTH00156 228405000914 Qi binding site; other site 228405000915 intrachain domain interface; other site 228405000916 interchain domain interface [polypeptide binding]; other site 228405000917 heme bH binding site [chemical binding]; other site 228405000918 heme bL binding site [chemical binding]; other site 228405000919 Qo binding site; other site 228405000920 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 228405000921 interchain domain interface [polypeptide binding]; other site 228405000922 intrachain domain interface; other site 228405000923 Qi binding site; other site 228405000924 Qo binding site; other site 228405000925 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 228405000926 Cytochrome c; Region: Cytochrom_C; cl11414 228405000927 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405000928 Coenzyme A binding pocket [chemical binding]; other site 228405000929 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 228405000930 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 228405000931 Fasciclin domain; Region: Fasciclin; pfam02469 228405000932 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 228405000933 Fasciclin domain; Region: Fasciclin; pfam02469 228405000934 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 228405000935 Fasciclin domain; Region: Fasciclin; pfam02469 228405000936 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 228405000937 DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]; Region: DjlA; COG1076 228405000938 putative metal binding site [ion binding]; other site 228405000939 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 228405000940 HSP70 interaction site [polypeptide binding]; other site 228405000941 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 228405000942 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 228405000943 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 228405000944 active site 228405000945 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 228405000946 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 228405000947 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 228405000948 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 228405000949 G1 box; other site 228405000950 putative GEF interaction site [polypeptide binding]; other site 228405000951 GTP/Mg2+ binding site [chemical binding]; other site 228405000952 Switch I region; other site 228405000953 G2 box; other site 228405000954 G3 box; other site 228405000955 Switch II region; other site 228405000956 G4 box; other site 228405000957 G5 box; other site 228405000958 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 228405000959 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 228405000960 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 228405000961 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 228405000962 recombination protein RecR; Reviewed; Region: recR; PRK00076 228405000963 RecR protein; Region: RecR; pfam02132 228405000964 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 228405000965 putative active site [active] 228405000966 putative metal-binding site [ion binding]; other site 228405000967 tetramer interface [polypeptide binding]; other site 228405000968 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; pfam02575 228405000969 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 228405000970 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 228405000971 Walker A motif; other site 228405000972 ATP binding site [chemical binding]; other site 228405000973 Walker B motif; other site 228405000974 arginine finger; other site 228405000975 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 228405000976 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 228405000977 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 228405000978 dimer interface [polypeptide binding]; other site 228405000979 putative radical transfer pathway; other site 228405000980 diiron center [ion binding]; other site 228405000981 tyrosyl radical; other site 228405000982 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 228405000983 ADP-ribose binding site [chemical binding]; other site 228405000984 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 228405000985 active site 228405000986 REJ domain; Region: REJ; pfam02010 228405000987 TM2 domain; Region: TM2; pfam05154 228405000988 PRC-barrel domain; Region: PRC; pfam05239 228405000989 Methyltransferase domain; Region: Methyltransf_31; pfam13847 228405000990 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 228405000991 S-adenosylmethionine binding site [chemical binding]; other site 228405000992 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 228405000993 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 228405000994 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 228405000995 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 228405000996 active site 228405000997 Alpha-L-fucosidase; Region: Alpha_L_fucos; cl12119 228405000998 Alpha-L-fucosidase [Carbohydrate transport and metabolism]; Region: COG3669 228405000999 Protein of unknown function (DUF2459); Region: DUF2459; pfam09601 228405001000 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 228405001001 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 228405001002 Walker A/P-loop; other site 228405001003 ATP binding site [chemical binding]; other site 228405001004 Q-loop/lid; other site 228405001005 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 228405001006 ABC transporter signature motif; other site 228405001007 Walker B; other site 228405001008 D-loop; other site 228405001009 H-loop/switch region; other site 228405001010 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 228405001011 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 228405001012 nucleotide binding pocket [chemical binding]; other site 228405001013 K-X-D-G motif; other site 228405001014 catalytic site [active] 228405001015 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 228405001016 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 228405001017 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 228405001018 Dimer interface [polypeptide binding]; other site 228405001019 BRCT sequence motif; other site 228405001020 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 228405001021 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405001022 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 228405001023 non-specific DNA binding site [nucleotide binding]; other site 228405001024 salt bridge; other site 228405001025 sequence-specific DNA binding site [nucleotide binding]; other site 228405001026 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 228405001027 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 228405001028 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 228405001029 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 228405001030 nucleotide binding site [chemical binding]; other site 228405001031 SulA interaction site; other site 228405001032 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 228405001033 Cell division protein FtsA; Region: FtsA; smart00842 228405001034 Cell division protein FtsA; Region: FtsA; pfam14450 228405001035 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 228405001036 Cell division protein FtsQ; Region: FtsQ; pfam03799 228405001037 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 228405001038 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 228405001039 ATP-grasp domain; Region: ATP-grasp_4; cl17255 228405001040 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405001041 Protein of unknown function (Hypoth_ymh); Region: Hypoth_Ymh; pfam09509 228405001042 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 228405001043 FAD binding domain; Region: FAD_binding_4; pfam01565 228405001044 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 228405001045 EF-hand domain pair; Region: EF_hand_5; pfam13499 228405001046 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 228405001047 Ca2+ binding site [ion binding]; other site 228405001048 PAS fold; Region: PAS_7; pfam12860 228405001049 PAS fold; Region: PAS_7; pfam12860 228405001050 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405001051 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 228405001052 dimer interface [polypeptide binding]; other site 228405001053 phosphorylation site [posttranslational modification] 228405001054 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 228405001055 ATP binding site [chemical binding]; other site 228405001056 Mg2+ binding site [ion binding]; other site 228405001057 G-X-G motif; other site 228405001058 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 228405001059 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 228405001060 ATP-dependent helicase HrpB; Region: DEAH_box_HrpB; TIGR01970 228405001061 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 228405001062 ATP binding site [chemical binding]; other site 228405001063 putative Mg++ binding site [ion binding]; other site 228405001064 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 228405001065 nucleotide binding region [chemical binding]; other site 228405001066 ATP-binding site [chemical binding]; other site 228405001067 ATP-dependent helicase C-terminal; Region: HrpB_C; pfam08482 228405001068 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; cl17429 228405001069 Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; Region: SsnA; COG0402 228405001070 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 228405001071 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 228405001072 active site 228405001073 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 228405001074 Helix-turn-helix domain; Region: HTH_18; pfam12833 228405001075 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405001076 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 228405001077 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 228405001078 active site 228405001079 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405001080 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 228405001081 ATP binding site [chemical binding]; other site 228405001082 Mg2+ binding site [ion binding]; other site 228405001083 G-X-G motif; other site 228405001084 mercuric reductase; Validated; Region: PRK06370 228405001085 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405001086 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 228405001087 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 228405001088 Uncharacterized conserved protein [Function unknown]; Region: COG0398 228405001089 Protein of unknown function, DUF547; Region: DUF547; pfam04784 228405001090 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405001091 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405001092 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 228405001093 Ribonuclease P; Region: Ribonuclease_P; pfam00825 228405001094 membrane protein insertase; Provisional; Region: PRK01318 228405001095 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 228405001096 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 228405001097 G1 box; other site 228405001098 GTP/Mg2+ binding site [chemical binding]; other site 228405001099 Switch I region; other site 228405001100 G2 box; other site 228405001101 G3 box; other site 228405001102 Switch II region; other site 228405001103 G4 box; other site 228405001104 G5 box; other site 228405001105 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 228405001106 Coenzyme A binding pocket [chemical binding]; other site 228405001107 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 228405001108 feedback inhibition sensing region; other site 228405001109 homohexameric interface [polypeptide binding]; other site 228405001110 nucleotide binding site [chemical binding]; other site 228405001111 N-acetyl-L-glutamate binding site [chemical binding]; other site 228405001112 Protein of unknown function (DUF1036); Region: DUF1036; pfam06282 228405001113 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 228405001114 Protein of unknown function (DUF1036); Region: DUF1036; cl02296 228405001115 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 228405001116 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 228405001117 motif II; other site 228405001118 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 228405001119 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 228405001120 active site 228405001121 substrate binding site [chemical binding]; other site 228405001122 trimer interface [polypeptide binding]; other site 228405001123 CoA binding site [chemical binding]; other site 228405001124 Domain of unknown function (DUF4287); Region: DUF4287; pfam14117 228405001125 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 228405001126 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 228405001127 HWE histidine kinase; Region: HWE_HK; smart00911 228405001128 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405001129 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 228405001130 catalytic site [active] 228405001131 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 228405001132 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 228405001133 putative ADP-binding pocket [chemical binding]; other site 228405001134 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405001135 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 228405001136 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 228405001137 putative active site [active] 228405001138 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin; Region: ZnMc_MMP_like_2; cd04276 228405001139 active site 228405001140 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 228405001141 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 228405001142 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 228405001143 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 228405001144 HWE histidine kinase; Region: HWE_HK; smart00911 228405001145 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 228405001146 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 228405001147 23S rRNA binding site [nucleotide binding]; other site 228405001148 L21 binding site [polypeptide binding]; other site 228405001149 L13 binding site [polypeptide binding]; other site 228405001150 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 228405001151 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 228405001152 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 228405001153 dimer interface [polypeptide binding]; other site 228405001154 motif 1; other site 228405001155 active site 228405001156 motif 2; other site 228405001157 motif 3; other site 228405001158 ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to...; Region: ASCH_Ef3133_like; cd06553 228405001159 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 228405001160 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 228405001161 putative tRNA-binding site [nucleotide binding]; other site 228405001162 B3/4 domain; Region: B3_4; pfam03483 228405001163 tRNA synthetase B5 domain; Region: B5; smart00874 228405001164 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 228405001165 dimer interface [polypeptide binding]; other site 228405001166 motif 1; other site 228405001167 motif 3; other site 228405001168 motif 2; other site 228405001169 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 228405001170 Ion channel; Region: Ion_trans_2; pfam07885 228405001171 dihydrodipicolinate reductase; Provisional; Region: PRK00048 228405001172 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 228405001173 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 228405001174 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cl00025 228405001175 active pocket/dimerization site; other site 228405001176 active site 228405001177 phosphorylation site [posttranslational modification] 228405001178 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 228405001179 dimerization domain swap beta strand [polypeptide binding]; other site 228405001180 regulatory protein interface [polypeptide binding]; other site 228405001181 active site 228405001182 regulatory phosphorylation site [posttranslational modification]; other site 228405001183 2-isopropylmalate synthase; Validated; Region: PRK00915 228405001184 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 228405001185 active site 228405001186 catalytic residues [active] 228405001187 metal binding site [ion binding]; metal-binding site 228405001188 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 228405001189 Uncharacterized conserved protein [Function unknown]; Region: COG0398 228405001190 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 228405001191 oxidoreductase; Provisional; Region: PRK06196 228405001192 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 228405001193 putative NAD(P) binding site [chemical binding]; other site 228405001194 active site 228405001195 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 228405001196 Sel1 repeat; Region: Sel1; cl02723 228405001197 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 228405001198 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis...; Region: GH25_muramidase_1; cd06413 228405001199 active site 228405001200 Glycosyl hydrolases family 25; Region: Glyco_hydro_25; pfam01183 228405001201 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405001202 Coenzyme A binding pocket [chemical binding]; other site 228405001203 ketol-acid reductoisomerase; Provisional; Region: PRK05479 228405001204 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 228405001205 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 228405001206 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 228405001207 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 228405001208 putative valine binding site [chemical binding]; other site 228405001209 dimer interface [polypeptide binding]; other site 228405001210 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 228405001211 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK09107 228405001212 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 228405001213 PYR/PP interface [polypeptide binding]; other site 228405001214 dimer interface [polypeptide binding]; other site 228405001215 TPP binding site [chemical binding]; other site 228405001216 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 228405001217 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 228405001218 TPP-binding site [chemical binding]; other site 228405001219 dimer interface [polypeptide binding]; other site 228405001220 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 228405001221 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 228405001222 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 228405001223 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 228405001224 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_21; cd04680 228405001225 nudix motif; other site 228405001226 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 228405001227 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 228405001228 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 228405001229 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 228405001230 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 228405001231 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 228405001232 metal ion-dependent adhesion site (MIDAS); other site 228405001233 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 228405001234 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 228405001235 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 228405001236 von Willebrand factor type A domain; Region: VWA_2; pfam13519 228405001237 thymidylate synthase; Reviewed; Region: thyA; PRK01827 228405001238 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 228405001239 dimerization interface [polypeptide binding]; other site 228405001240 active site 228405001241 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cd00333 228405001242 amphipathic channel; other site 228405001243 Asn-Pro-Ala signature motifs; other site 228405001244 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 228405001245 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 228405001246 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 228405001247 folate binding site [chemical binding]; other site 228405001248 NADP+ binding site [chemical binding]; other site 228405001249 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 228405001250 Strictosidine synthase; Region: Str_synth; pfam03088 228405001251 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 228405001252 homotrimer interaction site [polypeptide binding]; other site 228405001253 putative active site [active] 228405001254 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 228405001255 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 228405001256 Walker A motif; other site 228405001257 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 228405001258 HflK protein; Region: hflK; TIGR01933 228405001259 HflC protein; Region: hflC; TIGR01932 228405001260 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 228405001261 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 228405001262 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 228405001263 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 228405001264 protein binding site [polypeptide binding]; other site 228405001265 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 228405001266 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 228405001267 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 228405001268 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 228405001269 short chain dehydrogenase; Provisional; Region: PRK09134 228405001270 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405001271 NAD(P) binding site [chemical binding]; other site 228405001272 active site 228405001273 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 228405001274 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 228405001275 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405001276 catalytic residue [active] 228405001277 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 228405001278 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 228405001279 FMN binding site [chemical binding]; other site 228405001280 substrate binding site [chemical binding]; other site 228405001281 putative catalytic residue [active] 228405001282 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 228405001283 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 228405001284 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 228405001285 amidase catalytic site [active] 228405001286 Zn binding residues [ion binding]; other site 228405001287 substrate binding site [chemical binding]; other site 228405001288 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 228405001289 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 228405001290 EamA-like transporter family; Region: EamA; pfam00892 228405001291 EamA-like transporter family; Region: EamA; pfam00892 228405001292 Helix-turn-helix domain; Region: HTH_28; pfam13518 228405001293 Winged helix-turn helix; Region: HTH_29; pfam13551 228405001294 Homeodomain-like domain; Region: HTH_32; pfam13565 228405001295 Integrase core domain; Region: rve; pfam00665 228405001296 Integrase core domain; Region: rve_3; pfam13683 228405001297 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 228405001298 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 228405001299 Methyltransferase domain; Region: Methyltransf_31; pfam13847 228405001300 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 228405001301 S-adenosylmethionine binding site [chemical binding]; other site 228405001302 Protein of unknown function (DUF3445); Region: DUF3445; pfam11927 228405001303 EVE domain; Region: EVE; cl00728 228405001304 Methyltransferase domain; Region: Methyltransf_18; pfam12847 228405001305 S-adenosylmethionine binding site [chemical binding]; other site 228405001306 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 228405001307 active site 228405001308 motif I; other site 228405001309 motif II; other site 228405001310 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 228405001311 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 228405001312 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 228405001313 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405001314 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405001315 metal binding site [ion binding]; metal-binding site 228405001316 active site 228405001317 I-site; other site 228405001318 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405001319 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 228405001320 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405001321 putative substrate translocation pore; other site 228405001322 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 228405001323 Predicted integral membrane protein (DUF2270); Region: DUF2270; pfam10028 228405001324 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 228405001325 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 228405001326 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 228405001327 Walker A motif; other site 228405001328 ATP binding site [chemical binding]; other site 228405001329 Walker B motif; other site 228405001330 arginine finger; other site 228405001331 Flagellar protein FlbT; Region: FlbT; pfam07378 228405001332 MarC family integral membrane protein; Region: MarC; pfam01914 228405001333 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 228405001334 flagellar motor switch protein FliM; Region: fliM_switch; TIGR01397 228405001335 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 228405001336 Uncharacterized conserved protein [Function unknown]; Region: COG2353 228405001337 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 228405001338 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405001339 PAS domain; Region: PAS_9; pfam13426 228405001340 putative active site [active] 228405001341 heme pocket [chemical binding]; other site 228405001342 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405001343 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 228405001344 dimer interface [polypeptide binding]; other site 228405001345 phosphorylation site [posttranslational modification] 228405001346 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 228405001347 ATP binding site [chemical binding]; other site 228405001348 Mg2+ binding site [ion binding]; other site 228405001349 G-X-G motif; other site 228405001350 Response regulator receiver domain; Region: Response_reg; pfam00072 228405001351 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 228405001352 active site 228405001353 phosphorylation site [posttranslational modification] 228405001354 intermolecular recognition site; other site 228405001355 dimerization interface [polypeptide binding]; other site 228405001356 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405001357 HAD superfamily, subfamily IIIB (Acid phosphatase); Region: Acid_phosphat_B; cl17236 228405001358 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 228405001359 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 228405001360 FMN binding site [chemical binding]; other site 228405001361 substrate binding site [chemical binding]; other site 228405001362 putative catalytic residue [active] 228405001363 RmuC family; Region: RmuC; pfam02646 228405001364 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 228405001365 active site 228405001366 catalytic residues [active] 228405001367 metal binding site [ion binding]; metal-binding site 228405001368 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 228405001369 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 228405001370 putative active site [active] 228405001371 substrate binding site [chemical binding]; other site 228405001372 putative cosubstrate binding site; other site 228405001373 catalytic site [active] 228405001374 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 228405001375 substrate binding site [chemical binding]; other site 228405001376 Predicted acetyltransferase [General function prediction only]; Region: COG3153 228405001377 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 228405001378 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 228405001379 dimerization interface 3.5A [polypeptide binding]; other site 228405001380 active site 228405001381 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405001382 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405001383 active site 228405001384 EthD domain; Region: EthD; pfam07110 228405001385 PII uridylyl-transferase; Provisional; Region: PRK05092 228405001386 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 228405001387 metal binding triad; other site 228405001388 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 228405001389 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 228405001390 Zn2+ binding site [ion binding]; other site 228405001391 Mg2+ binding site [ion binding]; other site 228405001392 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 228405001393 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 228405001394 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 228405001395 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 228405001396 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 228405001397 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 228405001398 active site 228405001399 HIGH motif; other site 228405001400 dimer interface [polypeptide binding]; other site 228405001401 KMSKS motif; other site 228405001402 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405001403 Uncharacterized protein conserved in bacteria (DUF2333); Region: DUF2333; cl11978 228405001404 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 228405001405 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 228405001406 Nitroreductase-like family 5. 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_5; cd02148 228405001407 putative FMN binding site [chemical binding]; other site 228405001408 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 228405001409 Glycoprotease family; Region: Peptidase_M22; pfam00814 228405001410 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 228405001411 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 228405001412 nucleotide binding site [chemical binding]; other site 228405001413 putative NEF/HSP70 interaction site [polypeptide binding]; other site 228405001414 SBD interface [polypeptide binding]; other site 228405001415 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 228405001416 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 228405001417 Coenzyme A binding pocket [chemical binding]; other site 228405001418 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 228405001419 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405001420 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 228405001421 metal binding site 2 [ion binding]; metal-binding site 228405001422 putative DNA binding helix; other site 228405001423 metal binding site 1 [ion binding]; metal-binding site 228405001424 dimer interface [polypeptide binding]; other site 228405001425 structural Zn2+ binding site [ion binding]; other site 228405001426 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 228405001427 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 228405001428 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 228405001429 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405001430 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 228405001431 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405001432 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 228405001433 Ligand Binding Site [chemical binding]; other site 228405001434 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 228405001435 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 228405001436 FeS/SAM binding site; other site 228405001437 queuosine biosynthesis protein QueD; Region: queuosine_QueD; TIGR03367 228405001438 active site 228405001439 Mechanosensitive ion channel; Region: MS_channel; pfam00924 228405001440 Pirin-related protein [General function prediction only]; Region: COG1741 228405001441 Pirin; Region: Pirin; pfam02678 228405001442 putative transposase OrfB; Reviewed; Region: PHA02517 228405001443 HTH-like domain; Region: HTH_21; pfam13276 228405001444 Integrase core domain; Region: rve; pfam00665 228405001445 Integrase core domain; Region: rve_3; cl15866 228405001446 Transposase; Region: HTH_Tnp_1; cl17663 228405001447 Abi-like protein; Region: Abi_2; pfam07751 228405001448 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 228405001449 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 228405001450 ATP binding site [chemical binding]; other site 228405001451 putative Mg++ binding site [ion binding]; other site 228405001452 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 228405001453 nucleotide binding region [chemical binding]; other site 228405001454 ATP-binding site [chemical binding]; other site 228405001455 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 228405001456 HRDC domain; Region: HRDC; pfam00570 228405001457 ATP-dependent Clp protease proteolytic subunit; Reviewed; Region: PRK12553 228405001458 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 228405001459 oligomer interface [polypeptide binding]; other site 228405001460 active site residues [active] 228405001461 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 228405001462 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405001463 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 228405001464 dimer interface [polypeptide binding]; other site 228405001465 phosphorylation site [posttranslational modification] 228405001466 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 228405001467 ATP binding site [chemical binding]; other site 228405001468 Mg2+ binding site [ion binding]; other site 228405001469 G-X-G motif; other site 228405001470 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 228405001471 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 228405001472 active site 228405001473 phosphorylation site [posttranslational modification] 228405001474 intermolecular recognition site; other site 228405001475 dimerization interface [polypeptide binding]; other site 228405001476 hypothetical protein; Provisional; Region: PRK10279 228405001477 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 228405001478 nucleophile elbow; other site 228405001479 Surface antigen; Region: Bac_surface_Ag; pfam01103 228405001480 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 228405001481 hydroxyglutarate oxidase; Provisional; Region: PRK11728 228405001482 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 228405001483 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405001484 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405001485 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 228405001486 Protein of unknwon function (DUF3008); Region: DUF3008; pfam11450 228405001487 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 228405001488 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 228405001489 Mg2+ binding site [ion binding]; other site 228405001490 G-X-G motif; other site 228405001491 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 228405001492 anchoring element; other site 228405001493 dimer interface [polypeptide binding]; other site 228405001494 ATP binding site [chemical binding]; other site 228405001495 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 228405001496 active site 228405001497 putative metal-binding site [ion binding]; other site 228405001498 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 228405001499 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 228405001500 DEAD-like helicases superfamily; Region: DEXDc; smart00487 228405001501 ATP binding site [chemical binding]; other site 228405001502 Mg++ binding site [ion binding]; other site 228405001503 motif III; other site 228405001504 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 228405001505 nucleotide binding region [chemical binding]; other site 228405001506 ATP-binding site [chemical binding]; other site 228405001507 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 228405001508 RNA binding site [nucleotide binding]; other site 228405001509 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 228405001510 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 228405001511 FeS/SAM binding site; other site 228405001512 S-formylglutathione hydrolase; Region: PLN02442 228405001513 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 228405001514 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 228405001515 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405001516 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405001517 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 228405001518 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 228405001519 substrate binding site [chemical binding]; other site 228405001520 catalytic Zn binding site [ion binding]; other site 228405001521 NAD binding site [chemical binding]; other site 228405001522 structural Zn binding site [ion binding]; other site 228405001523 dimer interface [polypeptide binding]; other site 228405001524 recombination protein F; Reviewed; Region: recF; PRK00064 228405001525 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405001526 Walker A/P-loop; other site 228405001527 ATP binding site [chemical binding]; other site 228405001528 Q-loop/lid; other site 228405001529 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405001530 ABC transporter signature motif; other site 228405001531 Walker B; other site 228405001532 D-loop; other site 228405001533 H-loop/switch region; other site 228405001534 Uncharacterized conserved protein [Function unknown]; Region: COG1359 228405001535 DNA polymerase III subunit beta; Validated; Region: PRK05643 228405001536 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 228405001537 putative DNA binding surface [nucleotide binding]; other site 228405001538 dimer interface [polypeptide binding]; other site 228405001539 beta-clamp/clamp loader binding surface; other site 228405001540 beta-clamp/translesion DNA polymerase binding surface; other site 228405001541 DnaA N-terminal domain; Region: DnaA_N; pfam11638 228405001542 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 228405001543 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 228405001544 Walker A motif; other site 228405001545 ATP binding site [chemical binding]; other site 228405001546 Walker B motif; other site 228405001547 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 228405001548 DnaA box-binding interface [nucleotide binding]; other site 228405001549 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 228405001550 enoyl-CoA hydratase; Provisional; Region: PRK05862 228405001551 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 228405001552 substrate binding site [chemical binding]; other site 228405001553 oxyanion hole (OAH) forming residues; other site 228405001554 trimer interface [polypeptide binding]; other site 228405001555 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 228405001556 ABC1 family; Region: ABC1; cl17513 228405001557 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 228405001558 active site 228405001559 ATP binding site [chemical binding]; other site 228405001560 substrate binding site [chemical binding]; other site 228405001561 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 228405001562 active site 228405001563 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 228405001564 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405001565 Cytochrome P450; Region: p450; cl12078 228405001566 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405001567 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405001568 Rubredoxin [Energy production and conversion]; Region: COG1773 228405001569 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 228405001570 iron binding site [ion binding]; other site 228405001571 Prokaryotic phospholipase A2; Region: Phospholip_A2_3; pfam09056 228405001572 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 228405001573 CoenzymeA binding site [chemical binding]; other site 228405001574 subunit interaction site [polypeptide binding]; other site 228405001575 PHB binding site; other site 228405001576 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 228405001577 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 228405001578 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 228405001579 Chromate transporter; Region: Chromate_transp; pfam02417 228405001580 histidyl-tRNA synthetase; Region: hisS; TIGR00442 228405001581 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 228405001582 dimer interface [polypeptide binding]; other site 228405001583 motif 1; other site 228405001584 active site 228405001585 motif 2; other site 228405001586 motif 3; other site 228405001587 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 228405001588 anticodon binding site; other site 228405001589 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 228405001590 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12295 228405001591 motif 1; other site 228405001592 dimer interface [polypeptide binding]; other site 228405001593 active site 228405001594 motif 2; other site 228405001595 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 228405001596 ATP phosphoribosyltransferase; Reviewed; Region: hisG; PRK00489 228405001597 ATP phosphoribosyltransferase; Region: HisG; cl15266 228405001598 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 228405001599 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 228405001600 inhibitor-cofactor binding pocket; inhibition site 228405001601 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405001602 catalytic residue [active] 228405001603 Predicted ATPase [General function prediction only]; Region: COG3911 228405001604 AAA domain; Region: AAA_28; pfam13521 228405001605 AAA ATPase domain; Region: AAA_16; pfam13191 228405001606 AAA domain; Region: AAA_22; pfam13401 228405001607 Tetratricopeptide repeat; Region: TPR_12; pfam13424 228405001608 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 228405001609 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405001610 DNA binding residues [nucleotide binding] 228405001611 Secretory lipase; Region: LIP; pfam03583 228405001612 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 228405001613 nitrilase; Region: PLN02798 228405001614 putative active site [active] 228405001615 catalytic triad [active] 228405001616 dimer interface [polypeptide binding]; other site 228405001617 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 228405001618 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 228405001619 dimer interface [polypeptide binding]; other site 228405001620 active site 228405001621 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 228405001622 catalytic residues [active] 228405001623 substrate binding site [chemical binding]; other site 228405001624 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 228405001625 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 228405001626 ornithine carbamoyltransferase; Provisional; Region: PRK00779 228405001627 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 228405001628 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 228405001629 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 228405001630 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 228405001631 FeS/SAM binding site; other site 228405001632 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 228405001633 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 228405001634 dimerization interface [polypeptide binding]; other site 228405001635 domain crossover interface; other site 228405001636 redox-dependent activation switch; other site 228405001637 Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR; Region: TER_DECR_SDR_a; cd05369 228405001638 short chain dehydrogenase; Provisional; Region: PRK07677 228405001639 NAD(P) binding site [chemical binding]; other site 228405001640 substrate binding site [chemical binding]; other site 228405001641 homotetramer interface [polypeptide binding]; other site 228405001642 active site 228405001643 homodimer interface [polypeptide binding]; other site 228405001644 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 228405001645 Mechanosensitive ion channel; Region: MS_channel; pfam00924 228405001646 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 228405001647 Mechanosensitive ion channel; Region: MS_channel; pfam00924 228405001648 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 228405001649 active site 228405001650 substrate binding sites [chemical binding]; other site 228405001651 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405001652 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405001653 DEXH box helicase, DNA ligase-associated; Region: DEXH_lig_assoc; TIGR04121 228405001654 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 228405001655 ATP binding site [chemical binding]; other site 228405001656 putative Mg++ binding site [ion binding]; other site 228405001657 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 228405001658 nucleotide binding region [chemical binding]; other site 228405001659 ATP-binding site [chemical binding]; other site 228405001660 DEAD/H associated; Region: DEAD_assoc; pfam08494 228405001661 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405001662 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 228405001663 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 228405001664 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 228405001665 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain; Region: MPP_PF1019; cd07391 228405001666 putative active site [active] 228405001667 putative metal binding site [ion binding]; other site 228405001668 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 228405001669 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 228405001670 Sulfate transporter family; Region: Sulfate_transp; pfam00916 228405001671 Predicted transcriptional regulator [Transcription]; Region: COG2932 228405001672 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 228405001673 Catalytic site [active] 228405001674 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 228405001675 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405001676 catalytic residue [active] 228405001677 hypothetical protein; Provisional; Region: PRK08262 228405001678 M20 Peptidase, carboxypeptidase yscS; Region: M20_yscS; cd05674 228405001679 metal binding site [ion binding]; metal-binding site 228405001680 MFS/sugar transport protein; Region: MFS_2; pfam13347 228405001681 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 228405001682 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 228405001683 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 228405001684 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; cl17726 228405001685 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 228405001686 S-adenosylmethionine binding site [chemical binding]; other site 228405001687 aspartate kinase; Reviewed; Region: PRK06635 228405001688 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 228405001689 putative nucleotide binding site [chemical binding]; other site 228405001690 putative catalytic residues [active] 228405001691 putative Mg ion binding site [ion binding]; other site 228405001692 putative aspartate binding site [chemical binding]; other site 228405001693 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 228405001694 putative allosteric regulatory site; other site 228405001695 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 228405001696 putative allosteric regulatory residue; other site 228405001697 Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; Region: PtsP; COG3605 228405001698 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 228405001699 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 228405001700 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 228405001701 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 228405001702 Helix-turn-helix domain; Region: HTH_25; pfam13413 228405001703 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 228405001704 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 228405001705 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 228405001706 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 228405001707 Protein of unknown function (DUF1214); Region: DUF1214; cl08447 228405001708 Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3458 228405001709 MAPEG family; Region: MAPEG; pfam01124 228405001710 peptide chain release factor 1; Validated; Region: prfA; PRK00591 228405001711 This domain is found in peptide chain release factors; Region: PCRF; smart00937 228405001712 RF-1 domain; Region: RF-1; pfam00472 228405001713 Uncharacterized Fe-S protein [General function prediction only]; Region: COG3217 228405001714 MOSC N-terminal beta barrel domain; Region: MOSC_N; pfam03476 228405001715 MOSC domain; Region: MOSC; pfam03473 228405001716 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 228405001717 catalytic motif [active] 228405001718 Catalytic residue [active] 228405001719 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 228405001720 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 228405001721 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 228405001722 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 228405001723 Clp amino terminal domain; Region: Clp_N; pfam02861 228405001724 Clp amino terminal domain; Region: Clp_N; pfam02861 228405001725 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 228405001726 Walker A motif; other site 228405001727 ATP binding site [chemical binding]; other site 228405001728 Walker B motif; other site 228405001729 arginine finger; other site 228405001730 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 228405001731 Walker A motif; other site 228405001732 ATP binding site [chemical binding]; other site 228405001733 Walker B motif; other site 228405001734 arginine finger; other site 228405001735 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 228405001736 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 228405001737 Peptidase family M23; Region: Peptidase_M23; pfam01551 228405001738 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 228405001739 Peptidase family M23; Region: Peptidase_M23; pfam01551 228405001740 ATP12 chaperone protein; Region: ATP12; cl02228 228405001741 Dicarboxylate transport; Region: DctA-YdbH; pfam11739 228405001742 YnbE-like lipoprotein; Region: Lipoprotein_19; pfam13617 228405001743 Protein of unknown function (DUF1318); Region: DUF1318; pfam07027 228405001744 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 228405001745 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 228405001746 Response regulator receiver domain; Region: Response_reg; pfam00072 228405001747 active site 228405001748 phosphorylation site [posttranslational modification] 228405001749 intermolecular recognition site; other site 228405001750 dimerization interface [polypeptide binding]; other site 228405001751 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 228405001752 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 228405001753 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 228405001754 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 228405001755 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 228405001756 Ligand Binding Site [chemical binding]; other site 228405001757 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 228405001758 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 228405001759 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 228405001760 Uncharacterized conserved protein, YhbC family [Function unknown]; Region: COG0782 228405001761 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 228405001762 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 228405001763 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 228405001764 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 228405001765 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 228405001766 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 228405001767 ATP-grasp domain; Region: ATP-grasp_4; cl17255 228405001768 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 228405001769 IMP binding site; other site 228405001770 dimer interface [polypeptide binding]; other site 228405001771 partial ornithine binding site; other site 228405001772 REDY-like protein HapK; Region: HapK; pfam11639 228405001773 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 228405001774 Peptidase family M48; Region: Peptidase_M48; pfam01435 228405001775 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405001776 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405001777 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 228405001778 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 228405001779 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405001780 homodimer interface [polypeptide binding]; other site 228405001781 catalytic residue [active] 228405001782 Protein of unknown function (DUF1330); Region: DUF1330; pfam07045 228405001783 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 228405001784 active site 228405001785 Thioesterase-like superfamily; Region: 4HBT_2; pfam13279 228405001786 active site 2 [active] 228405001787 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 228405001788 metal binding site 2 [ion binding]; metal-binding site 228405001789 putative DNA binding helix; other site 228405001790 metal binding site 1 [ion binding]; metal-binding site 228405001791 dimer interface [polypeptide binding]; other site 228405001792 structural Zn2+ binding site [ion binding]; other site 228405001793 MarR family; Region: MarR; pfam01047 228405001794 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 228405001795 NlpC/P60 family; Region: NLPC_P60; cl17555 228405001796 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 228405001797 Cytochrome c2 [Energy production and conversion]; Region: COG3474 228405001798 prephenate dehydratase; Provisional; Region: PRK11899 228405001799 Prephenate dehydratase; Region: PDT; pfam00800 228405001800 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 228405001801 putative L-Phe binding site [chemical binding]; other site 228405001802 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405001803 transcriptional activator TtdR; Provisional; Region: PRK09801 228405001804 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 228405001805 putative effector binding pocket; other site 228405001806 dimerization interface [polypeptide binding]; other site 228405001807 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 228405001808 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]; Region: NPY1; COG2816 228405001809 NADH pyrophosphatase-like rudimentary NUDIX domain; Region: NUDIX-like; pfam09296 228405001810 NADH pyrophosphatase zinc ribbon domain; Region: zf-NADH-PPase; pfam09297 228405001811 NADH pyrophosphatase, a member of the Nudix hydrolase superfamily, catalyzes the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP. Like other members of the Nudix family, it requires a divalent cation, such as Mg2+ or Mn2+, for...; Region: NADH_pyrophosphatase; cd03429 228405001812 putative NADH binding site [chemical binding]; other site 228405001813 putative active site [active] 228405001814 nudix motif; other site 228405001815 putative metal binding site [ion binding]; other site 228405001816 Beta propeller domain; Region: Beta_propel; pfam09826 228405001817 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 228405001818 Sel1-like repeats; Region: SEL1; smart00671 228405001819 Sel1-like repeats; Region: SEL1; smart00671 228405001820 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 228405001821 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 228405001822 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 228405001823 DNA binding residues [nucleotide binding] 228405001824 putative dimer interface [polypeptide binding]; other site 228405001825 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 228405001826 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 228405001827 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405001828 active site 228405001829 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 228405001830 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405001831 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405001832 active site 228405001833 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 228405001834 CoenzymeA binding site [chemical binding]; other site 228405001835 subunit interaction site [polypeptide binding]; other site 228405001836 PHB binding site; other site 228405001837 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 228405001838 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 228405001839 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 228405001840 dimer interface [polypeptide binding]; other site 228405001841 active site 228405001842 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 228405001843 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 228405001844 substrate binding site [chemical binding]; other site 228405001845 oxyanion hole (OAH) forming residues; other site 228405001846 trimer interface [polypeptide binding]; other site 228405001847 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 228405001848 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 228405001849 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 228405001850 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 228405001851 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 228405001852 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 228405001853 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 228405001854 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 228405001855 active site 228405001856 metal binding site [ion binding]; metal-binding site 228405001857 TPR repeat; Region: TPR_11; pfam13414 228405001858 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 228405001859 binding surface 228405001860 TPR motif; other site 228405001861 TPR repeat; Region: TPR_11; pfam13414 228405001862 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 228405001863 Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound...; Region: GT_MraY-like; cl10571 228405001864 Mg++ binding site [ion binding]; other site 228405001865 putative catalytic motif [active] 228405001866 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 228405001867 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 228405001868 substrate binding pocket [chemical binding]; other site 228405001869 chain length determination region; other site 228405001870 substrate-Mg2+ binding site; other site 228405001871 catalytic residues [active] 228405001872 aspartate-rich region 1; other site 228405001873 active site lid residues [active] 228405001874 aspartate-rich region 2; other site 228405001875 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 228405001876 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 228405001877 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 228405001878 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 228405001879 dimer interface [polypeptide binding]; other site 228405001880 motif 1; other site 228405001881 active site 228405001882 motif 2; other site 228405001883 motif 3; other site 228405001884 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 228405001885 DALR anticodon binding domain; Region: DALR_1; smart00836 228405001886 pyruvate phosphate dikinase; Provisional; Region: PRK09279 228405001887 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 228405001888 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 228405001889 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 228405001890 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 228405001891 short chain dehydrogenase; Provisional; Region: PRK08267 228405001892 classical (c) SDR, subgroup 9; Region: SDR_c9; cd08931 228405001893 putative NAD(P) binding site [chemical binding]; other site 228405001894 active site 228405001895 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06106 228405001896 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 228405001897 dimerization interface [polypeptide binding]; other site 228405001898 active site 228405001899 L-aspartate oxidase; Provisional; Region: PRK07512 228405001900 L-aspartate oxidase; Provisional; Region: PRK06175 228405001901 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 228405001902 quinolinate synthetase; Provisional; Region: PRK09375 228405001903 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 228405001904 Sel1-like repeats; Region: SEL1; smart00671 228405001905 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 228405001906 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like6; cd05664 228405001907 metal binding site [ion binding]; metal-binding site 228405001908 putative dimer interface [polypeptide binding]; other site 228405001909 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 228405001910 DEAD-like helicases superfamily; Region: DEXDc; smart00487 228405001911 ATP binding site [chemical binding]; other site 228405001912 Mg++ binding site [ion binding]; other site 228405001913 motif III; other site 228405001914 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 228405001915 nucleotide binding region [chemical binding]; other site 228405001916 ATP-binding site [chemical binding]; other site 228405001917 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 228405001918 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 228405001919 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 228405001920 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 228405001921 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 228405001922 putative acyl-acceptor binding pocket; other site 228405001923 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 228405001924 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 228405001925 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 228405001926 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 228405001927 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 228405001928 putative acyl-acceptor binding pocket; other site 228405001929 phosphoglycolate phosphatase; Provisional; Region: PRK13222 228405001930 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 228405001931 motif II; other site 228405001932 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 228405001933 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 228405001934 Substrate binding site; other site 228405001935 Mg++ binding site; other site 228405001936 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 228405001937 active site 228405001938 substrate binding site [chemical binding]; other site 228405001939 CoA binding site [chemical binding]; other site 228405001940 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 228405001941 tetramer (dimer of dimers) interface [polypeptide binding]; other site 228405001942 active site 228405001943 dimer interface [polypeptide binding]; other site 228405001944 glutathione reductase; Validated; Region: PRK06116 228405001945 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405001946 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 228405001947 TIR domain; Region: TIR_2; pfam13676 228405001948 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 228405001949 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405001950 P-loop; other site 228405001951 Magnesium ion binding site [ion binding]; other site 228405001952 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405001953 Magnesium ion binding site [ion binding]; other site 228405001954 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 228405001955 CAAX protease self-immunity; Region: Abi; pfam02517 228405001956 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 228405001957 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 228405001958 cation binding site [ion binding]; other site 228405001959 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 228405001960 IHF - DNA interface [nucleotide binding]; other site 228405001961 IHF dimer interface [polypeptide binding]; other site 228405001962 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional; Region: PRK14495 228405001963 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 228405001964 Prostaglandin dehydrogenases; Region: PGDH; cd05288 228405001965 NAD(P) binding site [chemical binding]; other site 228405001966 substrate binding site [chemical binding]; other site 228405001967 dimer interface [polypeptide binding]; other site 228405001968 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 228405001969 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 228405001970 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 228405001971 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405001972 NAD(P) binding site [chemical binding]; other site 228405001973 active site 228405001974 amidophosphoribosyltransferase; Provisional; Region: PRK09123 228405001975 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 228405001976 active site 228405001977 tetramer interface [polypeptide binding]; other site 228405001978 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 228405001979 active site 228405001980 Colicin V production protein; Region: Colicin_V; pfam02674 228405001981 DNA repair protein RadA; Provisional; Region: PRK11823 228405001982 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 228405001983 Walker A motif; other site 228405001984 ATP binding site [chemical binding]; other site 228405001985 Walker B motif; other site 228405001986 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 228405001987 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 228405001988 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 228405001989 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405001990 Walker A/P-loop; other site 228405001991 ATP binding site [chemical binding]; other site 228405001992 Q-loop/lid; other site 228405001993 ABC transporter signature motif; other site 228405001994 Walker B; other site 228405001995 D-loop; other site 228405001996 H-loop/switch region; other site 228405001997 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 228405001998 Permease; Region: Permease; pfam02405 228405001999 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 228405002000 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 228405002001 active site 228405002002 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 228405002003 dimer interface [polypeptide binding]; other site 228405002004 substrate binding site [chemical binding]; other site 228405002005 catalytic residues [active] 228405002006 Transmembrane secretion effector; Region: MFS_3; pfam05977 228405002007 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 228405002008 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 228405002009 Na+/H+ ion antiporter subunit; Region: MNHE; pfam01899 228405002010 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12599 228405002011 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; pfam03334 228405002012 Domain of unknown function (DUF4040); Region: DUF4040; pfam13244 228405002013 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 228405002014 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12508 228405002015 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 228405002016 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 228405002017 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 228405002018 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 228405002019 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 228405002020 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12668 228405002021 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 228405002022 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 228405002023 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 228405002024 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 228405002025 DnaA box-binding interface [nucleotide binding]; other site 228405002026 Fe-S metabolism associated domain; Region: SufE; cl00951 228405002027 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 228405002028 dimer interface [polypeptide binding]; other site 228405002029 phosphorylation site [posttranslational modification] 228405002030 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 228405002031 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 228405002032 ATP binding site [chemical binding]; other site 228405002033 Mg2+ binding site [ion binding]; other site 228405002034 G-X-G motif; other site 228405002035 Protein of unknown function (DUF1491); Region: DUF1491; pfam07372 228405002036 Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]; Region: PrfC; COG4108 228405002037 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 228405002038 G1 box; other site 228405002039 putative GEF interaction site [polypeptide binding]; other site 228405002040 GTP/Mg2+ binding site [chemical binding]; other site 228405002041 Switch I region; other site 228405002042 G2 box; other site 228405002043 G3 box; other site 228405002044 Switch II region; other site 228405002045 G4 box; other site 228405002046 G5 box; other site 228405002047 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 228405002048 PAN domain; Region: PAN_4; pfam14295 228405002049 putative binding site; other site 228405002050 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 228405002051 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405002052 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405002053 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 228405002054 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 228405002055 active site 228405002056 uracil binding [chemical binding]; other site 228405002057 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 228405002058 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 228405002059 S-adenosylmethionine binding site [chemical binding]; other site 228405002060 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405002061 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405002062 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 228405002063 acetyl-CoA acetyltransferase; Provisional; Region: PRK06025 228405002064 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 228405002065 dimer interface [polypeptide binding]; other site 228405002066 active site 228405002067 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 228405002068 TadE-like protein; Region: TadE; pfam07811 228405002069 Predicted membrane protein [Function unknown]; Region: COG4655 228405002070 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 228405002071 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 228405002072 chaperone protein DnaJ; Provisional; Region: PRK10767 228405002073 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 228405002074 HSP70 interaction site [polypeptide binding]; other site 228405002075 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 228405002076 substrate binding site [polypeptide binding]; other site 228405002077 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 228405002078 Zn binding sites [ion binding]; other site 228405002079 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 228405002080 dimer interface [polypeptide binding]; other site 228405002081 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 228405002082 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 228405002083 putative ligand binding site [chemical binding]; other site 228405002084 Predicted methyltransferases [General function prediction only]; Region: COG0313 228405002085 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 228405002086 putative SAM binding site [chemical binding]; other site 228405002087 putative homodimer interface [polypeptide binding]; other site 228405002088 Uncharacterized protein family UPF0102; Region: UPF0102; cl00516 228405002089 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 228405002090 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 228405002091 active site 228405002092 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 228405002093 Cytochrome c; Region: Cytochrom_C; pfam00034 228405002094 Transglycosylase; Region: Transgly; pfam00912 228405002095 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 228405002096 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 228405002097 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405002098 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405002099 metal binding site [ion binding]; metal-binding site 228405002100 active site 228405002101 I-site; other site 228405002102 NnrU protein; Region: NnrU; pfam07298 228405002103 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 228405002104 oligomerization interface [polypeptide binding]; other site 228405002105 active site 228405002106 metal binding site [ion binding]; metal-binding site 228405002107 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 228405002108 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 228405002109 Trp docking motif [polypeptide binding]; other site 228405002110 active site 228405002111 PQQ-like domain; Region: PQQ_2; pfam13360 228405002112 GTP-binding protein Der; Reviewed; Region: PRK00093 228405002113 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 228405002114 G1 box; other site 228405002115 GTP/Mg2+ binding site [chemical binding]; other site 228405002116 Switch I region; other site 228405002117 G2 box; other site 228405002118 Switch II region; other site 228405002119 G3 box; other site 228405002120 G4 box; other site 228405002121 G5 box; other site 228405002122 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 228405002123 G1 box; other site 228405002124 GTP/Mg2+ binding site [chemical binding]; other site 228405002125 Switch I region; other site 228405002126 G2 box; other site 228405002127 G3 box; other site 228405002128 Switch II region; other site 228405002129 G4 box; other site 228405002130 G5 box; other site 228405002131 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 228405002132 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 228405002133 Substrate binding site; other site 228405002134 Cupin domain; Region: Cupin_2; cl17218 228405002135 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 228405002136 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 228405002137 CysD dimerization site [polypeptide binding]; other site 228405002138 G1 box; other site 228405002139 putative GEF interaction site [polypeptide binding]; other site 228405002140 GTP/Mg2+ binding site [chemical binding]; other site 228405002141 Switch I region; other site 228405002142 G2 box; other site 228405002143 G3 box; other site 228405002144 Switch II region; other site 228405002145 G4 box; other site 228405002146 G5 box; other site 228405002147 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 228405002148 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 228405002149 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form...; Region: APSK; cd02027 228405002150 ligand-binding site [chemical binding]; other site 228405002151 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 228405002152 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 228405002153 Active Sites [active] 228405002154 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 228405002155 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 228405002156 glutaminase active site [active] 228405002157 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 228405002158 dimer interface [polypeptide binding]; other site 228405002159 active site 228405002160 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 228405002161 dimer interface [polypeptide binding]; other site 228405002162 active site 228405002163 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 228405002164 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 228405002165 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 228405002166 NADP binding site [chemical binding]; other site 228405002167 active site 228405002168 putative substrate binding site [chemical binding]; other site 228405002169 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 228405002170 dimerization interface [polypeptide binding]; other site 228405002171 putative active cleft [active] 228405002172 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 228405002173 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 228405002174 inhibitor-cofactor binding pocket; inhibition site 228405002175 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405002176 catalytic residue [active] 228405002177 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 228405002178 non-specific DNA binding site [nucleotide binding]; other site 228405002179 salt bridge; other site 228405002180 sequence-specific DNA binding site [nucleotide binding]; other site 228405002181 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 228405002182 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405002183 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 228405002184 DNA binding residues [nucleotide binding] 228405002185 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 228405002186 S-adenosylmethionine synthetase; Validated; Region: PRK05250 228405002187 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 228405002188 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 228405002189 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 228405002190 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 228405002191 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 228405002192 putative active site [active] 228405002193 putative substrate binding site [chemical binding]; other site 228405002194 putative cosubstrate binding site; other site 228405002195 catalytic site [active] 228405002196 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 228405002197 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 228405002198 homotetramer interface [polypeptide binding]; other site 228405002199 ligand binding site [chemical binding]; other site 228405002200 catalytic site [active] 228405002201 NAD binding site [chemical binding]; other site 228405002202 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 228405002203 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 228405002204 substrate binding site; other site 228405002205 tetramer interface; other site 228405002206 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 228405002207 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 228405002208 NAD binding site [chemical binding]; other site 228405002209 substrate binding site [chemical binding]; other site 228405002210 homodimer interface [polypeptide binding]; other site 228405002211 active site 228405002212 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 228405002213 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 228405002214 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405002215 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 228405002216 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 228405002217 NADP-binding site; other site 228405002218 homotetramer interface [polypeptide binding]; other site 228405002219 substrate binding site [chemical binding]; other site 228405002220 homodimer interface [polypeptide binding]; other site 228405002221 active site 228405002222 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405002223 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405002224 NAD(P) binding site [chemical binding]; other site 228405002225 active site 228405002226 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 228405002227 ABC-2 type transporter; Region: ABC2_membrane; cl17235 228405002228 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 228405002229 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 228405002230 Walker A/P-loop; other site 228405002231 ATP binding site [chemical binding]; other site 228405002232 Q-loop/lid; other site 228405002233 ABC transporter signature motif; other site 228405002234 Walker B; other site 228405002235 D-loop; other site 228405002236 H-loop/switch region; other site 228405002237 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 228405002238 putative carbohydrate binding site [chemical binding]; other site 228405002239 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 228405002240 Methyltransferase domain; Region: Methyltransf_23; pfam13489 228405002241 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 228405002242 S-adenosylmethionine binding site [chemical binding]; other site 228405002243 glycosyltransferase, TIGR04182 family; Region: glyco_TIGR04182 228405002244 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 228405002245 Ligand binding site; other site 228405002246 Putative Catalytic site; other site 228405002247 DXD motif; other site 228405002248 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 228405002249 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 228405002250 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405002251 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 228405002252 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405002253 This family is most closely related to the GT1 family of glycosyltransferases. mtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the...; Region: GT1_mtfB_like; cd03809 228405002254 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405002255 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 228405002256 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 228405002257 Probable Catalytic site; other site 228405002258 metal-binding site 228405002259 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 228405002260 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 228405002261 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405002262 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 228405002263 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405002264 active site 228405002265 tryptophanase/L-cysteine desulfhydrase, PLP-dependent; Provisional; Region: tnaA; PRK13238 228405002266 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 228405002267 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405002268 catalytic residue [active] 228405002269 Zinc dependent phospholipase C/S1-P1 nuclease; Region: ZnPC_S1P1; cd10981 228405002270 Zn binding site [ion binding]; other site 228405002271 Domain of unknown function (DUF4332); Region: DUF4332; pfam14229 228405002272 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 228405002273 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 228405002274 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 228405002275 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 228405002276 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405002277 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405002278 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 228405002279 Amidase; Region: Amidase; cl11426 228405002280 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 228405002281 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 228405002282 S-adenosylmethionine binding site [chemical binding]; other site 228405002283 Protein of unknown function (DUF461); Region: DUF461; pfam04314 228405002284 Methyltransferase domain; Region: Methyltransf_31; pfam13847 228405002285 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 228405002286 S-adenosylmethionine binding site [chemical binding]; other site 228405002287 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 228405002288 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 228405002289 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 228405002290 Tetramer interface [polypeptide binding]; other site 228405002291 active site 228405002292 FMN-binding site [chemical binding]; other site 228405002293 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 228405002294 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 228405002295 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 228405002296 Domain of unknown function (DUF4345); Region: DUF4345; pfam14248 228405002297 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 228405002298 Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins; Region: GDPD_AtGDE_like; cd08566 228405002299 putative active site [active] 228405002300 catalytic site [active] 228405002301 putative metal binding site [ion binding]; other site 228405002302 oligomer interface [polypeptide binding]; other site 228405002303 putative acyl-CoA synthetase; Provisional; Region: PRK06018 228405002304 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 228405002305 dimer interface [polypeptide binding]; other site 228405002306 acyl-activating enzyme (AAE) consensus motif; other site 228405002307 putative active site [active] 228405002308 AMP binding site [chemical binding]; other site 228405002309 putative CoA binding site [chemical binding]; other site 228405002310 Protein of unknown function (DUF3088); Region: DUF3088; pfam11287 228405002311 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 228405002312 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 228405002313 CoenzymeA binding site [chemical binding]; other site 228405002314 subunit interaction site [polypeptide binding]; other site 228405002315 PHB binding site; other site 228405002316 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 228405002317 dimer interface [polypeptide binding]; other site 228405002318 putative tRNA-binding site [nucleotide binding]; other site 228405002319 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 228405002320 classical (c) SDRs; Region: SDR_c; cd05233 228405002321 NAD(P) binding site [chemical binding]; other site 228405002322 active site 228405002323 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405002324 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 228405002325 N-terminal plug; other site 228405002326 ligand-binding site [chemical binding]; other site 228405002327 YCII-related domain; Region: YCII; cl00999 228405002328 Protein of unknown function DUF262; Region: DUF262; pfam03235 228405002329 Uncharacterized conserved protein [Function unknown]; Region: COG1479 228405002330 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 228405002331 Domain of unknown function (DUF2437); Region: DUF2437; pfam10370 228405002332 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 228405002333 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 228405002334 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405002335 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 228405002336 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 228405002337 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 228405002338 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 228405002339 dimer interaction site [polypeptide binding]; other site 228405002340 substrate-binding tunnel; other site 228405002341 active site 228405002342 catalytic site [active] 228405002343 substrate binding site [chemical binding]; other site 228405002344 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 228405002345 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 228405002346 active site 228405002347 Riboflavin kinase; Region: Flavokinase; pfam01687 228405002348 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 228405002349 Putative bacterial sensory transduction regulator; Region: YbjN; pfam10722 228405002350 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 228405002351 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405002352 active site 228405002353 HIGH motif; other site 228405002354 nucleotide binding site [chemical binding]; other site 228405002355 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405002356 active site 228405002357 KMSKS motif; other site 228405002358 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 228405002359 tRNA binding surface [nucleotide binding]; other site 228405002360 anticodon binding site; other site 228405002361 lipoprotein signal peptidase; Provisional; Region: PRK14787 228405002362 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 228405002363 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 228405002364 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 228405002365 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 228405002366 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 228405002367 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 228405002368 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 228405002369 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 228405002370 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 228405002371 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 228405002372 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 228405002373 dimer interface [polypeptide binding]; other site 228405002374 active site 228405002375 CoA binding pocket [chemical binding]; other site 228405002376 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 228405002377 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 228405002378 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 228405002379 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 228405002380 dihydroorotase; Validated; Region: PRK09060 228405002381 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 228405002382 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 228405002383 active site 228405002384 hypothetical protein; Provisional; Region: PRK09133 228405002385 M20 Peptidase, carboxypeptidase yscS-like; Region: M20_yscS_like; cd05675 228405002386 putative metal binding site [ion binding]; other site 228405002387 feruloyl-CoA synthase; Reviewed; Region: PRK08180 228405002388 Feruloyl-CoA synthetase (FCS); Region: FCS; cd05921 228405002389 acyl-activating enzyme (AAE) consensus motif; other site 228405002390 putative AMP binding site [chemical binding]; other site 228405002391 putative active site [active] 228405002392 putative CoA binding site [chemical binding]; other site 228405002393 hypothetical protein; Validated; Region: PRK07586 228405002394 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 228405002395 PYR/PP interface [polypeptide binding]; other site 228405002396 dimer interface [polypeptide binding]; other site 228405002397 TPP binding site [chemical binding]; other site 228405002398 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 228405002399 TPP-binding site [chemical binding]; other site 228405002400 dimer interface [polypeptide binding]; other site 228405002401 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 228405002402 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 228405002403 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405002404 Orthopoxvirus protein of unknown function (DUF830); Region: DUF830; cl13998 228405002405 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 228405002406 Class I ribonucleotide reductase; Region: RNR_I; cd01679 228405002407 active site 228405002408 dimer interface [polypeptide binding]; other site 228405002409 catalytic residues [active] 228405002410 effector binding site; other site 228405002411 R2 peptide binding site; other site 228405002412 Uncharacterized conserved protein [Function unknown]; Region: COG1432 228405002413 LabA_like proteins; Region: LabA; cd10911 228405002414 putative metal binding site [ion binding]; other site 228405002415 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 228405002416 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 228405002417 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 228405002418 Zn2+ binding site [ion binding]; other site 228405002419 Mg2+ binding site [ion binding]; other site 228405002420 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 228405002421 synthetase active site [active] 228405002422 NTP binding site [chemical binding]; other site 228405002423 metal binding site [ion binding]; metal-binding site 228405002424 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 228405002425 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 228405002426 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 228405002427 active site 228405002428 pyridoxine 5'-phosphate synthase; Provisional; Region: PRK05265 228405002429 active site 228405002430 hydrophilic channel; other site 228405002431 dimerization interface [polypeptide binding]; other site 228405002432 catalytic residues [active] 228405002433 active site lid [active] 228405002434 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 228405002435 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 228405002436 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 228405002437 dimerization interface [polypeptide binding]; other site 228405002438 active site 228405002439 metal binding site [ion binding]; metal-binding site 228405002440 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 228405002441 dsRNA binding site [nucleotide binding]; other site 228405002442 GTPase Era; Reviewed; Region: era; PRK00089 228405002443 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 228405002444 G1 box; other site 228405002445 GTP/Mg2+ binding site [chemical binding]; other site 228405002446 Switch I region; other site 228405002447 G2 box; other site 228405002448 Switch II region; other site 228405002449 G3 box; other site 228405002450 G4 box; other site 228405002451 G5 box; other site 228405002452 KH domain; Region: KH_2; pfam07650 228405002453 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 228405002454 Recombination protein O N terminal; Region: RecO_N; pfam11967 228405002455 Recombination protein O C terminal; Region: RecO_C; pfam02565 228405002456 Extensin-like protein C-terminus; Region: Extensin-like_C; pfam06904 228405002457 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 228405002458 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 228405002459 CAP-like domain; other site 228405002460 active site 228405002461 primary dimer interface [polypeptide binding]; other site 228405002462 NAD-dependent deacetylase; Provisional; Region: PRK00481 228405002463 SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2-fam; cd01407 228405002464 NAD+ binding site [chemical binding]; other site 228405002465 substrate binding site [chemical binding]; other site 228405002466 Zn binding site [ion binding]; other site 228405002467 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_8; cd08901 228405002468 putative hydrophobic ligand binding site [chemical binding]; other site 228405002469 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 228405002470 dimerization interface [polypeptide binding]; other site 228405002471 putative DNA binding site [nucleotide binding]; other site 228405002472 putative Zn2+ binding site [ion binding]; other site 228405002473 Nodulin-21 and CCC1-related protein family; Region: Nodulin-21_like_1; cd02432 228405002474 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 228405002475 aspartate aminotransferase; Provisional; Region: PRK05764 228405002476 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 228405002477 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405002478 homodimer interface [polypeptide binding]; other site 228405002479 catalytic residue [active] 228405002480 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 228405002481 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 228405002482 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; cl01181 228405002483 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 228405002484 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 228405002485 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 228405002486 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 228405002487 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 228405002488 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 228405002489 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 228405002490 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405002491 ligand binding site [chemical binding]; other site 228405002492 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 228405002493 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 228405002494 Domain of unknown function (DUF389); Region: DUF389; cl00781 228405002495 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 228405002496 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 228405002497 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 228405002498 dimer interface [polypeptide binding]; other site 228405002499 allosteric magnesium binding site [ion binding]; other site 228405002500 active site 228405002501 aspartate-rich active site metal binding site; other site 228405002502 Schiff base residues; other site 228405002503 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405002504 Coenzyme A binding pocket [chemical binding]; other site 228405002505 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405002506 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 228405002507 substrate binding pocket [chemical binding]; other site 228405002508 FAD binding site [chemical binding]; other site 228405002509 catalytic base [active] 228405002510 hypothetical protein; Provisional; Region: PRK06194 228405002511 classical (c) SDRs; Region: SDR_c; cd05233 228405002512 NAD(P) binding site [chemical binding]; other site 228405002513 active site 228405002514 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial homologs of mammalian glycerophosphodiester phosphodiesterase GDE4; Region: GDPD_GDE4_like_1; cd08613 228405002515 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 228405002516 putative active site [active] 228405002517 catalytic site [active] 228405002518 putative metal binding site [ion binding]; other site 228405002519 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 228405002520 heme-binding site [chemical binding]; other site 228405002521 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 228405002522 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 228405002523 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 228405002524 PilZ domain; Region: PilZ; pfam07238 228405002525 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 228405002526 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 228405002527 substrate binding site [chemical binding]; other site 228405002528 oxyanion hole (OAH) forming residues; other site 228405002529 trimer interface [polypeptide binding]; other site 228405002530 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 228405002531 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 228405002532 Transcriptional regulators [Transcription]; Region: MarR; COG1846 228405002533 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 228405002534 Domain of Unknown Function (DUF1543); Region: DUF1543; pfam07566 228405002535 Cytochrome c2 [Energy production and conversion]; Region: COG3474 228405002536 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 228405002537 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 228405002538 Mg2+ binding site [ion binding]; other site 228405002539 G-X-G motif; other site 228405002540 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 228405002541 ATP binding site [chemical binding]; other site 228405002542 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 228405002543 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405002544 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405002545 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 228405002546 putative active site [active] 228405002547 putative catalytic site [active] 228405002548 putative Mg binding site IVb [ion binding]; other site 228405002549 putative phosphate binding site [ion binding]; other site 228405002550 putative DNA binding site [nucleotide binding]; other site 228405002551 putative Mg binding site IVa [ion binding]; other site 228405002552 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 228405002553 FAD binding domain; Region: FAD_binding_4; pfam01565 228405002554 Putative FMN-binding domain; Region: FMN_bind_2; pfam04299 228405002555 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 228405002556 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 228405002557 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 228405002558 generic binding surface II; other site 228405002559 generic binding surface I; other site 228405002560 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 228405002561 S-adenosylmethionine binding site [chemical binding]; other site 228405002562 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 228405002563 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 228405002564 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 228405002565 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 228405002566 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 228405002567 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH8; cd08262 228405002568 putative NAD(P) binding site [chemical binding]; other site 228405002569 catalytic Zn binding site [ion binding]; other site 228405002570 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 228405002571 classical (c) SDRs; Region: SDR_c; cd05233 228405002572 NAD(P) binding site [chemical binding]; other site 228405002573 active site 228405002574 Cupin domain; Region: Cupin_2; cl17218 228405002575 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405002576 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405002577 Protein of unknown function (DUF3297); Region: DUF3297; pfam11730 228405002578 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 228405002579 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 228405002580 Phosphotransferase enzyme family; Region: APH; pfam01636 228405002581 putative active site [active] 228405002582 putative substrate binding site [chemical binding]; other site 228405002583 ATP binding site [chemical binding]; other site 228405002584 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 228405002585 putative substrate translocation pore; other site 228405002586 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405002587 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 228405002588 active site 2 [active] 228405002589 active site 1 [active] 228405002590 Uncharacterized protein conserved in bacteria [Function unknown]; Region: MmcQ; COG2315 228405002591 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 228405002592 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 228405002593 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 228405002594 active site 228405002595 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405002596 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 228405002597 ligand binding site [chemical binding]; other site 228405002598 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 228405002599 Protein of unknown function (DUF2855); Region: DUF2855; pfam11017 228405002600 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 228405002601 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 228405002602 substrate binding site [chemical binding]; other site 228405002603 oxyanion hole (OAH) forming residues; other site 228405002604 trimer interface [polypeptide binding]; other site 228405002605 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405002606 Cytochrome P450; Region: p450; cl12078 228405002607 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405002608 Cytochrome P450; Region: p450; cl12078 228405002609 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 228405002610 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 228405002611 RNA binding surface [nucleotide binding]; other site 228405002612 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 228405002613 active site 228405002614 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 228405002615 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 228405002616 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 228405002617 P-loop; other site 228405002618 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 228405002619 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405002620 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 228405002621 active site 228405002622 phosphorylation site [posttranslational modification] 228405002623 intermolecular recognition site; other site 228405002624 dimerization interface [polypeptide binding]; other site 228405002625 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 228405002626 DNA binding site [nucleotide binding] 228405002627 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 228405002628 RNA/DNA hybrid binding site [nucleotide binding]; other site 228405002629 active site 228405002630 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 228405002631 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 228405002632 putative active site [active] 228405002633 putative substrate binding site [chemical binding]; other site 228405002634 ATP binding site [chemical binding]; other site 228405002635 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 228405002636 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405002637 putative substrate translocation pore; other site 228405002638 benzoate transport; Region: 2A0115; TIGR00895 228405002639 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 228405002640 putative substrate translocation pore; other site 228405002641 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 228405002642 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405002643 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405002644 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405002645 Walker A/P-loop; other site 228405002646 ATP binding site [chemical binding]; other site 228405002647 Q-loop/lid; other site 228405002648 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405002649 ABC transporter signature motif; other site 228405002650 Walker B; other site 228405002651 D-loop; other site 228405002652 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 228405002653 active site 228405002654 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405002655 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405002656 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 228405002657 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 228405002658 putative MPT binding site; other site 228405002659 enoyl-CoA hydratase; Provisional; Region: PRK06190 228405002660 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 228405002661 substrate binding site [chemical binding]; other site 228405002662 oxyanion hole (OAH) forming residues; other site 228405002663 trimer interface [polypeptide binding]; other site 228405002664 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 228405002665 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 228405002666 putative active site [active] 228405002667 metal binding site [ion binding]; metal-binding site 228405002668 acetyl-CoA acetyltransferase; Provisional; Region: PRK06205 228405002669 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 228405002670 dimer interface [polypeptide binding]; other site 228405002671 active site 228405002672 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 228405002673 DNA-binding site [nucleotide binding]; DNA binding site 228405002674 RNA-binding motif; other site 228405002675 Protein of unknown function (DUF2490); Region: DUF2490; pfam10677 228405002676 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 228405002677 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 228405002678 transmembrane helices; other site 228405002679 HPP family; Region: HPP; pfam04982 228405002680 FOG: CBS domain [General function prediction only]; Region: COG0517 228405002681 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 228405002682 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 228405002683 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 228405002684 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 228405002685 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 228405002686 Pirin-related protein [General function prediction only]; Region: COG1741 228405002687 Pirin; Region: Pirin; pfam02678 228405002688 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 228405002689 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 228405002690 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 228405002691 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 228405002692 active site 228405002693 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 228405002694 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 228405002695 hexamer interface [polypeptide binding]; other site 228405002696 ligand binding site [chemical binding]; other site 228405002697 putative active site [active] 228405002698 NAD(P) binding site [chemical binding]; other site 228405002699 Bacterial protein of unknown function (Gcw_chp); Region: Gcw_chp; cl09901 228405002700 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 228405002701 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405002702 NAD(P) binding site [chemical binding]; other site 228405002703 active site 228405002704 Sensors of blue-light using FAD; Region: BLUF; smart01034 228405002705 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 228405002706 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 228405002707 ATP binding site [chemical binding]; other site 228405002708 Mg2+ binding site [ion binding]; other site 228405002709 G-X-G motif; other site 228405002710 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 228405002711 anchoring element; other site 228405002712 dimer interface [polypeptide binding]; other site 228405002713 ATP binding site [chemical binding]; other site 228405002714 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 228405002715 active site 228405002716 metal binding site [ion binding]; metal-binding site 228405002717 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 228405002718 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 228405002719 Found in ATP-dependent protease La (LON); Region: LON; smart00464 228405002720 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 228405002721 Walker A motif; other site 228405002722 ATP binding site [chemical binding]; other site 228405002723 Walker B motif; other site 228405002724 arginine finger; other site 228405002725 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 228405002726 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 228405002727 Predicted membrane protein [Function unknown]; Region: COG3650 228405002728 META domain; Region: META; pfam03724 228405002729 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 228405002730 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 228405002731 enoyl-CoA hydratase; Provisional; Region: PRK06142 228405002732 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 228405002733 substrate binding site [chemical binding]; other site 228405002734 oxyanion hole (OAH) forming residues; other site 228405002735 trimer interface [polypeptide binding]; other site 228405002736 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 228405002737 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 228405002738 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 228405002739 acetyl-CoA acetyltransferase; Validated; Region: PRK08257 228405002740 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 228405002741 active site 228405002742 haloalkane dehalogenase; Provisional; Region: PRK00870 228405002743 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 228405002744 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 228405002745 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 228405002746 putative catalytic residue [active] 228405002747 geranylgeranyl reductase family; Region: GG-red-SF; TIGR02032 228405002748 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 228405002749 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cd00531 228405002750 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 228405002751 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 228405002752 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 228405002753 ArsC family; Region: ArsC; pfam03960 228405002754 catalytic residues [active] 228405002755 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 228405002756 arsenical-resistance protein; Region: acr3; TIGR00832 228405002757 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 228405002758 dimerization interface [polypeptide binding]; other site 228405002759 putative DNA binding site [nucleotide binding]; other site 228405002760 putative Zn2+ binding site [ion binding]; other site 228405002761 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 228405002762 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405002763 putative substrate translocation pore; other site 228405002764 Methyltransferase domain; Region: Methyltransf_26; pfam13659 228405002765 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 228405002766 Ligand Binding Site [chemical binding]; other site 228405002767 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 228405002768 Ligand Binding Site [chemical binding]; other site 228405002769 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 228405002770 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 228405002771 Sulfate transporter family; Region: Sulfate_transp; pfam00916 228405002772 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 228405002773 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 228405002774 camphor resistance protein CrcB; Provisional; Region: PRK14195 228405002775 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 228405002776 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 228405002777 RNA binding surface [nucleotide binding]; other site 228405002778 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 228405002779 active site 228405002780 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 228405002781 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 228405002782 motif II; other site 228405002783 ATP12 chaperone protein; Region: ATP12; cl02228 228405002784 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 228405002785 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 228405002786 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 228405002787 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 228405002788 Amidohydrolase; Region: Amidohydro_4; pfam13147 228405002789 active site 228405002790 Family of unknown function (DUF695); Region: DUF695; pfam05117 228405002791 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 228405002792 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405002793 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 228405002794 Transcriptional regulators [Transcription]; Region: MarR; COG1846 228405002795 MarR family; Region: MarR_2; pfam12802 228405002796 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 228405002797 putative C-terminal domain interface [polypeptide binding]; other site 228405002798 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405002799 putative dimer interface [polypeptide binding]; other site 228405002800 putative GSH binding site (G-site) [chemical binding]; other site 228405002801 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 228405002802 dimer interface [polypeptide binding]; other site 228405002803 N-terminal domain interface [polypeptide binding]; other site 228405002804 putative substrate binding pocket (H-site) [chemical binding]; other site 228405002805 YCII-related domain; Region: YCII; cl00999 228405002806 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 228405002807 dimer interface [polypeptide binding]; other site 228405002808 Domain of unknown function (DUF4287); Region: DUF4287; pfam14117 228405002809 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_8; cd07246 228405002810 putative dimer interface [polypeptide binding]; other site 228405002811 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 228405002812 Protein of unknown function (DUF1428); Region: DUF1428; pfam07237 228405002813 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 228405002814 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 228405002815 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 228405002816 NAD(P) binding site [chemical binding]; other site 228405002817 homodimer interface [polypeptide binding]; other site 228405002818 substrate binding site [chemical binding]; other site 228405002819 active site 228405002820 Uncharacterized conserved protein [Function unknown]; Region: COG2968 228405002821 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 228405002822 KpsF/GutQ family protein; Region: kpsF; TIGR00393 228405002823 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 228405002824 putative active site [active] 228405002825 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 228405002826 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 228405002827 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 228405002828 phasin; Region: phasin_2; TIGR01985 228405002829 StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been...; Region: StaR_like; cd05804 228405002830 Protein of unknown function (DUF1499); Region: DUF1499; pfam07386 228405002831 Uncharacterized conserved protein [Function unknown]; Region: COG2127 228405002832 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 228405002833 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 228405002834 Walker A motif; other site 228405002835 ATP binding site [chemical binding]; other site 228405002836 Walker B motif; other site 228405002837 arginine finger; other site 228405002838 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 228405002839 Walker A motif; other site 228405002840 ATP binding site [chemical binding]; other site 228405002841 Walker B motif; other site 228405002842 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 228405002843 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405002844 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405002845 Protein of unknown function (DUF454); Region: DUF454; cl01063 228405002846 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 228405002847 active site residue [active] 228405002848 protease TldD; Provisional; Region: tldD; PRK10735 228405002849 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405002850 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405002851 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 228405002852 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405002853 NAD(P) binding site [chemical binding]; other site 228405002854 active site 228405002855 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 228405002856 TPR motif; other site 228405002857 TPR repeat; Region: TPR_11; pfam13414 228405002858 binding surface 228405002859 TPR repeat; Region: TPR_11; pfam13414 228405002860 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 228405002861 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 228405002862 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 228405002863 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 228405002864 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 228405002865 Subunit I/III interface [polypeptide binding]; other site 228405002866 D-pathway; other site 228405002867 Subunit I/VIIc interface [polypeptide binding]; other site 228405002868 Subunit I/IV interface [polypeptide binding]; other site 228405002869 Subunit I/II interface [polypeptide binding]; other site 228405002870 Low-spin heme (heme a) binding site [chemical binding]; other site 228405002871 Subunit I/VIIa interface [polypeptide binding]; other site 228405002872 Subunit I/VIa interface [polypeptide binding]; other site 228405002873 Dimer interface; other site 228405002874 Putative water exit pathway; other site 228405002875 Binuclear center (heme a3/CuB) [ion binding]; other site 228405002876 K-pathway; other site 228405002877 Subunit I/Vb interface [polypeptide binding]; other site 228405002878 Putative proton exit pathway; other site 228405002879 Subunit I/VIb interface; other site 228405002880 Subunit I/VIc interface [polypeptide binding]; other site 228405002881 Electron transfer pathway; other site 228405002882 Subunit I/VIIIb interface [polypeptide binding]; other site 228405002883 Subunit I/VIIb interface [polypeptide binding]; other site 228405002884 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 228405002885 UbiA prenyltransferase family; Region: UbiA; pfam01040 228405002886 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 228405002887 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 228405002888 Subunit III/VIIa interface [polypeptide binding]; other site 228405002889 Phospholipid binding site [chemical binding]; other site 228405002890 Subunit I/III interface [polypeptide binding]; other site 228405002891 Subunit III/VIb interface [polypeptide binding]; other site 228405002892 Subunit III/VIa interface; other site 228405002893 Subunit III/Vb interface [polypeptide binding]; other site 228405002894 SURF1 family; Region: SURF1; pfam02104 228405002895 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 228405002896 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 228405002897 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405002898 catalytic residue [active] 228405002899 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 228405002900 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 228405002901 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405002902 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 228405002903 Uncharacterized ACR, COG1678; Region: DUF179; pfam02622 228405002904 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 228405002905 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 228405002906 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405002907 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 228405002908 N-terminal plug; other site 228405002909 ligand-binding site [chemical binding]; other site 228405002910 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 228405002911 catalytic triad [active] 228405002912 dimer interface [polypeptide binding]; other site 228405002913 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 228405002914 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 228405002915 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 228405002916 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405002917 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405002918 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405002919 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405002920 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405002921 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 228405002922 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 228405002923 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 228405002924 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 228405002925 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 228405002926 carboxyltransferase (CT) interaction site; other site 228405002927 biotinylation site [posttranslational modification]; other site 228405002928 Protein of unknown function (DUF805); Region: DUF805; pfam05656 228405002929 Protein of unknown function (DUF805); Region: DUF805; pfam05656 228405002930 lipoate-protein ligase B; Provisional; Region: PRK14341 228405002931 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 228405002932 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 228405002933 trimer interface [polypeptide binding]; other site 228405002934 dimer interface [polypeptide binding]; other site 228405002935 putative active site [active] 228405002936 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 228405002937 MPT binding site; other site 228405002938 trimer interface [polypeptide binding]; other site 228405002939 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 228405002940 MoaE homodimer interface [polypeptide binding]; other site 228405002941 MoaD interaction [polypeptide binding]; other site 228405002942 active site residues [active] 228405002943 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 228405002944 MoaE interaction surface [polypeptide binding]; other site 228405002945 MoeB interaction surface [polypeptide binding]; other site 228405002946 thiocarboxylated glycine; other site 228405002947 molybdenum cofactor biosynthesis protein A; Provisional; Region: PRK13361 228405002948 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 228405002949 FeS/SAM binding site; other site 228405002950 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 228405002951 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 228405002952 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 228405002953 XdhC Rossmann domain; Region: XdhC_C; pfam13478 228405002954 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 228405002955 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 228405002956 Ligand binding site; other site 228405002957 metal-binding site 228405002958 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 228405002959 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 228405002960 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 228405002961 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 228405002962 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 228405002963 aldehyde oxidoreductase 2Fe-2S subunit; Provisional; Region: PRK11433 228405002964 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 228405002965 catalytic loop [active] 228405002966 iron binding site [ion binding]; other site 228405002967 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 228405002968 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 228405002969 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 228405002970 intracellular protease, PfpI family; Region: PfpI; TIGR01382 228405002971 proposed catalytic triad [active] 228405002972 conserved cys residue [active] 228405002973 isopropylmalate isomerase large subunit; Provisional; Region: PRK12466 228405002974 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 228405002975 substrate binding site [chemical binding]; other site 228405002976 ligand binding site [chemical binding]; other site 228405002977 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 228405002978 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 228405002979 substrate binding site [chemical binding]; other site 228405002980 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405002981 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405002982 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 228405002983 active site 228405002984 catalytic residues [active] 228405002985 metal binding site [ion binding]; metal-binding site 228405002986 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 228405002987 Na binding site [ion binding]; other site 228405002988 Protein of unknown function (DUF1838); Region: DUF1838; pfam08894 228405002989 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405002990 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 228405002991 N-terminal plug; other site 228405002992 ligand-binding site [chemical binding]; other site 228405002993 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 228405002994 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405002995 putative substrate translocation pore; other site 228405002996 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 228405002997 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405002998 Prostaglandin dehydrogenases; Region: PGDH; cd05288 228405002999 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 228405003000 NAD(P) binding site [chemical binding]; other site 228405003001 substrate binding site [chemical binding]; other site 228405003002 dimer interface [polypeptide binding]; other site 228405003003 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 228405003004 Methyltransferase domain; Region: Methyltransf_31; pfam13847 228405003005 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 228405003006 S-adenosylmethionine binding site [chemical binding]; other site 228405003007 REDY-like protein HapK; Region: HapK; pfam11639 228405003008 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405003009 classical (c) SDRs; Region: SDR_c; cd05233 228405003010 NAD(P) binding site [chemical binding]; other site 228405003011 active site 228405003012 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 228405003013 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 228405003014 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405003015 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 228405003016 active site 228405003017 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 228405003018 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 228405003019 putative active site [active] 228405003020 putative catalytic site [active] 228405003021 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405003022 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405003023 active site 228405003024 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405003025 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405003026 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 228405003027 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405003028 DNA-binding site [nucleotide binding]; DNA binding site 228405003029 UTRA domain; Region: UTRA; pfam07702 228405003030 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 228405003031 Uncharacterized protein involved in propionate catabolism [General function prediction only]; Region: PrpD; COG2079 228405003032 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 228405003033 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405003034 acyl-activating enzyme (AAE) consensus motif; other site 228405003035 AMP binding site [chemical binding]; other site 228405003036 active site 228405003037 CoA binding site [chemical binding]; other site 228405003038 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 228405003039 Amidase; Region: Amidase; cl11426 228405003040 enoyl-CoA hydratase; Provisional; Region: PRK06127 228405003041 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 228405003042 substrate binding site [chemical binding]; other site 228405003043 oxyanion hole (OAH) forming residues; other site 228405003044 trimer interface [polypeptide binding]; other site 228405003045 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 228405003046 Methylomonas sp. 4,4'-diapolycopene-dialdehyde dehydrogenase-like; Region: ALDH_DDALDH; cd07099 228405003047 NAD(P) binding site [chemical binding]; other site 228405003048 catalytic residues [active] 228405003049 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 228405003050 FAD binding domain; Region: FAD_binding_4; pfam01565 228405003051 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 228405003052 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405003053 DNA-binding site [nucleotide binding]; DNA binding site 228405003054 UTRA domain; Region: UTRA; pfam07702 228405003055 Protein of unknown function (DUF1838); Region: DUF1838; pfam08894 228405003056 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_4; cd07582 228405003057 Predicted amidohydrolase [General function prediction only]; Region: COG0388 228405003058 putative active site [active] 228405003059 catalytic triad [active] 228405003060 putative dimer interface [polypeptide binding]; other site 228405003061 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases; Region: CE4_PuuE_like; cd10979 228405003062 putative active site [active] 228405003063 putative catalytic site [active] 228405003064 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 228405003065 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases; Region: CE4_PuuE_like; cd10979 228405003066 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 228405003067 putative active site [active] 228405003068 putative catalytic site [active] 228405003069 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; cl00220 228405003070 Isochorismatase family; Region: Isochorismatase; pfam00857 228405003071 catalytic triad [active] 228405003072 conserved cis-peptide bond; other site 228405003073 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405003074 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 228405003075 N-terminal plug; other site 228405003076 ligand-binding site [chemical binding]; other site 228405003077 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 228405003078 DEAD-like helicases superfamily; Region: DEXDc; smart00487 228405003079 ATP binding site [chemical binding]; other site 228405003080 Mg++ binding site [ion binding]; other site 228405003081 motif III; other site 228405003082 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 228405003083 nucleotide binding region [chemical binding]; other site 228405003084 ATP-binding site [chemical binding]; other site 228405003085 PaaX-like protein C-terminal domain; Region: PaaX_C; pfam08223 228405003086 This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine...; Region: Rhizobitoxine-FADS-like; cd03510 228405003087 putative di-iron ligands [ion binding]; other site 228405003088 This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine...; Region: Rhizobitoxine-FADS-like; cd03510 228405003089 Transcriptional regulators [Transcription]; Region: PurR; COG1609 228405003090 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 228405003091 DNA binding site [nucleotide binding] 228405003092 domain linker motif; other site 228405003093 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 228405003094 putative dimerization interface [polypeptide binding]; other site 228405003095 putative ligand binding site [chemical binding]; other site 228405003096 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 228405003097 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405003098 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405003099 LysR substrate binding domain; Region: LysR_substrate; pfam03466 228405003100 dimerization interface [polypeptide binding]; other site 228405003101 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 228405003102 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 228405003103 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405003104 homodimer interface [polypeptide binding]; other site 228405003105 catalytic residue [active] 228405003106 pantoate--beta-alanine ligase; Region: panC; TIGR00018 228405003107 Pantoate-beta-alanine ligase; Region: PanC; cd00560 228405003108 active site 228405003109 ATP-binding site [chemical binding]; other site 228405003110 pantoate-binding site; other site 228405003111 HXXH motif; other site 228405003112 ATPase MipZ; Region: MipZ; pfam09140 228405003113 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405003114 P-loop; other site 228405003115 Magnesium ion binding site [ion binding]; other site 228405003116 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405003117 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405003118 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 228405003119 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 228405003120 Domain of unknown function (DUF4112); Region: DUF4112; pfam13430 228405003121 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405003122 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405003123 active site 228405003124 LuxR family transcriptional regulatory, chaperone HchA-associated; Region: reg_near_HchA; TIGR03541 228405003125 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405003126 DNA binding residues [nucleotide binding] 228405003127 dimerization interface [polypeptide binding]; other site 228405003128 UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]; Region: MurC; COG0773 228405003129 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 228405003130 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 228405003131 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 228405003132 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 228405003133 dimer interface [polypeptide binding]; other site 228405003134 catalytic triad [active] 228405003135 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 228405003136 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 228405003137 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 228405003138 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 228405003139 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 228405003140 ligand binding site [chemical binding]; other site 228405003141 homodimer interface [polypeptide binding]; other site 228405003142 NAD(P) binding site [chemical binding]; other site 228405003143 trimer interface B [polypeptide binding]; other site 228405003144 trimer interface A [polypeptide binding]; other site 228405003145 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 228405003146 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405003147 NAD(P) binding site [chemical binding]; other site 228405003148 active site 228405003149 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 228405003150 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 228405003151 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405003152 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 228405003153 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 228405003154 intersubunit interface [polypeptide binding]; other site 228405003155 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 228405003156 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 228405003157 dimer interface [polypeptide binding]; other site 228405003158 ABC-ATPase subunit interface; other site 228405003159 putative PBP binding regions; other site 228405003160 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 228405003161 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 228405003162 Walker A/P-loop; other site 228405003163 ATP binding site [chemical binding]; other site 228405003164 Q-loop/lid; other site 228405003165 ABC transporter signature motif; other site 228405003166 Walker B; other site 228405003167 D-loop; other site 228405003168 H-loop/switch region; other site 228405003169 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 228405003170 active site 228405003171 tetramer interface; other site 228405003172 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 228405003173 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 228405003174 tetramer interface [polypeptide binding]; other site 228405003175 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405003176 catalytic residue [active] 228405003177 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 228405003178 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 228405003179 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 228405003180 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 228405003181 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 228405003182 AAA domain; Region: AAA_31; pfam13614 228405003183 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 228405003184 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 228405003185 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 228405003186 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 228405003187 ATP binding site [chemical binding]; other site 228405003188 Walker A motif; other site 228405003189 hexamer interface [polypeptide binding]; other site 228405003190 Walker B motif; other site 228405003191 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 228405003192 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405003193 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 228405003194 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405003195 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 228405003196 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 228405003197 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 228405003198 ATP binding site [chemical binding]; other site 228405003199 dimerization interface [polypeptide binding]; other site 228405003200 thiamine-monophosphate kinase; Region: thiL; TIGR01379 228405003201 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 228405003202 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 228405003203 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 228405003204 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 228405003205 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; pfam03981 228405003206 putative phosphate acyltransferase; Provisional; Region: PRK05331 228405003207 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 228405003208 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 228405003209 dimer interface [polypeptide binding]; other site 228405003210 active site 228405003211 CoA binding pocket [chemical binding]; other site 228405003212 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 228405003213 IHF - DNA interface [nucleotide binding]; other site 228405003214 IHF dimer interface [polypeptide binding]; other site 228405003215 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 228405003216 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 228405003217 DNA binding residues [nucleotide binding] 228405003218 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229; cl15841 228405003219 SelR domain; Region: SelR; pfam01641 228405003220 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 228405003221 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405003222 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 228405003223 putative active site [active] 228405003224 putative catalytic site [active] 228405003225 Predicted membrane protein [Function unknown]; Region: COG3671 228405003226 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 228405003227 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 228405003228 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405003229 catalytic residue [active] 228405003230 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 228405003231 apolar tunnel; other site 228405003232 heme binding site [chemical binding]; other site 228405003233 dimerization interface [polypeptide binding]; other site 228405003234 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 228405003235 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405003236 Coenzyme A binding pocket [chemical binding]; other site 228405003237 Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]; Region: NadR; COG3172 228405003238 AAA domain; Region: AAA_28; pfam13521 228405003239 Nicotinamide mononucleotide transporter; Region: NMN_transporter; pfam04973 228405003240 isocitrate dehydrogenase; Validated; Region: PRK08299 228405003241 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 228405003242 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 228405003243 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 228405003244 enoyl-CoA hydratase; Provisional; Region: PRK08252 228405003245 substrate binding site [chemical binding]; other site 228405003246 oxyanion hole (OAH) forming residues; other site 228405003247 trimer interface [polypeptide binding]; other site 228405003248 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405003249 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405003250 active site 228405003251 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405003252 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405003253 active site 228405003254 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 228405003255 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 228405003256 active site 228405003257 intersubunit interface [polypeptide binding]; other site 228405003258 catalytic residue [active] 228405003259 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_tuaB_like; cd13127 228405003260 N-terminal formyl transferase catalytic core domain of NRPS_like proteins, one of the proteins involved in the synthesis of Oxazolomycin; Region: FMT_core_NRPS_like; cd08649 228405003261 putative active site [active] 228405003262 putative substrate binding site [chemical binding]; other site 228405003263 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 228405003264 putative cosubstrate binding site; other site 228405003265 catalytic site [active] 228405003266 C-terminal subdomain of the Formyltransferase-like domain found in OzmH-like proteins; Region: FMT_C_OzmH_like; cd08700 228405003267 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405003268 acyl-activating enzyme (AAE) consensus motif; other site 228405003269 natural product biosynthesis luciferase-like monooxygenase domain; Region: seco_metab_LLM; TIGR04020 228405003270 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 228405003271 The adenylation domain of nonribosomal peptide synthetases (NRPS); Region: A_NRPS; cd05930 228405003272 AMP binding site [chemical binding]; other site 228405003273 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 228405003274 Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3321 228405003275 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 228405003276 active site 228405003277 Acyl transferase domain in polyketide synthase (PKS) enzymes; Region: PKS_AT; smart00827 228405003278 ketoreductase (KR), subgroup 2, complex (x) SDRs; Region: KR_2_SDR_x; cd08953 228405003279 This enzymatic domain is part of bacterial polyketide synthases; Region: PKS_KR; smart00822 228405003280 putative NADP binding site [chemical binding]; other site 228405003281 active site 228405003282 Dehydratase domain in polyketide synthase (PKS) enzymes; Region: PKS_DH; smart00826 228405003283 Phosphopantetheine attachment site; Region: PP-binding; pfam00550 228405003284 Thioesterase domains of type I polyketide synthases or non-ribosomal peptide synthetases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3319 228405003285 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405003286 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405003287 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 228405003288 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 228405003289 phosphate binding site [ion binding]; other site 228405003290 Uncharacterized protein conserved in bacteria (DUF2320); Region: DUF2320; pfam10082 228405003291 Chain length determinant protein; Region: Wzz; pfam02706 228405003292 exopolysaccharide transport protein family; Region: eps_transp_fam; TIGR01005 228405003293 Chain length determinant protein; Region: Wzz; cl15801 228405003294 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 228405003295 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405003296 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 228405003297 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 228405003298 Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans; Region: Endoglucanase_E_like; cd01831 228405003299 active site 228405003300 catalytic triad [active] 228405003301 oxyanion hole [active] 228405003302 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405003303 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 228405003304 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 228405003305 NAD binding site [chemical binding]; other site 228405003306 homodimer interface [polypeptide binding]; other site 228405003307 active site 228405003308 substrate binding site [chemical binding]; other site 228405003309 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 228405003310 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 228405003311 active site 228405003312 Predicted membrane protein/domain [Function unknown]; Region: COG1714 228405003313 Uncharacterized membrane protein [Function unknown]; Region: SpoIIM; COG1300 228405003314 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 228405003315 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 228405003316 metal ion-dependent adhesion site (MIDAS); other site 228405003317 MoxR-like ATPases [General function prediction only]; Region: COG0714 228405003318 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 228405003319 Walker A motif; other site 228405003320 ATP binding site [chemical binding]; other site 228405003321 Walker B motif; other site 228405003322 arginine finger; other site 228405003323 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 228405003324 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 228405003325 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405003326 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 228405003327 active site 228405003328 catalytic tetrad [active] 228405003329 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 228405003330 Carboxylesterase family; Region: COesterase; pfam00135 228405003331 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 228405003332 substrate binding pocket [chemical binding]; other site 228405003333 catalytic triad [active] 228405003334 cystathionine gamma-lyase; Validated; Region: PRK07582 228405003335 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 228405003336 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405003337 catalytic residue [active] 228405003338 Glutathione S-transferase, C-terminal domain; Region: GST_C_2; pfam13410 228405003339 N-terminal domain interface [polypeptide binding]; other site 228405003340 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405003341 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 228405003342 dimer interface [polypeptide binding]; other site 228405003343 ADP-ribose binding site [chemical binding]; other site 228405003344 active site 228405003345 nudix motif; other site 228405003346 metal binding site [ion binding]; metal-binding site 228405003347 Dipeptidyl peptidase IV (DPP IV) N-terminal region; Region: DPPIV_N; pfam00930 228405003348 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405003349 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405003350 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 228405003351 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405003352 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405003353 Walker A/P-loop; other site 228405003354 ATP binding site [chemical binding]; other site 228405003355 Q-loop/lid; other site 228405003356 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405003357 ABC transporter signature motif; other site 228405003358 Walker B; other site 228405003359 D-loop; other site 228405003360 ABC transporter; Region: ABC_tran_2; pfam12848 228405003361 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405003362 Amidase; Region: Amidase; cl11426 228405003363 amidase; Provisional; Region: PRK08137 228405003364 Predicted transcriptional regulator [Transcription]; Region: COG2378 228405003365 HTH domain; Region: HTH_11; pfam08279 228405003366 WYL domain; Region: WYL; pfam13280 228405003367 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405003368 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 228405003369 putative C-terminal domain interface [polypeptide binding]; other site 228405003370 putative GSH binding site (G-site) [chemical binding]; other site 228405003371 putative dimer interface [polypeptide binding]; other site 228405003372 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405003373 N-terminal domain interface [polypeptide binding]; other site 228405003374 dimer interface [polypeptide binding]; other site 228405003375 substrate binding pocket (H-site) [chemical binding]; other site 228405003376 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 228405003377 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 228405003378 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 228405003379 metal-binding site [ion binding] 228405003380 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 228405003381 Predicted integral membrane protein linked to a cation pump [Inorganic ion transport and metabolism]; Region: COG5456 228405003382 FixH; Region: FixH; pfam05751 228405003383 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 228405003384 4Fe-4S binding domain; Region: Fer4_5; pfam12801 228405003385 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 228405003386 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 228405003387 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 228405003388 Cytochrome c; Region: Cytochrom_C; cl11414 228405003389 Cytochrome c; Region: Cytochrom_C; pfam00034 228405003390 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 228405003391 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cd01324 228405003392 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 228405003393 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; pfam02433 228405003394 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 228405003395 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 228405003396 Low-spin heme binding site [chemical binding]; other site 228405003397 Putative water exit pathway; other site 228405003398 Binuclear center (active site) [active] 228405003399 Putative proton exit pathway; other site 228405003400 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 228405003401 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405003402 putative active site [active] 228405003403 heme pocket [chemical binding]; other site 228405003404 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 228405003405 dimer interface [polypeptide binding]; other site 228405003406 phosphorylation site [posttranslational modification] 228405003407 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 228405003408 ATP binding site [chemical binding]; other site 228405003409 Mg2+ binding site [ion binding]; other site 228405003410 G-X-G motif; other site 228405003411 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 228405003412 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 228405003413 active site 228405003414 phosphorylation site [posttranslational modification] 228405003415 intermolecular recognition site; other site 228405003416 dimerization interface [polypeptide binding]; other site 228405003417 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405003418 DNA binding residues [nucleotide binding] 228405003419 dimerization interface [polypeptide binding]; other site 228405003420 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 228405003421 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 228405003422 active site 228405003423 phosphorylation site [posttranslational modification] 228405003424 intermolecular recognition site; other site 228405003425 dimerization interface [polypeptide binding]; other site 228405003426 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405003427 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 228405003428 non-specific DNA binding site [nucleotide binding]; other site 228405003429 salt bridge; other site 228405003430 sequence-specific DNA binding site [nucleotide binding]; other site 228405003431 Predicted transcriptional regulator [General function prediction only]; Region: COG3800 228405003432 Domain of unknown function (DUF955); Region: DUF955; pfam06114 228405003433 Predicted transcriptional regulator (DUF2083); Region: DUF2083; pfam09856 228405003434 malate synthase A; Region: malate_syn_A; TIGR01344 228405003435 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 228405003436 active site 228405003437 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 228405003438 tetramer interface [polypeptide binding]; other site 228405003439 active site 228405003440 Mg2+/Mn2+ binding site [ion binding]; other site 228405003441 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 228405003442 Possible lysine decarboxylase; Region: Lysine_decarbox; pfam03641 228405003443 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 228405003444 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 228405003445 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405003446 Walker A/P-loop; other site 228405003447 ATP binding site [chemical binding]; other site 228405003448 Q-loop/lid; other site 228405003449 ABC transporter signature motif; other site 228405003450 Walker B; other site 228405003451 D-loop; other site 228405003452 H-loop/switch region; other site 228405003453 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 228405003454 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405003455 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 228405003456 DNA binding site [nucleotide binding] 228405003457 Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair]; Region: SPS1; COG0515 228405003458 Catalytic domain of Protein Kinases; Region: PKc; cd00180 228405003459 active site 228405003460 ATP binding site [chemical binding]; other site 228405003461 substrate binding site [chemical binding]; other site 228405003462 activation loop (A-loop); other site 228405003463 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 228405003464 TPR motif; other site 228405003465 binding surface 228405003466 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 228405003467 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 228405003468 inhibitor-cofactor binding pocket; inhibition site 228405003469 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405003470 catalytic residue [active] 228405003471 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 228405003472 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 228405003473 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405003474 catalytic residue [active] 228405003475 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 228405003476 AAA domain; Region: AAA_26; pfam13500 228405003477 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405003478 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405003479 Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; Region: ArgE; COG0624 228405003480 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 228405003481 putative metal binding site [ion binding]; other site 228405003482 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 228405003483 pyrimidine utilization protein A; Region: RutA; TIGR03612 228405003484 active site 228405003485 dimer interface [polypeptide binding]; other site 228405003486 non-prolyl cis peptide bond; other site 228405003487 insertion regions; other site 228405003488 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405003489 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 228405003490 putative substrate translocation pore; other site 228405003491 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 228405003492 putative substrate translocation pore; other site 228405003493 H+ Antiporter protein; Region: 2A0121; TIGR00900 228405003494 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 228405003495 putative substrate translocation pore; other site 228405003496 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 228405003497 M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins; Region: M20_PAAh_like; cd03896 228405003498 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase; Region: DapE-ArgE; TIGR01910 228405003499 putative metal binding site [ion binding]; other site 228405003500 Isochorismatase family; Region: Isochorismatase; pfam00857 228405003501 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 228405003502 catalytic triad [active] 228405003503 conserved cis-peptide bond; other site 228405003504 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405003505 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405003506 Transcriptional regulators [Transcription]; Region: GntR; COG1802 228405003507 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405003508 DNA-binding site [nucleotide binding]; DNA binding site 228405003509 FCD domain; Region: FCD; pfam07729 228405003510 PhoD-like phosphatase; Region: PhoD; pfam09423 228405003511 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 228405003512 putative active site [active] 228405003513 putative metal binding site [ion binding]; other site 228405003514 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 228405003515 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405003516 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405003517 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 228405003518 Histidine kinase; Region: HisKA_3; pfam07730 228405003519 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 228405003520 ATP binding site [chemical binding]; other site 228405003521 Mg2+ binding site [ion binding]; other site 228405003522 G-X-G motif; other site 228405003523 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 228405003524 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 228405003525 active site 228405003526 phosphorylation site [posttranslational modification] 228405003527 intermolecular recognition site; other site 228405003528 dimerization interface [polypeptide binding]; other site 228405003529 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405003530 DNA binding residues [nucleotide binding] 228405003531 dimerization interface [polypeptide binding]; other site 228405003532 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 228405003533 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405003534 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 228405003535 MgtE intracellular N domain; Region: MgtE_N; pfam03448 228405003536 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 228405003537 Divalent cation transporter; Region: MgtE; cl00786 228405003538 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 228405003539 catalytic residues [active] 228405003540 isovaleryl-CoA dehydrogenase; Region: PLN02519 228405003541 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 228405003542 substrate binding site [chemical binding]; other site 228405003543 FAD binding site [chemical binding]; other site 228405003544 catalytic base [active] 228405003545 Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; Region: PYR_PYL_RCAR_like; cd07821 228405003546 putative hydrophobic ligand binding site [chemical binding]; other site 228405003547 protein interface [polypeptide binding]; other site 228405003548 gate; other site 228405003549 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 228405003550 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405003551 putative active site [active] 228405003552 heme pocket [chemical binding]; other site 228405003553 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 228405003554 dimer interface [polypeptide binding]; other site 228405003555 phosphorylation site [posttranslational modification] 228405003556 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 228405003557 ATP binding site [chemical binding]; other site 228405003558 Mg2+ binding site [ion binding]; other site 228405003559 G-X-G motif; other site 228405003560 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 228405003561 Response regulator receiver domain; Region: Response_reg; pfam00072 228405003562 active site 228405003563 phosphorylation site [posttranslational modification] 228405003564 intermolecular recognition site; other site 228405003565 dimerization interface [polypeptide binding]; other site 228405003566 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 228405003567 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 228405003568 ligand binding site [chemical binding]; other site 228405003569 flexible hinge region; other site 228405003570 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 228405003571 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 228405003572 nucleophile elbow; other site 228405003573 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 228405003574 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 228405003575 Uncharacterized stress protein (general stress protein 26) [General function prediction only]; Region: COG3871 228405003576 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 228405003577 Ca2+ binding site [ion binding]; other site 228405003578 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405003579 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 228405003580 enoyl-CoA hydratase; Provisional; Region: PRK05995 228405003581 substrate binding site [chemical binding]; other site 228405003582 oxyanion hole (OAH) forming residues; other site 228405003583 trimer interface [polypeptide binding]; other site 228405003584 The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; Region: OBF_DNA_ligase_family; cl08424 228405003585 Protein of unknown function (DUF817); Region: DUF817; pfam05675 228405003586 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 228405003587 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 228405003588 ATP-grasp domain; Region: ATP-grasp_4; cl17255 228405003589 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 228405003590 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 228405003591 carboxyltransferase (CT) interaction site; other site 228405003592 biotinylation site [posttranslational modification]; other site 228405003593 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 228405003594 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 228405003595 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405003596 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 228405003597 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 228405003598 Type III secretion system lipoprotein chaperone (YscW); Region: YscW; cl15825 228405003599 META domain; Region: META; pfam03724 228405003600 META domain; Region: META; pfam03724 228405003601 META domain; Region: META; pfam03724 228405003602 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 228405003603 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 228405003604 ligand binding site [chemical binding]; other site 228405003605 flexible hinge region; other site 228405003606 ribonuclease Z; Reviewed; Region: PRK00055 228405003607 AMP nucleosidase; Provisional; Region: PRK08292 228405003608 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 228405003609 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 228405003610 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 228405003611 active site 228405003612 catalytic motif [active] 228405003613 Zn binding site [ion binding]; other site 228405003614 Tyrosine phosphatase family; Region: Y_phosphatase3; pfam13350 228405003615 Tyrosine phosphatase family C-terminal region; Region: Y_phosphatase3C; pfam13348 228405003616 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 228405003617 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405003618 P-loop; other site 228405003619 Magnesium ion binding site [ion binding]; other site 228405003620 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405003621 Magnesium ion binding site [ion binding]; other site 228405003622 curved DNA-binding protein CbpA; Provisional; Region: PRK10266 228405003623 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 228405003624 HSP70 interaction site [polypeptide binding]; other site 228405003625 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 228405003626 dimer interface [polypeptide binding]; other site 228405003627 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 228405003628 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405003629 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 228405003630 active site 228405003631 phosphorylation site [posttranslational modification] 228405003632 intermolecular recognition site; other site 228405003633 dimerization interface [polypeptide binding]; other site 228405003634 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 228405003635 DNA binding site [nucleotide binding] 228405003636 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405003637 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 228405003638 ATP binding site [chemical binding]; other site 228405003639 Mg2+ binding site [ion binding]; other site 228405003640 G-X-G motif; other site 228405003641 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 228405003642 TPR motif; other site 228405003643 binding surface 228405003644 CcmE; Region: CcmE; pfam03100 228405003645 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 228405003646 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405003647 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 228405003648 dimerization interface [polypeptide binding]; other site 228405003649 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 228405003650 dimer interface [polypeptide binding]; other site 228405003651 phosphorylation site [posttranslational modification] 228405003652 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 228405003653 ATP binding site [chemical binding]; other site 228405003654 Mg2+ binding site [ion binding]; other site 228405003655 G-X-G motif; other site 228405003656 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405003657 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 228405003658 active site 228405003659 phosphorylation site [posttranslational modification] 228405003660 intermolecular recognition site; other site 228405003661 dimerization interface [polypeptide binding]; other site 228405003662 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 228405003663 DNA binding site [nucleotide binding] 228405003664 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 228405003665 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 228405003666 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 228405003667 protein binding site [polypeptide binding]; other site 228405003668 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 228405003669 protein binding site [polypeptide binding]; other site 228405003670 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 228405003671 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 228405003672 metal binding triad; other site 228405003673 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 228405003674 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 228405003675 metal binding triad; other site 228405003676 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 228405003677 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405003678 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 228405003679 DNA binding residues [nucleotide binding] 228405003680 Heavy-metal resistance; Region: Metal_resist; pfam13801 228405003681 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405003682 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 228405003683 Amidase; Region: Amidase; cl11426 228405003684 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 228405003685 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 228405003686 Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein; Region: MMP_ACEL2062; cd12952 228405003687 Uncharacterized conserved protein [Function unknown]; Region: COG0393 228405003688 methylmalonyl-CoA mutase; Reviewed; Region: PRK09426 228405003689 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 228405003690 active site 228405003691 substrate binding site [chemical binding]; other site 228405003692 coenzyme B12 binding site [chemical binding]; other site 228405003693 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 228405003694 B12 binding site [chemical binding]; other site 228405003695 cobalt ligand [ion binding]; other site 228405003696 methylmalonyl-CoA mutase, heterodimeric type, beta chain; Region: mmCoA_mut_beta; TIGR00642 228405003697 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 228405003698 heterodimer interface [polypeptide binding]; other site 228405003699 substrate interaction site [chemical binding]; other site 228405003700 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 228405003701 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 228405003702 FMN binding site [chemical binding]; other site 228405003703 substrate binding site [chemical binding]; other site 228405003704 putative catalytic residue [active] 228405003705 Peptidase M15; Region: Peptidase_M15_3; cl01194 228405003706 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 228405003707 active site 228405003708 Protein of unknown function (DUF3423); Region: DUF3423; pfam11903 228405003709 amidase; Provisional; Region: PRK06170 228405003710 Amidase; Region: Amidase; cl11426 228405003711 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 228405003712 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 228405003713 N- and C-terminal domain interface [polypeptide binding]; other site 228405003714 active site 228405003715 MgATP binding site [chemical binding]; other site 228405003716 catalytic site [active] 228405003717 metal binding site [ion binding]; metal-binding site 228405003718 glycerol binding site [chemical binding]; other site 228405003719 homotetramer interface [polypeptide binding]; other site 228405003720 homodimer interface [polypeptide binding]; other site 228405003721 FBP binding site [chemical binding]; other site 228405003722 protein IIAGlc interface [polypeptide binding]; other site 228405003723 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 228405003724 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405003725 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405003726 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405003727 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405003728 amino acid transporter; Region: 2A0306; TIGR00909 228405003729 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405003730 Cytochrome P450; Region: p450; cl12078 228405003731 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 228405003732 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 228405003733 hinge; other site 228405003734 active site 228405003735 Protein of unknown function (DUF2948); Region: DUF2948; pfam11164 228405003736 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 228405003737 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 228405003738 NAD binding site [chemical binding]; other site 228405003739 dimerization interface [polypeptide binding]; other site 228405003740 product binding site; other site 228405003741 substrate binding site [chemical binding]; other site 228405003742 zinc binding site [ion binding]; other site 228405003743 catalytic residues [active] 228405003744 hypothetical protein; Provisional; Region: PRK02853 228405003745 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405003746 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405003747 NAD(P) binding site [chemical binding]; other site 228405003748 active site 228405003749 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405003750 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405003751 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 228405003752 dimerization interface [polypeptide binding]; other site 228405003753 The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the...; Region: Membrane-FADS-like; cl00615 228405003754 Fatty acid desaturase; Region: FA_desaturase; pfam00487 228405003755 putative di-iron ligands [ion binding]; other site 228405003756 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 228405003757 LytTr DNA-binding domain; Region: LytTR; smart00850 228405003758 glucans biosynthesis protein; Provisional; Region: opgC; PRK03854 228405003759 Acyltransferase family; Region: Acyl_transf_3; pfam01757 228405003760 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 228405003761 rRNA binding site [nucleotide binding]; other site 228405003762 predicted 30S ribosome binding site; other site 228405003763 Maf-like protein; Region: Maf; pfam02545 228405003764 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 228405003765 active site 228405003766 dimer interface [polypeptide binding]; other site 228405003767 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 228405003768 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405003769 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 228405003770 DNA binding residues [nucleotide binding] 228405003771 Putative phosphatase (DUF442); Region: DUF442; cl17385 228405003772 MAPEG family; Region: MAPEG; cl09190 228405003773 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 228405003774 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 228405003775 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 228405003776 active site 228405003777 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 228405003778 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 228405003779 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 228405003780 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405003781 Walker A/P-loop; other site 228405003782 ATP binding site [chemical binding]; other site 228405003783 Q-loop/lid; other site 228405003784 ABC transporter signature motif; other site 228405003785 Walker B; other site 228405003786 D-loop; other site 228405003787 H-loop/switch region; other site 228405003788 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 228405003789 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 228405003790 catalytic residues [active] 228405003791 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 228405003792 UbiA prenyltransferase family; Region: UbiA; pfam01040 228405003793 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 228405003794 RNA methyltransferase, RsmE family; Region: TIGR00046 228405003795 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 228405003796 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405003797 putative substrate translocation pore; other site 228405003798 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 228405003799 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405003800 active site 228405003801 catalytic tetrad [active] 228405003802 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405003803 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405003804 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 228405003805 dimerization interface [polypeptide binding]; other site 228405003806 RibD C-terminal domain; Region: RibD_C; cl17279 228405003807 glutamate--cysteine ligase; Region: PLN02611 228405003808 Uncharacterized conserved protein [Function unknown]; Region: COG2135 228405003809 POT family; Region: PTR2; cl17359 228405003810 POT family; Region: PTR2; cl17359 228405003811 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 228405003812 Mechanosensitive ion channel; Region: MS_channel; pfam00924 228405003813 Pseudouridine synthase, Escherichia coli RluE; Region: PseudoU_synth_RluE; cd02566 228405003814 pseudouridine synthase; Region: TIGR00093 228405003815 probable active site [active] 228405003816 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 228405003817 tetramerization interface [polypeptide binding]; other site 228405003818 active site 228405003819 zinc-responsive transcriptional regulator; Provisional; Region: zntR; PRK09514 228405003820 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator; Region: HTH_MerR1; cd04783 228405003821 DNA binding residues [nucleotide binding] 228405003822 dimer interface [polypeptide binding]; other site 228405003823 mercury binding site [ion binding]; other site 228405003824 Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]; Region: GrxC; COG0695 228405003825 Methylamine utilisation protein MauE; Region: MauE; pfam07291 228405003826 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 228405003827 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 228405003828 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cd00347 228405003829 Uncharacterized conserved protein [Function unknown]; Region: COG1565 228405003830 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 228405003831 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 228405003832 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 228405003833 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 228405003834 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 228405003835 Phosphotransferase enzyme family; Region: APH; pfam01636 228405003836 Ecdysteroid kinase; Region: EcKinase; cl17738 228405003837 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 228405003838 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 228405003839 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 228405003840 FliG C-terminal domain; Region: FliG_C; pfam01706 228405003841 flagellar motor switch protein FliN; Region: fliN; TIGR02480 228405003842 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 228405003843 cofactor binding site; other site 228405003844 metal binding site [ion binding]; metal-binding site 228405003845 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 228405003846 putative active site [active] 228405003847 catalytic residue [active] 228405003848 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 228405003849 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 228405003850 5S rRNA interface [nucleotide binding]; other site 228405003851 CTC domain interface [polypeptide binding]; other site 228405003852 L16 interface [polypeptide binding]; other site 228405003853 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405003854 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405003855 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 228405003856 Amidohydrolase; Region: Amidohydro_2; pfam04909 228405003857 putative solute:sodium symporter small subunit; Region: Na_symport_sm; TIGR03647 228405003858 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 228405003859 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 228405003860 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 228405003861 Na binding site [ion binding]; other site 228405003862 acetyl-CoA synthetase; Provisional; Region: PRK00174 228405003863 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 228405003864 active site 228405003865 CoA binding site [chemical binding]; other site 228405003866 acyl-activating enzyme (AAE) consensus motif; other site 228405003867 AMP binding site [chemical binding]; other site 228405003868 acetate binding site [chemical binding]; other site 228405003869 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 228405003870 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 228405003871 active site 228405003872 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 228405003873 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 228405003874 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 228405003875 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 228405003876 dimer interface [polypeptide binding]; other site 228405003877 phosphorylation site [posttranslational modification] 228405003878 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 228405003879 ATP binding site [chemical binding]; other site 228405003880 Mg2+ binding site [ion binding]; other site 228405003881 G-X-G motif; other site 228405003882 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 228405003883 active site 228405003884 Protein of unknown function (DUF3995); Region: DUF3995; pfam13160 228405003885 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 228405003886 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405003887 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 228405003888 active site 228405003889 phosphorylation site [posttranslational modification] 228405003890 intermolecular recognition site; other site 228405003891 dimerization interface [polypeptide binding]; other site 228405003892 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 228405003893 DNA binding site [nucleotide binding] 228405003894 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 228405003895 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; cl00342 228405003896 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405003897 catalytic residue [active] 228405003898 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 228405003899 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 228405003900 DNA polymerase I; Provisional; Region: PRK05755 228405003901 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 228405003902 active site 228405003903 metal binding site 1 [ion binding]; metal-binding site 228405003904 putative 5' ssDNA interaction site; other site 228405003905 metal binding site 3; metal-binding site 228405003906 metal binding site 2 [ion binding]; metal-binding site 228405003907 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 228405003908 putative DNA binding site [nucleotide binding]; other site 228405003909 putative metal binding site [ion binding]; other site 228405003910 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 228405003911 active site 228405003912 catalytic site [active] 228405003913 substrate binding site [chemical binding]; other site 228405003914 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 228405003915 active site 228405003916 DNA binding site [nucleotide binding] 228405003917 catalytic site [active] 228405003918 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 228405003919 Prostaglandin dehydrogenases; Region: PGDH; cd05288 228405003920 NAD(P) binding site [chemical binding]; other site 228405003921 substrate binding site [chemical binding]; other site 228405003922 dimer interface [polypeptide binding]; other site 228405003923 Peptidase C13 family; Region: Peptidase_C13; cl02159 228405003924 cystathionine beta-lyase, bacterial; Region: cysta_beta_ly_B; TIGR01324 228405003925 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 228405003926 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405003927 catalytic residue [active] 228405003928 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 228405003929 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 228405003930 active site residue [active] 228405003931 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 228405003932 active site residue [active] 228405003933 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 228405003934 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 228405003935 dimer interface [polypeptide binding]; other site 228405003936 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405003937 catalytic residue [active] 228405003938 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 228405003939 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 228405003940 PAS domain S-box; Region: sensory_box; TIGR00229 228405003941 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405003942 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405003943 metal binding site [ion binding]; metal-binding site 228405003944 active site 228405003945 I-site; other site 228405003946 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405003947 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 228405003948 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 228405003949 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 228405003950 non-specific DNA binding site [nucleotide binding]; other site 228405003951 salt bridge; other site 228405003952 sequence-specific DNA binding site [nucleotide binding]; other site 228405003953 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 228405003954 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 228405003955 active site 228405003956 Int/Topo IB signature motif; other site 228405003957 catalytic residues [active] 228405003958 DNA binding site [nucleotide binding] 228405003959 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 228405003960 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405003961 ligand binding site [chemical binding]; other site 228405003962 short chain dehydrogenase; Provisional; Region: PRK07478 228405003963 classical (c) SDRs; Region: SDR_c; cd05233 228405003964 NAD(P) binding site [chemical binding]; other site 228405003965 active site 228405003966 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 228405003967 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 228405003968 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 228405003969 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405003970 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 228405003971 N-terminal domain interface [polypeptide binding]; other site 228405003972 Protein of unknown function (DUF736); Region: DUF736; pfam05284 228405003973 Protein of unknown function (DUF3620); Region: DUF3620; pfam12281 228405003974 Protein of unknown function (DUF3363); Region: DUF3363; pfam11843 228405003975 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 228405003976 Walker A motif; other site 228405003977 ATP binding site [chemical binding]; other site 228405003978 Walker B motif; other site 228405003979 Staphylococcal nuclease homologues; Region: SNc; smart00318 228405003980 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 228405003981 Catalytic site; other site 228405003982 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 228405003983 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405003984 DNA binding residues [nucleotide binding] 228405003985 dimerization interface [polypeptide binding]; other site 228405003986 flavocytochrome c; Region: flavo_cyto_c; TIGR01813 228405003987 Predicted oxidoreductase [General function prediction only]; Region: COG3573 228405003988 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405003989 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405003990 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 228405003991 dimerization interface [polypeptide binding]; other site 228405003992 YciI-like protein; Reviewed; Region: PRK12863 228405003993 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 228405003994 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 228405003995 putative catalytic site [active] 228405003996 putative metal binding site [ion binding]; other site 228405003997 putative phosphate binding site [ion binding]; other site 228405003998 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 228405003999 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405004000 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 228405004001 dimerization interface [polypeptide binding]; other site 228405004002 Protein of unknown function (DUF1330); Region: DUF1330; pfam07045 228405004003 SnoaL-like domain; Region: SnoaL_2; pfam12680 228405004004 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 228405004005 CoenzymeA binding site [chemical binding]; other site 228405004006 subunit interaction site [polypeptide binding]; other site 228405004007 PHB binding site; other site 228405004008 Cupin domain; Region: Cupin_2; cl17218 228405004009 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405004010 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405004011 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405004012 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405004013 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405004014 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 228405004015 N-terminal plug; other site 228405004016 ligand-binding site [chemical binding]; other site 228405004017 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405004018 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405004019 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405004020 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405004021 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 228405004022 dimerization interface [polypeptide binding]; other site 228405004023 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 228405004024 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 228405004025 ligand binding site [chemical binding]; other site 228405004026 flexible hinge region; other site 228405004027 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 228405004028 putative switch regulator; other site 228405004029 non-specific DNA interactions [nucleotide binding]; other site 228405004030 DNA binding site [nucleotide binding] 228405004031 sequence specific DNA binding site [nucleotide binding]; other site 228405004032 putative cAMP binding site [chemical binding]; other site 228405004033 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405004034 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 228405004035 N-terminal plug; other site 228405004036 ligand-binding site [chemical binding]; other site 228405004037 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 228405004038 Domain of unknown function (DUF4387); Region: DUF4387; pfam14330 228405004039 aldolase II superfamily protein; Provisional; Region: PRK07044 228405004040 intersubunit interface [polypeptide binding]; other site 228405004041 active site 228405004042 Zn2+ binding site [ion binding]; other site 228405004043 MFS/sugar transport protein; Region: MFS_2; pfam13347 228405004044 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 228405004045 putative substrate translocation pore; other site 228405004046 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 228405004047 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_like_2; cd12172 228405004048 putative ligand binding site [chemical binding]; other site 228405004049 putative NAD binding site [chemical binding]; other site 228405004050 catalytic site [active] 228405004051 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 228405004052 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 228405004053 substrate binding site [chemical binding]; other site 228405004054 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 228405004055 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 228405004056 substrate binding site [chemical binding]; other site 228405004057 ligand binding site [chemical binding]; other site 228405004058 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]; Region: COG5001 228405004059 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405004060 metal binding site [ion binding]; metal-binding site 228405004061 active site 228405004062 I-site; other site 228405004063 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405004064 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 228405004065 Domain of unknown function (DUF305); Region: DUF305; cl17794 228405004066 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 228405004067 YHS domain; Region: YHS; pfam04945 228405004068 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 228405004069 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 228405004070 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 228405004071 motif II; other site 228405004072 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 228405004073 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 228405004074 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 228405004075 Multicopper oxidase; Region: Cu-oxidase; pfam00394 228405004076 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 228405004077 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 228405004078 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 228405004079 putative homodimer interface [polypeptide binding]; other site 228405004080 putative homotetramer interface [polypeptide binding]; other site 228405004081 putative allosteric switch controlling residues; other site 228405004082 putative metal binding site [ion binding]; other site 228405004083 putative homodimer-homodimer interface [polypeptide binding]; other site 228405004084 Protein of unknown function (DUF3620); Region: DUF3620; cl02233 228405004085 BCCT family transporter; Region: BCCT; pfam02028 228405004086 Pirin-related protein [General function prediction only]; Region: COG1741 228405004087 Pirin; Region: Pirin; pfam02678 228405004088 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 228405004089 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405004090 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 228405004091 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 228405004092 catalytic Zn binding site [ion binding]; other site 228405004093 NAD binding site [chemical binding]; other site 228405004094 structural Zn binding site [ion binding]; other site 228405004095 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405004096 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405004097 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 228405004098 putative effector binding pocket; other site 228405004099 dimerization interface [polypeptide binding]; other site 228405004100 RNA polymerase sigma factor, TIGR02999 family; Region: Sig-70_X6 228405004101 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 228405004102 Catalytic domain of Protein Kinases; Region: PKc; cd00180 228405004103 active site 228405004104 ATP binding site [chemical binding]; other site 228405004105 substrate binding site [chemical binding]; other site 228405004106 activation loop (A-loop); other site 228405004107 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 228405004108 binding surface 228405004109 TPR motif; other site 228405004110 Tetratricopeptide repeat; Region: TPR_12; pfam13424 228405004111 Domain of unknown function (DUF4412); Region: DUF4412; pfam14371 228405004112 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405004113 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405004114 Domain of unknown function (DU1801); Region: DUF1801; cl17490 228405004115 Domain of unknown function (DUF1772); Region: DUF1772; pfam08592 228405004116 Response regulator receiver domain; Region: Response_reg; pfam00072 228405004117 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 228405004118 active site 228405004119 phosphorylation site [posttranslational modification] 228405004120 intermolecular recognition site; other site 228405004121 dimerization interface [polypeptide binding]; other site 228405004122 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405004123 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405004124 metal binding site [ion binding]; metal-binding site 228405004125 active site 228405004126 I-site; other site 228405004127 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405004128 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 228405004129 dimer interface [polypeptide binding]; other site 228405004130 phosphorylation site [posttranslational modification] 228405004131 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 228405004132 ATP binding site [chemical binding]; other site 228405004133 Mg2+ binding site [ion binding]; other site 228405004134 G-X-G motif; other site 228405004135 Response regulator receiver domain; Region: Response_reg; pfam00072 228405004136 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 228405004137 active site 228405004138 phosphorylation site [posttranslational modification] 228405004139 intermolecular recognition site; other site 228405004140 dimerization interface [polypeptide binding]; other site 228405004141 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 228405004142 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 228405004143 active site 228405004144 phosphorylation site [posttranslational modification] 228405004145 intermolecular recognition site; other site 228405004146 dimerization interface [polypeptide binding]; other site 228405004147 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 228405004148 putative binding surface; other site 228405004149 active site 228405004150 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 228405004151 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 228405004152 putative dimer interface [polypeptide binding]; other site 228405004153 active site pocket [active] 228405004154 putative cataytic base [active] 228405004155 cobalamin synthase; Reviewed; Region: cobS; PRK00235 228405004156 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 228405004157 catalytic core [active] 228405004158 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 228405004159 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 228405004160 homodimer interface [polypeptide binding]; other site 228405004161 Walker A motif; other site 228405004162 ATP binding site [chemical binding]; other site 228405004163 hydroxycobalamin binding site [chemical binding]; other site 228405004164 Walker B motif; other site 228405004165 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 228405004166 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 228405004167 N-terminal plug; other site 228405004168 ligand-binding site [chemical binding]; other site 228405004169 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 228405004170 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; cd00636 228405004171 intersubunit interface [polypeptide binding]; other site 228405004172 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 228405004173 ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]; Region: FepG; COG4779 228405004174 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 228405004175 ABC-ATPase subunit interface; other site 228405004176 dimer interface [polypeptide binding]; other site 228405004177 putative PBP binding regions; other site 228405004178 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 228405004179 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 228405004180 Walker A/P-loop; other site 228405004181 ATP binding site [chemical binding]; other site 228405004182 Q-loop/lid; other site 228405004183 ABC transporter signature motif; other site 228405004184 Walker B; other site 228405004185 D-loop; other site 228405004186 H-loop/switch region; other site 228405004187 CobD/Cbib protein; Region: CobD_Cbib; pfam03186 228405004188 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 228405004189 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 228405004190 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405004191 catalytic residue [active] 228405004192 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 228405004193 homotrimer interface [polypeptide binding]; other site 228405004194 Walker A motif; other site 228405004195 GTP binding site [chemical binding]; other site 228405004196 Walker B motif; other site 228405004197 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 228405004198 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4337 228405004199 Histidine kinase; Region: HisKA_3; pfam07730 228405004200 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 228405004201 ATP binding site [chemical binding]; other site 228405004202 Mg2+ binding site [ion binding]; other site 228405004203 G-X-G motif; other site 228405004204 Domain of unknown function (DUF897); Region: DUF897; cl01312 228405004205 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 228405004206 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 228405004207 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405004208 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 228405004209 dimerization interface [polypeptide binding]; other site 228405004210 Fic/DOC family; Region: Fic; pfam02661 228405004211 Fic family protein [Function unknown]; Region: COG3177 228405004212 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 228405004213 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405004214 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405004215 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 228405004216 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 228405004217 Walker A/P-loop; other site 228405004218 ATP binding site [chemical binding]; other site 228405004219 Q-loop/lid; other site 228405004220 ABC transporter signature motif; other site 228405004221 Walker B; other site 228405004222 D-loop; other site 228405004223 H-loop/switch region; other site 228405004224 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 228405004225 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405004226 Walker A/P-loop; other site 228405004227 ATP binding site [chemical binding]; other site 228405004228 Q-loop/lid; other site 228405004229 ABC transporter signature motif; other site 228405004230 Walker B; other site 228405004231 D-loop; other site 228405004232 H-loop/switch region; other site 228405004233 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 228405004234 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 228405004235 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 228405004236 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 228405004237 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405004238 Domain of unknown function (DUF1956); Region: DUF1956; pfam09209 228405004239 Cupin domain; Region: Cupin_2; cl17218 228405004240 Hemerythrin-like domain; Region: Hr-like; cd12108 228405004241 Fe binding site [ion binding]; other site 228405004242 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 228405004243 apolar tunnel; other site 228405004244 heme binding site [chemical binding]; other site 228405004245 dimerization interface [polypeptide binding]; other site 228405004246 Rrf2 family protein; Region: rrf2_super; TIGR00738 228405004247 Transcriptional regulator; Region: Rrf2; cl17282 228405004248 Hexameric tyrosine-coordinated heme protein (HTHP); Region: HTHP; pfam11534 228405004249 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 228405004250 NnrU protein; Region: NnrU; pfam07298 228405004251 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 228405004252 MoaE interaction surface [polypeptide binding]; other site 228405004253 MoeB interaction surface [polypeptide binding]; other site 228405004254 thiocarboxylated glycine; other site 228405004255 Predicted integral membrane protein [Function unknown]; Region: COG5615 228405004256 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 228405004257 MoaE homodimer interface [polypeptide binding]; other site 228405004258 MoaD interaction [polypeptide binding]; other site 228405004259 active site residues [active] 228405004260 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 228405004261 MPT binding site; other site 228405004262 trimer interface [polypeptide binding]; other site 228405004263 molybdenum cofactor biosynthesis protein MoaC; Provisional; Region: moaC; PRK09364 228405004264 trimer interface [polypeptide binding]; other site 228405004265 dimer interface [polypeptide binding]; other site 228405004266 putative active site [active] 228405004267 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 228405004268 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 228405004269 dimer interface [polypeptide binding]; other site 228405004270 putative functional site; other site 228405004271 putative MPT binding site; other site 228405004272 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 228405004273 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 228405004274 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 228405004275 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 228405004276 active site 228405004277 dimer interface [polypeptide binding]; other site 228405004278 effector binding site; other site 228405004279 TSCPD domain; Region: TSCPD; pfam12637 228405004280 NnrS protein; Region: NnrS; pfam05940 228405004281 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 228405004282 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 228405004283 FeS/SAM binding site; other site 228405004284 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 228405004285 transcriptional activator FtrB; Provisional; Region: ftrB; PRK09392 228405004286 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 228405004287 ligand binding site [chemical binding]; other site 228405004288 flexible hinge region; other site 228405004289 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 228405004290 putative switch regulator; other site 228405004291 non-specific DNA interactions [nucleotide binding]; other site 228405004292 DNA binding site [nucleotide binding] 228405004293 sequence specific DNA binding site [nucleotide binding]; other site 228405004294 putative cAMP binding site [chemical binding]; other site 228405004295 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 228405004296 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 228405004297 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 228405004298 putative substrate translocation pore; other site 228405004299 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 228405004300 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 228405004301 [4Fe-4S] binding site [ion binding]; other site 228405004302 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 228405004303 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 228405004304 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 228405004305 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 228405004306 molybdopterin cofactor binding site; other site 228405004307 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 228405004308 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 228405004309 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 228405004310 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 228405004311 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 228405004312 Hemerythrin-like domain; Region: Hr-like; cd12108 228405004313 Fe binding site [ion binding]; other site 228405004314 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 228405004315 active site clefts [active] 228405004316 zinc binding site [ion binding]; other site 228405004317 dimer interface [polypeptide binding]; other site 228405004318 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 228405004319 dinuclear metal binding motif [ion binding]; other site 228405004320 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405004321 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405004322 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405004323 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405004324 active site 228405004325 choline dehydrogenase; Validated; Region: PRK02106 228405004326 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 228405004327 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 228405004328 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 228405004329 dimer interface [polypeptide binding]; other site 228405004330 putative functional site; other site 228405004331 putative MPT binding site; other site 228405004332 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 228405004333 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 228405004334 active site 228405004335 homotetramer interface [polypeptide binding]; other site 228405004336 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 228405004337 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 228405004338 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 228405004339 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 228405004340 Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline; Region: PC_cytidylyltransferase; cd02523 228405004341 active site 228405004342 metal-binding site 228405004343 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 228405004344 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 228405004345 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 228405004346 nucleotide binding site/active site [active] 228405004347 HIT family signature motif; other site 228405004348 catalytic residue [active] 228405004349 MobA-like NTP transferase domain; Region: NTP_transf_3; pfam12804 228405004350 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 228405004351 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 228405004352 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 228405004353 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 228405004354 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 228405004355 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 228405004356 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 228405004357 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 228405004358 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405004359 catalytic residue [active] 228405004360 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 228405004361 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 228405004362 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405004363 NAD(P) binding site [chemical binding]; other site 228405004364 active site 228405004365 acyl-CoA synthetase; Validated; Region: PRK09192 228405004366 Fatty acyl-AMP ligase (FAAL); Region: FAAL; cd05931 228405004367 acyl-activating enzyme (AAE) consensus motif; other site 228405004368 active site 228405004369 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 228405004370 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 228405004371 integrase; Provisional; Region: PRK09692 228405004372 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 228405004373 active site 228405004374 Int/Topo IB signature motif; other site 228405004375 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 228405004376 non-specific DNA binding site [nucleotide binding]; other site 228405004377 salt bridge; other site 228405004378 sequence-specific DNA binding site [nucleotide binding]; other site 228405004379 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 228405004380 Methyltransferase domain; Region: Methyltransf_26; pfam13659 228405004381 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 228405004382 Amidase; Region: Amidase; pfam01425 228405004383 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 228405004384 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases; Region: MDR_like_2; cd05289 228405004385 putative NAD(P) binding site [chemical binding]; other site 228405004386 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405004387 NADH(P)-binding; Region: NAD_binding_10; pfam13460 228405004388 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405004389 Coenzyme A binding pocket [chemical binding]; other site 228405004390 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405004391 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405004392 Transcriptional regulators [Transcription]; Region: FadR; COG2186 228405004393 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405004394 DNA-binding site [nucleotide binding]; DNA binding site 228405004395 FCD domain; Region: FCD; pfam07729 228405004396 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405004397 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405004398 Protein of unknown function (DUF819); Region: DUF819; cl02317 228405004399 L-Ala-D/L-Glu epimerase; Provisional; Region: PRK15129 228405004400 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 228405004401 active site 228405004402 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405004403 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 228405004404 N-terminal plug; other site 228405004405 ligand-binding site [chemical binding]; other site 228405004406 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 228405004407 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 228405004408 AsnC family; Region: AsnC_trans_reg; pfam01037 228405004409 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 228405004410 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 228405004411 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 228405004412 NAD binding site [chemical binding]; other site 228405004413 Phe binding site; other site 228405004414 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 228405004415 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405004416 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405004417 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405004418 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 228405004419 ANTAR domain; Region: ANTAR; pfam03861 228405004420 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 228405004421 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 228405004422 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 228405004423 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 228405004424 FMN binding site [chemical binding]; other site 228405004425 substrate binding site [chemical binding]; other site 228405004426 putative catalytic residue [active] 228405004427 AAA-like domain; Region: AAA_10; pfam12846 228405004428 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 228405004429 Walker A motif; other site 228405004430 ATP binding site [chemical binding]; other site 228405004431 Walker B motif; other site 228405004432 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 228405004433 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 228405004434 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 228405004435 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 228405004436 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 228405004437 dimerization interface [polypeptide binding]; other site 228405004438 putative DNA binding site [nucleotide binding]; other site 228405004439 putative Zn2+ binding site [ion binding]; other site 228405004440 Predicted membrane protein [Function unknown]; Region: COG2119 228405004441 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 228405004442 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 228405004443 Protein of unknown function (DUF3299); Region: DUF3299; pfam11736 228405004444 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 228405004445 Catalytic domain of Protein Kinases; Region: PKc; cd00180 228405004446 active site 228405004447 ATP binding site [chemical binding]; other site 228405004448 substrate binding site [chemical binding]; other site 228405004449 activation loop (A-loop); other site 228405004450 RNA polymerase sigma factor, TIGR02999 family; Region: Sig-70_X6 228405004451 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 228405004452 DNA binding residues [nucleotide binding] 228405004453 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 228405004454 Double zinc ribbon; Region: DZR; pfam12773 228405004455 Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins...; Region: FHA; cl00062 228405004456 phosphopeptide binding site; other site 228405004457 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 228405004458 Catalytic domain of Protein Kinases; Region: PKc; cd00180 228405004459 active site 228405004460 ATP binding site [chemical binding]; other site 228405004461 substrate binding site [chemical binding]; other site 228405004462 activation loop (A-loop); other site 228405004463 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cd02619 228405004464 active site 228405004465 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 228405004466 MarR family; Region: MarR_2; pfam12802 228405004467 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405004468 Coenzyme A binding pocket [chemical binding]; other site 228405004469 diaminobutyrate--2-oxoglutarate aminotransferase; Validated; Region: PRK09264 228405004470 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 228405004471 inhibitor-cofactor binding pocket; inhibition site 228405004472 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405004473 catalytic residue [active] 228405004474 Ectoine synthase; Region: Ectoine_synth; pfam06339 228405004475 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 228405004476 aspartate kinase; Validated; Region: PRK09181 228405004477 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 228405004478 nucleotide binding site [chemical binding]; other site 228405004479 substrate binding site [chemical binding]; other site 228405004480 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway; Region: ACT_AK-Ectoine_1; cd04910 228405004481 allosteric regulatory residue; other site 228405004482 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway; Region: ACT_AK-Ectoine_2; cd04915 228405004483 putative MFS family transporter protein; Provisional; Region: PRK03633 228405004484 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 228405004485 Na binding site [ion binding]; other site 228405004486 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405004487 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405004488 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 228405004489 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 228405004490 Walker A/P-loop; other site 228405004491 ATP binding site [chemical binding]; other site 228405004492 Q-loop/lid; other site 228405004493 ABC transporter signature motif; other site 228405004494 Walker B; other site 228405004495 D-loop; other site 228405004496 H-loop/switch region; other site 228405004497 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 228405004498 FtsX-like permease family; Region: FtsX; pfam02687 228405004499 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 228405004500 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 228405004501 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 228405004502 Predicted periplasmic protein (DUF2271); Region: DUF2271; pfam10029 228405004503 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 228405004504 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 228405004505 ApbE family; Region: ApbE; pfam02424 228405004506 Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; Region: FepA; COG4771 228405004507 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 228405004508 N-terminal plug; other site 228405004509 ligand-binding site [chemical binding]; other site 228405004510 D-lactate dehydrogenase; Provisional; Region: PRK11183 228405004511 FAD binding domain; Region: FAD_binding_4; pfam01565 228405004512 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 228405004513 Transcriptional regulators [Transcription]; Region: FadR; COG2186 228405004514 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405004515 DNA-binding site [nucleotide binding]; DNA binding site 228405004516 FCD domain; Region: FCD; cl11656 228405004517 Membrane bound YbgT-like protein; Region: YbgT_YccB; pfam08173 228405004518 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 228405004519 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 228405004520 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 228405004521 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 228405004522 thiol reductant ABC exporter, CydD subunit; Region: CydD; TIGR02857 228405004523 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 228405004524 Walker A/P-loop; other site 228405004525 ATP binding site [chemical binding]; other site 228405004526 Q-loop/lid; other site 228405004527 ABC transporter signature motif; other site 228405004528 Walker B; other site 228405004529 D-loop; other site 228405004530 H-loop/switch region; other site 228405004531 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405004532 Walker A/P-loop; other site 228405004533 ATP binding site [chemical binding]; other site 228405004534 ABC transporter; Region: ABC_tran; pfam00005 228405004535 Q-loop/lid; other site 228405004536 ABC transporter signature motif; other site 228405004537 Walker B; other site 228405004538 D-loop; other site 228405004539 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 228405004540 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 228405004541 Protein of unknown function (DUF1330); Region: DUF1330; cl02288 228405004542 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405004543 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 228405004544 Uncharacterized conserved protein [Function unknown]; Region: COG1262 228405004545 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 228405004546 Sulfatase; Region: Sulfatase; pfam00884 228405004547 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 228405004548 Sulfatase; Region: Sulfatase; pfam00884 228405004549 putative exonuclease, DNA ligase-associated; Region: Xnuc_lig_assoc; TIGR04122 228405004550 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 228405004551 DNA ligase, ATP-dependent, PP_1105 family; Region: DNA_lig_bact; TIGR04120 228405004552 Adenylation domain of putative bacterial ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_Bac1; cd07897 228405004553 active site 228405004554 DNA binding site [nucleotide binding] 228405004555 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_Arch_LigB; cd07972 228405004556 DNA binding site [nucleotide binding] 228405004557 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2015 228405004558 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405004559 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 228405004560 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 228405004561 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405004562 Coenzyme A binding pocket [chemical binding]; other site 228405004563 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 228405004564 catalytic nucleophile [active] 228405004565 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 228405004566 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 228405004567 HIGH motif; other site 228405004568 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 228405004569 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 228405004570 active site 228405004571 KMSKS motif; other site 228405004572 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 228405004573 tRNA binding surface [nucleotide binding]; other site 228405004574 anticodon binding site; other site 228405004575 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 228405004576 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 228405004577 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 228405004578 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 228405004579 Methyltransferase domain; Region: Methyltransf_18; pfam12847 228405004580 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 228405004581 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405004582 Coenzyme A binding pocket [chemical binding]; other site 228405004583 short chain dehydrogenase; Provisional; Region: PRK06523 228405004584 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405004585 NAD(P) binding site [chemical binding]; other site 228405004586 active site 228405004587 SnoaL-like domain; Region: SnoaL_2; pfam12680 228405004588 Predicted transcriptional regulators [Transcription]; Region: COG1733 228405004589 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 228405004590 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 228405004591 salt bridge; other site 228405004592 non-specific DNA binding site [nucleotide binding]; other site 228405004593 sequence-specific DNA binding site [nucleotide binding]; other site 228405004594 Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators; Region: HTH_CadR-PbrR-like; cd04785 228405004595 DNA binding residues [nucleotide binding] 228405004596 Hg(II)-responsive transcriptional regulator; Region: MerR; TIGR02051 228405004597 dimer interface [polypeptide binding]; other site 228405004598 putative metal binding site [ion binding]; other site 228405004599 MerT mercuric transport protein; Region: MerT; cl03578 228405004600 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 228405004601 metal-binding site [ion binding] 228405004602 mercuric reductase; Region: MerA; TIGR02053 228405004603 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405004604 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 228405004605 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 228405004606 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 228405004607 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 228405004608 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405004609 Outer membrane efflux protein; Region: OEP; pfam02321 228405004610 RNA polymerase sigma factor; Provisional; Region: PRK12539 228405004611 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405004612 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 228405004613 DNA binding residues [nucleotide binding] 228405004614 Protein of unknown function (DUF1109); Region: DUF1109; pfam06532 228405004615 YHS domain; Region: YHS; pfam04945 228405004616 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 228405004617 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 228405004618 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 228405004619 motif II; other site 228405004620 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 228405004621 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 228405004622 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 228405004623 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405004624 SnoaL-like domain; Region: SnoaL_3; pfam13474 228405004625 Copper resistance protein D; Region: CopD; pfam05425 228405004626 CopC domain; Region: CopC; pfam04234 228405004627 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 228405004628 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 228405004629 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 228405004630 Multicopper oxidase; Region: Cu-oxidase; pfam00394 228405004631 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 228405004632 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 228405004633 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 228405004634 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 228405004635 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 228405004636 putative homodimer interface [polypeptide binding]; other site 228405004637 putative homotetramer interface [polypeptide binding]; other site 228405004638 putative allosteric switch controlling residues; other site 228405004639 putative metal binding site [ion binding]; other site 228405004640 putative homodimer-homodimer interface [polypeptide binding]; other site 228405004641 Protein of unknown function (DUF3703); Region: DUF3703; pfam12487 228405004642 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 228405004643 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 228405004644 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 228405004645 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 228405004646 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 228405004647 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405004648 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405004649 Outer membrane efflux protein; Region: OEP; pfam02321 228405004650 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 228405004651 Uncharacterized conserved protein [Function unknown]; Region: COG5489 228405004652 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 228405004653 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 228405004654 VirB7 interaction site; other site 228405004655 helicase superfamily c-terminal domain; Region: HELICc; smart00490 228405004656 nucleotide binding region [chemical binding]; other site 228405004657 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 228405004658 DNA binding residues [nucleotide binding] 228405004659 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 228405004660 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 228405004661 lipoprotein signal peptidase; Provisional; Region: PRK14787 228405004662 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 228405004663 integrase; Provisional; Region: PRK09692 228405004664 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 228405004665 active site 228405004666 Int/Topo IB signature motif; other site 228405004667 Domain of unknown function (DUF329); Region: DUF329; pfam03884 228405004668 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 228405004669 RNA binding site [nucleotide binding]; other site 228405004670 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 228405004671 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 228405004672 active site 228405004673 dimer interface [polypeptide binding]; other site 228405004674 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 228405004675 dimer interface [polypeptide binding]; other site 228405004676 active site 228405004677 elongation factor Tu; Reviewed; Region: PRK00049 228405004678 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 228405004679 G1 box; other site 228405004680 GEF interaction site [polypeptide binding]; other site 228405004681 GTP/Mg2+ binding site [chemical binding]; other site 228405004682 Switch I region; other site 228405004683 G2 box; other site 228405004684 G3 box; other site 228405004685 Switch II region; other site 228405004686 G4 box; other site 228405004687 G5 box; other site 228405004688 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 228405004689 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 228405004690 Antibiotic Binding Site [chemical binding]; other site 228405004691 Uncharacterized conserved protein [Function unknown]; Region: COG2128 228405004692 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 228405004693 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 228405004694 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 228405004695 active site 228405004696 catalytic site [active] 228405004697 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 228405004698 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 228405004699 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 228405004700 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 228405004701 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 228405004702 putative active site [active] 228405004703 phosphogluconate dehydratase; Validated; Region: PRK09054 228405004704 6-phosphogluconate dehydratase; Region: edd; TIGR01196 228405004705 glucokinase, proteobacterial type; Region: glk; TIGR00749 228405004706 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 228405004707 nucleotide binding site [chemical binding]; other site 228405004708 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 228405004709 NADH dehydrogenase subunit B; Validated; Region: PRK06411 228405004710 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 228405004711 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 228405004712 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 228405004713 NADH dehydrogenase subunit D; Validated; Region: PRK06075 228405004714 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 228405004715 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 228405004716 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405004717 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 228405004718 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 228405004719 putative dimer interface [polypeptide binding]; other site 228405004720 [2Fe-2S] cluster binding site [ion binding]; other site 228405004721 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 228405004722 SLBB domain; Region: SLBB; pfam10531 228405004723 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 228405004724 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 228405004725 NADH dehydrogenase subunit G; Validated; Region: PRK09130 228405004726 catalytic loop [active] 228405004727 iron binding site [ion binding]; other site 228405004728 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 228405004729 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 228405004730 molybdopterin cofactor binding site; other site 228405004731 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 228405004732 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 228405004733 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 228405004734 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 228405004735 4Fe-4S binding domain; Region: Fer4; pfam00037 228405004736 4Fe-4S binding domain; Region: Fer4; pfam00037 228405004737 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 228405004738 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 228405004739 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 228405004740 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 228405004741 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 228405004742 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 228405004743 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 228405004744 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 228405004745 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 228405004746 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 228405004747 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 228405004748 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 228405004749 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 228405004750 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 228405004751 nucleotide binding site [chemical binding]; other site 228405004752 Type III pantothenate kinase; Region: Pan_kinase; cl17198 228405004753 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 228405004754 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405004755 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 228405004756 Methylmalonyl-CoA epimerase (MMCE); Region: MMCE; cd07249 228405004757 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405004758 dimer interface [polypeptide binding]; other site 228405004759 substrate binding site [chemical binding]; other site 228405004760 metal binding site [ion binding]; metal-binding site 228405004761 Protein of unknown function (DUF1467); Region: DUF1467; pfam07330 228405004762 prolyl-tRNA synthetase; Provisional; Region: PRK12325 228405004763 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 228405004764 dimer interface [polypeptide binding]; other site 228405004765 motif 1; other site 228405004766 active site 228405004767 motif 2; other site 228405004768 motif 3; other site 228405004769 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 228405004770 anticodon binding site; other site 228405004771 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 228405004772 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 228405004773 FtsX-like permease family; Region: FtsX; pfam02687 228405004774 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 228405004775 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 228405004776 Walker A/P-loop; other site 228405004777 ATP binding site [chemical binding]; other site 228405004778 Q-loop/lid; other site 228405004779 ABC transporter signature motif; other site 228405004780 Walker B; other site 228405004781 D-loop; other site 228405004782 H-loop/switch region; other site 228405004783 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 228405004784 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 228405004785 putative active site [active] 228405004786 putative PHP Thumb interface [polypeptide binding]; other site 228405004787 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 228405004788 generic binding surface I; other site 228405004789 generic binding surface II; other site 228405004790 Domain of unknown function DUF59; Region: DUF59; cl00941 228405004791 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 228405004792 rRNA interaction site [nucleotide binding]; other site 228405004793 S8 interaction site; other site 228405004794 putative laminin-1 binding site; other site 228405004795 elongation factor Ts; Provisional; Region: tsf; PRK09377 228405004796 UBA/TS-N domain; Region: UBA; pfam00627 228405004797 Elongation factor TS; Region: EF_TS; pfam00889 228405004798 Elongation factor TS; Region: EF_TS; pfam00889 228405004799 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 228405004800 putative nucleotide binding site [chemical binding]; other site 228405004801 uridine monophosphate binding site [chemical binding]; other site 228405004802 homohexameric interface [polypeptide binding]; other site 228405004803 ribosome recycling factor; Reviewed; Region: frr; PRK00083 228405004804 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 228405004805 hinge region; other site 228405004806 undecaprenyl pyrophosphate synthase; Provisional; Region: PRK14834 228405004807 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 228405004808 catalytic residue [active] 228405004809 putative FPP diphosphate binding site; other site 228405004810 putative FPP binding hydrophobic cleft; other site 228405004811 dimer interface [polypeptide binding]; other site 228405004812 putative IPP diphosphate binding site; other site 228405004813 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 228405004814 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 228405004815 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 228405004816 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 228405004817 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 228405004818 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 228405004819 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 228405004820 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 228405004821 active site 228405004822 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 228405004823 protein binding site [polypeptide binding]; other site 228405004824 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 228405004825 putative substrate binding region [chemical binding]; other site 228405004826 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 228405004827 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 228405004828 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 228405004829 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 228405004830 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 228405004831 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 228405004832 Surface antigen; Region: Bac_surface_Ag; pfam01103 228405004833 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 228405004834 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 228405004835 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 228405004836 trimer interface [polypeptide binding]; other site 228405004837 active site 228405004838 UDP-GlcNAc binding site [chemical binding]; other site 228405004839 lipid binding site [chemical binding]; lipid-binding site 228405004840 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 228405004841 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 228405004842 active site 228405004843 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 228405004844 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 228405004845 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 228405004846 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 228405004847 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 228405004848 dimer interface [polypeptide binding]; other site 228405004849 active site 228405004850 citrylCoA binding site [chemical binding]; other site 228405004851 NADH binding [chemical binding]; other site 228405004852 cationic pore residues; other site 228405004853 oxalacetate/citrate binding site [chemical binding]; other site 228405004854 coenzyme A binding site [chemical binding]; other site 228405004855 catalytic triad [active] 228405004856 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 228405004857 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 228405004858 active site 228405004859 HIGH motif; other site 228405004860 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 228405004861 active site 228405004862 KMSKS motif; other site 228405004863 LexA repressor; Validated; Region: PRK00215 228405004864 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 228405004865 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 228405004866 Catalytic site [active] 228405004867 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 228405004868 active site 228405004869 ribulose/triose binding site [chemical binding]; other site 228405004870 phosphate binding site [ion binding]; other site 228405004871 substrate (anthranilate) binding pocket [chemical binding]; other site 228405004872 product (indole) binding pocket [chemical binding]; other site 228405004873 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 228405004874 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 228405004875 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 228405004876 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 228405004877 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 228405004878 glutamine binding [chemical binding]; other site 228405004879 catalytic triad [active] 228405004880 anthranilate synthase component I; Provisional; Region: PRK13573 228405004881 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 228405004882 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 228405004883 SurA N-terminal domain; Region: SurA_N_3; cl07813 228405004884 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 228405004885 triosephosphate isomerase; Provisional; Region: PRK14565 228405004886 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 228405004887 substrate binding site [chemical binding]; other site 228405004888 dimer interface [polypeptide binding]; other site 228405004889 catalytic triad [active] 228405004890 Preprotein translocase SecG subunit; Region: SecG; pfam03840 228405004891 CTP synthetase; Validated; Region: pyrG; PRK05380 228405004892 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 228405004893 Catalytic site [active] 228405004894 active site 228405004895 UTP binding site [chemical binding]; other site 228405004896 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 228405004897 active site 228405004898 putative oxyanion hole; other site 228405004899 catalytic triad [active] 228405004900 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 228405004901 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 228405004902 S-adenosylmethionine binding site [chemical binding]; other site 228405004903 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 228405004904 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 228405004905 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 228405004906 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405004907 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 228405004908 DNA photolyase; Region: DNA_photolyase; pfam00875 228405004909 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 228405004910 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 228405004911 putative ribose interaction site [chemical binding]; other site 228405004912 putative ADP binding site [chemical binding]; other site 228405004913 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 228405004914 active site 228405004915 nucleotide binding site [chemical binding]; other site 228405004916 HIGH motif; other site 228405004917 KMSKS motif; other site 228405004918 Hemimethylated DNA-binding protein YccV like; Region: YccV-like; pfam08755 228405004919 exopolyphosphatase; Region: exo_poly_only; TIGR03706 228405004920 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 228405004921 nucleotide binding site [chemical binding]; other site 228405004922 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 228405004923 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 228405004924 S-adenosylmethionine binding site [chemical binding]; other site 228405004925 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405004926 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 228405004927 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 228405004928 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 228405004929 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 228405004930 active site 228405004931 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 228405004932 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 228405004933 Coenzyme A binding pocket [chemical binding]; other site 228405004934 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 228405004935 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 228405004936 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 228405004937 TPR motif; other site 228405004938 Aspartyl/Asparaginyl beta-hydroxylase; Region: Asp_Arg_Hydrox; cl17820 228405004939 GMP synthase; Reviewed; Region: guaA; PRK00074 228405004940 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 228405004941 AMP/PPi binding site [chemical binding]; other site 228405004942 candidate oxyanion hole; other site 228405004943 catalytic triad [active] 228405004944 potential glutamine specificity residues [chemical binding]; other site 228405004945 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 228405004946 ATP Binding subdomain [chemical binding]; other site 228405004947 Ligand Binding sites [chemical binding]; other site 228405004948 Dimerization subdomain; other site 228405004949 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 228405004950 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 228405004951 putative hydrolase; Provisional; Region: PRK02113 228405004952 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 228405004953 active site 228405004954 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 228405004955 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 228405004956 DNA polymerase III subunit delta'; Validated; Region: PRK08485 228405004957 thymidylate kinase; Validated; Region: tmk; PRK00698 228405004958 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 228405004959 TMP-binding site; other site 228405004960 ATP-binding site [chemical binding]; other site 228405004961 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 228405004962 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 228405004963 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 228405004964 rare lipoprotein A; Region: rlpA; TIGR00413 228405004965 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 228405004966 Sporulation related domain; Region: SPOR; pfam05036 228405004967 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 228405004968 catalytic core [active] 228405004969 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding...; Region: NPD_FabD; cd04742 228405004970 FMN binding site [chemical binding]; other site 228405004971 substrate binding site [chemical binding]; other site 228405004972 putative catalytic residue [active] 228405004973 polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or...; Region: PKS; cd00833 228405004974 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: FabB; COG0304 228405004975 active site 228405004976 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 228405004977 active site 228405004978 Acyl transferase domain; Region: Acyl_transf_1; cl08282 228405004979 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 228405004980 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 228405004981 active site 1 [active] 228405004982 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 228405004983 active site 2 [active] 228405004984 active site 1 [active] 228405004985 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 228405004986 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 228405004987 active site 1 [active] 228405004988 dimer interface [polypeptide binding]; other site 228405004989 active site 2 [active] 228405004990 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 228405004991 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405004992 ligand binding site [chemical binding]; other site 228405004993 Uncharacterized conserved protein [Function unknown]; Region: COG3743 228405004994 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405004995 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405004996 enoyl-CoA hydratase; Provisional; Region: PRK09245 228405004997 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 228405004998 substrate binding site [chemical binding]; other site 228405004999 oxyanion hole (OAH) forming residues; other site 228405005000 trimer interface [polypeptide binding]; other site 228405005001 TIGR03084 family protein; Region: TIGR03084 228405005002 Mycothiol maleylpyruvate isomerase N-terminal domain; Region: MDMPI_N; pfam11716 228405005003 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 228405005004 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 228405005005 enoyl-CoA hydratase; Provisional; Region: PRK05862 228405005006 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 228405005007 substrate binding site [chemical binding]; other site 228405005008 oxyanion hole (OAH) forming residues; other site 228405005009 trimer interface [polypeptide binding]; other site 228405005010 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 228405005011 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 228405005012 tetrameric interface [polypeptide binding]; other site 228405005013 NAD binding site [chemical binding]; other site 228405005014 catalytic residues [active] 228405005015 Predicted membrane protein [Function unknown]; Region: COG2311 228405005016 Protein of unknown function (DUF418); Region: DUF418; pfam04235 228405005017 methionyl-tRNA synthetase; Reviewed; Region: PRK12268 228405005018 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 228405005019 active site 228405005020 HIGH motif; other site 228405005021 KMSKS motif; other site 228405005022 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 228405005023 tRNA binding surface [nucleotide binding]; other site 228405005024 anticodon binding site; other site 228405005025 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405005026 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 228405005027 S-adenosylmethionine binding site [chemical binding]; other site 228405005028 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 228405005029 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405005030 active site 228405005031 catalytic tetrad [active] 228405005032 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 228405005033 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405005034 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 228405005035 acyl-activating enzyme (AAE) consensus motif; other site 228405005036 acyl-activating enzyme (AAE) consensus motif; other site 228405005037 putative AMP binding site [chemical binding]; other site 228405005038 putative active site [active] 228405005039 putative CoA binding site [chemical binding]; other site 228405005040 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 228405005041 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 228405005042 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 228405005043 TPP-binding site; other site 228405005044 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 228405005045 PYR/PP interface [polypeptide binding]; other site 228405005046 dimer interface [polypeptide binding]; other site 228405005047 TPP binding site [chemical binding]; other site 228405005048 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 228405005049 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 228405005050 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 228405005051 substrate binding pocket [chemical binding]; other site 228405005052 chain length determination region; other site 228405005053 substrate-Mg2+ binding site; other site 228405005054 catalytic residues [active] 228405005055 aspartate-rich region 1; other site 228405005056 active site lid residues [active] 228405005057 aspartate-rich region 2; other site 228405005058 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 228405005059 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 228405005060 catalytic core [active] 228405005061 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 228405005062 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 228405005063 Catalytic site [active] 228405005064 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 228405005065 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 228405005066 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 228405005067 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 228405005068 RNA binding surface [nucleotide binding]; other site 228405005069 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 228405005070 active site 228405005071 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405005072 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405005073 active site 228405005074 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 228405005075 Uncharacterized conserved protein [Function unknown]; Region: COG2353 228405005076 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 228405005077 YceI-like domain; Region: YceI; pfam04264 228405005078 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 228405005079 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 228405005080 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 228405005081 serine acetyltransferase; Provisional; Region: cysE; PRK11132 228405005082 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 228405005083 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 228405005084 trimer interface [polypeptide binding]; other site 228405005085 active site 228405005086 substrate binding site [chemical binding]; other site 228405005087 CoA binding site [chemical binding]; other site 228405005088 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 228405005089 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 228405005090 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405005091 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405005092 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405005093 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405005094 WHG domain; Region: WHG; pfam13305 228405005095 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 228405005096 putative FMN binding site [chemical binding]; other site 228405005097 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 228405005098 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 228405005099 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 228405005100 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 228405005101 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 228405005102 Surface antigen; Region: Bac_surface_Ag; pfam01103 228405005103 Family of unknown function (DUF490); Region: DUF490; pfam04357 228405005104 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405005105 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 228405005106 non-specific DNA binding site [nucleotide binding]; other site 228405005107 salt bridge; other site 228405005108 sequence-specific DNA binding site [nucleotide binding]; other site 228405005109 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 228405005110 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 228405005111 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 228405005112 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405005113 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405005114 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 228405005115 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 228405005116 type II secretion system protein D; Region: type_II_gspD; TIGR02517 228405005117 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 228405005118 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 228405005119 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 228405005120 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 228405005121 type II secretion system protein E; Region: type_II_gspE; TIGR02533 228405005122 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 228405005123 Walker A motif; other site 228405005124 ATP binding site [chemical binding]; other site 228405005125 Walker B motif; other site 228405005126 type II secretion system protein F; Region: GspF; TIGR02120 228405005127 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405005128 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405005129 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 228405005130 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 228405005131 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 228405005132 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 228405005133 Type II transport protein GspH; Region: GspH; pfam12019 228405005134 type II secretion system protein I; Region: gspI; TIGR01707 228405005135 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 228405005136 type II secretion system protein J; Region: gspJ; TIGR01711 228405005137 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 228405005138 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 228405005139 type II secretion system protein L; Region: typeII_sec_gspL; TIGR01709 228405005140 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 228405005141 GspL periplasmic domain; Region: GspL_C; cl14909 228405005142 Type II secretion system (T2SS), protein M; Region: T2SM; pfam04612 228405005143 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 228405005144 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 228405005145 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405005146 non-specific DNA binding site [nucleotide binding]; other site 228405005147 salt bridge; other site 228405005148 sequence-specific DNA binding site [nucleotide binding]; other site 228405005149 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 228405005150 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 228405005151 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 228405005152 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 228405005153 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 228405005154 Zinc-finger domain; Region: zf-CHCC; pfam10276 228405005155 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 228405005156 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405005157 Walker A/P-loop; other site 228405005158 ATP binding site [chemical binding]; other site 228405005159 Q-loop/lid; other site 228405005160 ABC transporter signature motif; other site 228405005161 Walker B; other site 228405005162 D-loop; other site 228405005163 H-loop/switch region; other site 228405005164 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 228405005165 catalytic residues [active] 228405005166 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 228405005167 Part of AAA domain; Region: AAA_19; pfam13245 228405005168 Family description; Region: UvrD_C_2; pfam13538 228405005169 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 228405005170 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 228405005171 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 228405005172 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 228405005173 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 228405005174 Substrate binding site; other site 228405005175 metal-binding site 228405005176 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 228405005177 Phosphotransferase enzyme family; Region: APH; pfam01636 228405005178 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 228405005179 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional; Region: PRK09754 228405005180 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405005181 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405005182 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 228405005183 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 228405005184 catalytic loop [active] 228405005185 iron binding site [ion binding]; other site 228405005186 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 228405005187 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 228405005188 active site 2 [active] 228405005189 active site 1 [active] 228405005190 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK14736 228405005191 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 228405005192 gamma subunit interface [polypeptide binding]; other site 228405005193 epsilon subunit interface [polypeptide binding]; other site 228405005194 LBP interface [polypeptide binding]; other site 228405005195 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 228405005196 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 228405005197 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 228405005198 alpha subunit interaction interface [polypeptide binding]; other site 228405005199 Walker A motif; other site 228405005200 ATP binding site [chemical binding]; other site 228405005201 Walker B motif; other site 228405005202 inhibitor binding site; inhibition site 228405005203 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 228405005204 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 228405005205 core domain interface [polypeptide binding]; other site 228405005206 delta subunit interface [polypeptide binding]; other site 228405005207 epsilon subunit interface [polypeptide binding]; other site 228405005208 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 228405005209 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 228405005210 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 228405005211 beta subunit interaction interface [polypeptide binding]; other site 228405005212 Walker A motif; other site 228405005213 ATP binding site [chemical binding]; other site 228405005214 Walker B motif; other site 228405005215 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 228405005216 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 228405005217 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 228405005218 primosome assembly protein PriA; Validated; Region: PRK05580 228405005219 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 228405005220 ATP binding site [chemical binding]; other site 228405005221 putative Mg++ binding site [ion binding]; other site 228405005222 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405005223 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405005224 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 228405005225 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 228405005226 CoenzymeA binding site [chemical binding]; other site 228405005227 subunit interaction site [polypeptide binding]; other site 228405005228 PHB binding site; other site 228405005229 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 228405005230 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 228405005231 Walker A motif; other site 228405005232 ATP binding site [chemical binding]; other site 228405005233 Walker B motif; other site 228405005234 arginine finger; other site 228405005235 Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: CoxE; COG3552 228405005236 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 228405005237 DNA methylase; Region: N6_N4_Mtase; pfam01555 228405005238 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 228405005239 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 228405005240 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 228405005241 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 228405005242 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 228405005243 FeS/SAM binding site; other site 228405005244 Uncharacterized protein conserved in bacteria (DUF2064); Region: DUF2064; cl17492 228405005245 GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function; Region: GT_2_like_a; cd02522 228405005246 transferase 2, rSAM/selenodomain-associated; Region: glyco_like_mftF; TIGR04283 228405005247 Probable Catalytic site; other site 228405005248 Hemerythrin-like domain; Region: Hr-like; cd12108 228405005249 Fe binding site [ion binding]; other site 228405005250 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 228405005251 Fe-S cluster binding site [ion binding]; other site 228405005252 active site 228405005253 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 228405005254 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405005255 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 228405005256 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 228405005257 TPR motif; other site 228405005258 binding surface 228405005259 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 228405005260 Transglycosylase; Region: Transgly; pfam00912 228405005261 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 228405005262 peptide chain release factor 2; Validated; Region: prfB; PRK00578 228405005263 This domain is found in peptide chain release factors; Region: PCRF; smart00937 228405005264 RF-1 domain; Region: RF-1; pfam00472 228405005265 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 228405005266 DNA-binding site [nucleotide binding]; DNA binding site 228405005267 RNA-binding motif; other site 228405005268 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 228405005269 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 228405005270 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 228405005271 minor groove reading motif; other site 228405005272 helix-hairpin-helix signature motif; other site 228405005273 substrate binding pocket [chemical binding]; other site 228405005274 active site 228405005275 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 228405005276 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 228405005277 DNA binding and oxoG recognition site [nucleotide binding] 228405005278 Protein of unknown function (DUF721); Region: DUF721; pfam05258 228405005279 Thioredoxin; Region: Thioredoxin_4; pfam13462 228405005280 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 228405005281 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 228405005282 AAA domain; Region: AAA_23; pfam13476 228405005283 Walker A/P-loop; other site 228405005284 ATP binding site [chemical binding]; other site 228405005285 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 228405005286 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 228405005287 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 228405005288 ABC transporter signature motif; other site 228405005289 Walker B; other site 228405005290 D-loop; other site 228405005291 H-loop/switch region; other site 228405005292 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 228405005293 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 228405005294 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 228405005295 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 228405005296 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 228405005297 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 228405005298 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 228405005299 TIR domain; Region: TIR_2; pfam13676 228405005300 GTP-binding protein YchF; Reviewed; Region: PRK09601 228405005301 YchF GTPase; Region: YchF; cd01900 228405005302 G1 box; other site 228405005303 GTP/Mg2+ binding site [chemical binding]; other site 228405005304 Switch I region; other site 228405005305 G2 box; other site 228405005306 Switch II region; other site 228405005307 G3 box; other site 228405005308 G4 box; other site 228405005309 G5 box; other site 228405005310 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 228405005311 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 228405005312 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 228405005313 Protein export membrane protein; Region: SecD_SecF; pfam02355 228405005314 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 228405005315 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 228405005316 Preprotein translocase subunit; Region: YajC; pfam02699 228405005317 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 228405005318 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 228405005319 S-adenosylmethionine binding site [chemical binding]; other site 228405005320 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 228405005321 seryl-tRNA synthetase; Provisional; Region: PRK05431 228405005322 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 228405005323 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 228405005324 dimer interface [polypeptide binding]; other site 228405005325 active site 228405005326 motif 1; other site 228405005327 motif 2; other site 228405005328 motif 3; other site 228405005329 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 228405005330 twin arginine-targeting protein translocase TatB; Region: tatB; TIGR01410 228405005331 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 228405005332 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 228405005333 putative catalytic site [active] 228405005334 putative phosphate binding site [ion binding]; other site 228405005335 active site 228405005336 metal binding site A [ion binding]; metal-binding site 228405005337 DNA binding site [nucleotide binding] 228405005338 putative AP binding site [nucleotide binding]; other site 228405005339 putative metal binding site B [ion binding]; other site 228405005340 Protein of unknown function, DUF486; Region: DUF486; cl01236 228405005341 phosphoribosylformylglycinamidine synthase I; Provisional; Region: PRK03619 228405005342 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 228405005343 putative active site [active] 228405005344 catalytic triad [active] 228405005345 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 228405005346 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 228405005347 active site 228405005348 purine riboside binding site [chemical binding]; other site 228405005349 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 228405005350 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 228405005351 Tetratricopeptide repeat; Region: TPR_16; pfam13432 228405005352 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 228405005353 TPR motif; other site 228405005354 binding surface 228405005355 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 228405005356 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 228405005357 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 228405005358 dimerization interface [polypeptide binding]; other site 228405005359 ATP binding site [chemical binding]; other site 228405005360 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 228405005361 dimerization interface [polypeptide binding]; other site 228405005362 ATP binding site [chemical binding]; other site 228405005363 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 228405005364 Domain of unknown function (DUF1993); Region: DUF1993; pfam09351 228405005365 M28 Zn-Peptidases; Region: M28_like_2; cd05662 228405005366 Peptidase family M28; Region: Peptidase_M28; pfam04389 228405005367 metal binding site [ion binding]; metal-binding site 228405005368 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 228405005369 Peptidase family M2 Angiotensin converting enzyme (ACE); Region: M2_ACE; cd06461 228405005370 active site 228405005371 Zn binding site [ion binding]; other site 228405005372 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405005373 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405005374 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405005375 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 228405005376 putative GSH binding site [chemical binding]; other site 228405005377 catalytic residues [active] 228405005378 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 228405005379 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 228405005380 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 228405005381 FeS/SAM binding site; other site 228405005382 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 228405005383 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 228405005384 conserved cys residue [active] 228405005385 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 228405005386 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 228405005387 conserved cys residue [active] 228405005388 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405005389 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 228405005390 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 228405005391 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 228405005392 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 228405005393 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 228405005394 RNA binding surface [nucleotide binding]; other site 228405005395 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405005396 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405005397 NAD(P) binding site [chemical binding]; other site 228405005398 active site 228405005399 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG3837 228405005400 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405005401 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405005402 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405005403 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405005404 metal binding site [ion binding]; metal-binding site 228405005405 active site 228405005406 I-site; other site 228405005407 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 228405005408 oligomerisation interface [polypeptide binding]; other site 228405005409 mobile loop; other site 228405005410 roof hairpin; other site 228405005411 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 228405005412 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 228405005413 ring oligomerisation interface [polypeptide binding]; other site 228405005414 ATP/Mg binding site [chemical binding]; other site 228405005415 stacking interactions; other site 228405005416 hinge regions; other site 228405005417 acyl-CoA synthetase; Validated; Region: PRK07798 228405005418 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405005419 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_5; cd05924 228405005420 acyl-activating enzyme (AAE) consensus motif; other site 228405005421 acyl-activating enzyme (AAE) consensus motif; other site 228405005422 putative AMP binding site [chemical binding]; other site 228405005423 putative active site [active] 228405005424 putative CoA binding site [chemical binding]; other site 228405005425 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 228405005426 CoenzymeA binding site [chemical binding]; other site 228405005427 subunit interaction site [polypeptide binding]; other site 228405005428 PHB binding site; other site 228405005429 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 228405005430 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 228405005431 DNA-binding site [nucleotide binding]; DNA binding site 228405005432 RNA-binding motif; other site 228405005433 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 228405005434 DNA-binding site [nucleotide binding]; DNA binding site 228405005435 RNA-binding motif; other site 228405005436 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 228405005437 DHH family; Region: DHH; pfam01368 228405005438 DHHA1 domain; Region: DHHA1; pfam02272 228405005439 OB-fold nucleic acid binding domain; Region: tRNA_anti; pfam01336 228405005440 generic binding surface I; other site 228405005441 generic binding surface II; other site 228405005442 adenylosuccinate lyase; Provisional; Region: PRK07492 228405005443 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 228405005444 tetramer interface [polypeptide binding]; other site 228405005445 active site 228405005446 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 228405005447 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 228405005448 active site 228405005449 dimer interface [polypeptide binding]; other site 228405005450 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 228405005451 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 228405005452 classical (c) SDRs; Region: SDR_c; cd05233 228405005453 NAD(P) binding site [chemical binding]; other site 228405005454 active site 228405005455 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 228405005456 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405005457 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 228405005458 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 228405005459 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405005460 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 228405005461 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 228405005462 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 228405005463 E3 interaction surface; other site 228405005464 lipoyl attachment site [posttranslational modification]; other site 228405005465 e3 binding domain; Region: E3_binding; pfam02817 228405005466 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 228405005467 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 228405005468 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 228405005469 E3 interaction surface; other site 228405005470 lipoyl attachment site [posttranslational modification]; other site 228405005471 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 228405005472 alpha subunit interface [polypeptide binding]; other site 228405005473 TPP binding site [chemical binding]; other site 228405005474 heterodimer interface [polypeptide binding]; other site 228405005475 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 228405005476 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 228405005477 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 228405005478 tetramer interface [polypeptide binding]; other site 228405005479 TPP-binding site [chemical binding]; other site 228405005480 heterodimer interface [polypeptide binding]; other site 228405005481 phosphorylation loop region [posttranslational modification] 228405005482 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 228405005483 Septum formation initiator; Region: DivIC; pfam04977 228405005484 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405005485 metal binding site [ion binding]; metal-binding site 228405005486 active site 228405005487 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405005488 enolase; Provisional; Region: eno; PRK00077 228405005489 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 228405005490 dimer interface [polypeptide binding]; other site 228405005491 metal binding site [ion binding]; metal-binding site 228405005492 substrate binding pocket [chemical binding]; other site 228405005493 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 228405005494 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 228405005495 catalytic core [active] 228405005496 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405005497 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405005498 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405005499 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405005500 metal binding site [ion binding]; metal-binding site 228405005501 active site 228405005502 I-site; other site 228405005503 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 228405005504 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 228405005505 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 228405005506 ATP binding site [chemical binding]; other site 228405005507 putative Mg++ binding site [ion binding]; other site 228405005508 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 228405005509 nucleotide binding region [chemical binding]; other site 228405005510 ATP-binding site [chemical binding]; other site 228405005511 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 228405005512 Uncharacterized conserved protein [Function unknown]; Region: COG2938 228405005513 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 228405005514 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 228405005515 generic binding surface II; other site 228405005516 ssDNA binding site; other site 228405005517 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 228405005518 ATP binding site [chemical binding]; other site 228405005519 putative Mg++ binding site [ion binding]; other site 228405005520 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 228405005521 nucleotide binding region [chemical binding]; other site 228405005522 ATP-binding site [chemical binding]; other site 228405005523 Uncharacterized conserved protein [Function unknown]; Region: COG2928 228405005524 Phosphotransferase enzyme family; Region: APH; pfam01636 228405005525 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 228405005526 putative active site [active] 228405005527 ATP binding site [chemical binding]; other site 228405005528 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cl17270 228405005529 putative substrate binding site [chemical binding]; other site 228405005530 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 228405005531 maleylacetoacetate isomerase; Region: maiA; TIGR01262 228405005532 C-terminal domain interface [polypeptide binding]; other site 228405005533 GSH binding site (G-site) [chemical binding]; other site 228405005534 putative dimer interface [polypeptide binding]; other site 228405005535 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 228405005536 dimer interface [polypeptide binding]; other site 228405005537 N-terminal domain interface [polypeptide binding]; other site 228405005538 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 228405005539 succinylarginine dihydrolase; Provisional; Region: PRK13281 228405005540 Methyltransferase domain; Region: Methyltransf_31; pfam13847 228405005541 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 228405005542 succinylglutamic semialdehyde dehydrogenase; Reviewed; Region: astD; PRK09457 228405005543 N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like; Region: ALDH_SGSD_AstD; cd07095 228405005544 NAD(P) binding site [chemical binding]; other site 228405005545 catalytic residues [active] 228405005546 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 228405005547 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 228405005548 hypothetical protein; Provisional; Region: PRK07338 228405005549 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 228405005550 metal binding site [ion binding]; metal-binding site 228405005551 dimer interface [polypeptide binding]; other site 228405005552 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 228405005553 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 228405005554 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405005555 ligand binding site [chemical binding]; other site 228405005556 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 228405005557 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 228405005558 putative homodimer interface [polypeptide binding]; other site 228405005559 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 228405005560 heterodimer interface [polypeptide binding]; other site 228405005561 homodimer interface [polypeptide binding]; other site 228405005562 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 228405005563 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 228405005564 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 228405005565 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 228405005566 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 228405005567 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 228405005568 homodimer interface [polypeptide binding]; other site 228405005569 metal binding site [ion binding]; metal-binding site 228405005570 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 228405005571 homodimer interface [polypeptide binding]; other site 228405005572 active site 228405005573 putative chemical substrate binding site [chemical binding]; other site 228405005574 metal binding site [ion binding]; metal-binding site 228405005575 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 228405005576 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 228405005577 HflX GTPase family; Region: HflX; cd01878 228405005578 G1 box; other site 228405005579 GTP/Mg2+ binding site [chemical binding]; other site 228405005580 Switch I region; other site 228405005581 G2 box; other site 228405005582 G3 box; other site 228405005583 Switch II region; other site 228405005584 G4 box; other site 228405005585 G5 box; other site 228405005586 bacterial Hfq-like; Region: Hfq; cd01716 228405005587 hexamer interface [polypeptide binding]; other site 228405005588 Sm1 motif; other site 228405005589 RNA binding site [nucleotide binding]; other site 228405005590 Sm2 motif; other site 228405005591 Cation transport protein; Region: TrkH; cl17365 228405005592 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 228405005593 TrkA-N domain; Region: TrkA_N; pfam02254 228405005594 TrkA-C domain; Region: TrkA_C; pfam02080 228405005595 TrkA-N domain; Region: TrkA_N; pfam02254 228405005596 TrkA-C domain; Region: TrkA_C; pfam02080 228405005597 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 228405005598 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 228405005599 active site 228405005600 phosphorylation site [posttranslational modification] 228405005601 intermolecular recognition site; other site 228405005602 dimerization interface [polypeptide binding]; other site 228405005603 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 228405005604 Walker A motif; other site 228405005605 ATP binding site [chemical binding]; other site 228405005606 Walker B motif; other site 228405005607 arginine finger; other site 228405005608 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 228405005609 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 228405005610 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 228405005611 dimerization interface [polypeptide binding]; other site 228405005612 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 228405005613 dimer interface [polypeptide binding]; other site 228405005614 phosphorylation site [posttranslational modification] 228405005615 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 228405005616 ATP binding site [chemical binding]; other site 228405005617 Mg2+ binding site [ion binding]; other site 228405005618 G-X-G motif; other site 228405005619 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 228405005620 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 228405005621 active site 228405005622 phosphorylation site [posttranslational modification] 228405005623 intermolecular recognition site; other site 228405005624 dimerization interface [polypeptide binding]; other site 228405005625 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 228405005626 Walker A motif; other site 228405005627 ATP binding site [chemical binding]; other site 228405005628 Walker B motif; other site 228405005629 arginine finger; other site 228405005630 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 228405005631 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 228405005632 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 228405005633 putative active site [active] 228405005634 heme pocket [chemical binding]; other site 228405005635 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 228405005636 phosphorylation site [posttranslational modification] 228405005637 dimer interface [polypeptide binding]; other site 228405005638 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 228405005639 ATP binding site [chemical binding]; other site 228405005640 Mg2+ binding site [ion binding]; other site 228405005641 G-X-G motif; other site 228405005642 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 228405005643 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 228405005644 FMN binding site [chemical binding]; other site 228405005645 active site 228405005646 catalytic residues [active] 228405005647 substrate binding site [chemical binding]; other site 228405005648 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 228405005649 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 228405005650 substrate binding site; other site 228405005651 dimer interface; other site 228405005652 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 228405005653 homotrimer interaction site [polypeptide binding]; other site 228405005654 zinc binding site [ion binding]; other site 228405005655 CDP-binding sites; other site 228405005656 enoyl-CoA hydratase; Provisional; Region: PRK09245 228405005657 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 228405005658 substrate binding site [chemical binding]; other site 228405005659 oxyanion hole (OAH) forming residues; other site 228405005660 trimer interface [polypeptide binding]; other site 228405005661 Competence-damaged protein; Region: CinA; pfam02464 228405005662 Helix-turn-helix domain; Region: HTH_28; pfam13518 228405005663 Winged helix-turn helix; Region: HTH_29; pfam13551 228405005664 Homeodomain-like domain; Region: HTH_32; pfam13565 228405005665 Integrase core domain; Region: rve; pfam00665 228405005666 Integrase core domain; Region: rve_3; pfam13683 228405005667 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 228405005668 putative coenzyme Q binding site [chemical binding]; other site 228405005669 lipoyl synthase; Provisional; Region: PRK05481 228405005670 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 228405005671 FeS/SAM binding site; other site 228405005672 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 228405005673 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405005674 acyl-activating enzyme (AAE) consensus motif; other site 228405005675 AMP binding site [chemical binding]; other site 228405005676 active site 228405005677 CoA binding site [chemical binding]; other site 228405005678 poly(3-hydroxyalkanoate) depolymerase; Region: PHA_depoly_arom; TIGR02240 228405005679 poly(R)-hydroxyalkanoic acid synthase, class II; Region: PHA_synth_II; TIGR01839 228405005680 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 228405005681 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405005682 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405005683 Bacterial transcriptional repressor; Region: TetR; pfam13972 228405005684 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 228405005685 Class I aldolases; Region: Aldolase_Class_I; cl17187 228405005686 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 228405005687 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 228405005688 active site 228405005689 phosphorylation site [posttranslational modification] 228405005690 intermolecular recognition site; other site 228405005691 dimerization interface [polypeptide binding]; other site 228405005692 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 228405005693 DNA binding site [nucleotide binding] 228405005694 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 228405005695 PhoU domain; Region: PhoU; pfam01895 228405005696 PhoU domain; Region: PhoU; pfam01895 228405005697 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 228405005698 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 228405005699 Walker A/P-loop; other site 228405005700 ATP binding site [chemical binding]; other site 228405005701 Q-loop/lid; other site 228405005702 ABC transporter signature motif; other site 228405005703 Walker B; other site 228405005704 D-loop; other site 228405005705 H-loop/switch region; other site 228405005706 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 228405005707 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 228405005708 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 228405005709 dimer interface [polypeptide binding]; other site 228405005710 conserved gate region; other site 228405005711 putative PBP binding loops; other site 228405005712 ABC-ATPase subunit interface; other site 228405005713 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 228405005714 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 228405005715 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 228405005716 dimer interface [polypeptide binding]; other site 228405005717 conserved gate region; other site 228405005718 putative PBP binding loops; other site 228405005719 ABC-ATPase subunit interface; other site 228405005720 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 228405005721 active site 228405005722 HslU subunit interaction site [polypeptide binding]; other site 228405005723 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 228405005724 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 228405005725 Walker A motif; other site 228405005726 ATP binding site [chemical binding]; other site 228405005727 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 228405005728 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 228405005729 Predicted transcriptional regulators [Transcription]; Region: COG1733 228405005730 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 228405005731 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 228405005732 substrate binding site [chemical binding]; other site 228405005733 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 228405005734 ATP binding site [chemical binding]; other site 228405005735 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 228405005736 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 228405005737 Active site serine [active] 228405005738 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 228405005739 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 228405005740 minor groove reading motif; other site 228405005741 helix-hairpin-helix signature motif; other site 228405005742 substrate binding pocket [chemical binding]; other site 228405005743 active site 228405005744 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 228405005745 Integral membrane protein (DUF2244); Region: DUF2244; pfam10003 228405005746 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405005747 Cytochrome P450; Region: p450; cl12078 228405005748 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 228405005749 putative FMN binding site [chemical binding]; other site 228405005750 Domain of unknown function (DUF1287); Region: DUF1287; pfam06940 228405005751 Phosphopantetheinyl transferase [Coenzyme metabolism]; Region: Sfp; COG2091 228405005752 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; pfam01648 228405005753 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 228405005754 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 228405005755 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 228405005756 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 228405005757 Sporulation related domain; Region: SPOR; pfam05036 228405005758 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 228405005759 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 228405005760 Zn2+ binding site [ion binding]; other site 228405005761 Mg2+ binding site [ion binding]; other site 228405005762 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 228405005763 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 228405005764 Epoxide hydrolase N terminus; Region: EHN; pfam06441 228405005765 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405005766 transcription antitermination factor NusB; Region: nusB; TIGR01951 228405005767 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 228405005768 homopentamer interface [polypeptide binding]; other site 228405005769 active site 228405005770 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 228405005771 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 228405005772 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 228405005773 dimerization interface [polypeptide binding]; other site 228405005774 active site 228405005775 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 228405005776 Lumazine binding domain; Region: Lum_binding; pfam00677 228405005777 Lumazine binding domain; Region: Lum_binding; pfam00677 228405005778 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 228405005779 RibD C-terminal domain; Region: RibD_C; cl17279 228405005780 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 228405005781 Restriction alleviation protein Lar; Region: Lar_restr_allev; cl08047 228405005782 ATP cone domain; Region: ATP-cone; pfam03477 228405005783 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 228405005784 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 228405005785 dimer interface [polypeptide binding]; other site 228405005786 active site 228405005787 glycine-pyridoxal phosphate binding site [chemical binding]; other site 228405005788 folate binding site [chemical binding]; other site 228405005789 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 228405005790 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 228405005791 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 228405005792 substrate-cofactor binding pocket; other site 228405005793 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405005794 catalytic residue [active] 228405005795 aldolase II superfamily protein; Provisional; Region: PRK07044 228405005796 intersubunit interface [polypeptide binding]; other site 228405005797 active site 228405005798 Zn2+ binding site [ion binding]; other site 228405005799 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 228405005800 ATP-NAD kinase; Region: NAD_kinase; pfam01513 228405005801 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 228405005802 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5330 228405005803 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 228405005804 trigger factor; Provisional; Region: tig; PRK01490 228405005805 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 228405005806 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 228405005807 hypothetical protein; Validated; Region: PRK08238 228405005808 phosphoribose diphosphate:decaprenyl-phosphate phosphoribosyltransferase; Provisional; Region: PRK12324 228405005809 Predicted membrane protein [Function unknown]; Region: COG2246 228405005810 GtrA-like protein; Region: GtrA; pfam04138 228405005811 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 228405005812 O-succinylbenzoate-CoA ligase; Region: menE; TIGR01923 228405005813 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405005814 AMP binding site [chemical binding]; other site 228405005815 active site 228405005816 acyl-activating enzyme (AAE) consensus motif; other site 228405005817 CoA binding site [chemical binding]; other site 228405005818 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405005819 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405005820 NAD(P) binding site [chemical binding]; other site 228405005821 active site 228405005822 Protein of unknown function (DUF2029); Region: DUF2029; pfam09594 228405005823 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405005824 Coenzyme A binding pocket [chemical binding]; other site 228405005825 putative carbohydrate kinase; Provisional; Region: PRK10565 228405005826 YjeF-related protein N-terminus; Region: YjeF_N; pfam03853 228405005827 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 228405005828 putative substrate binding site [chemical binding]; other site 228405005829 putative ATP binding site [chemical binding]; other site 228405005830 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 228405005831 catalytic core [active] 228405005832 Coenzyme Q (ubiquinone) biosynthesis protein Coq4; Region: Coq4; cl02093 228405005833 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 228405005834 Nitrogen regulatory protein P-II; Region: P-II; smart00938 228405005835 glutamine synthetase; Provisional; Region: glnA; PRK09469 228405005836 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 228405005837 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 228405005838 phosphodiesterase YaeI; Provisional; Region: PRK11340 228405005839 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 228405005840 putative active site [active] 228405005841 putative metal binding site [ion binding]; other site 228405005842 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 228405005843 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 228405005844 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 228405005845 Walker A motif; other site 228405005846 ATP binding site [chemical binding]; other site 228405005847 Walker B motif; other site 228405005848 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 228405005849 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 228405005850 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 228405005851 oligomer interface [polypeptide binding]; other site 228405005852 active site residues [active] 228405005853 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 228405005854 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405005855 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 228405005856 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405005857 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 228405005858 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_2; cd04821 228405005859 Predicted aminopeptidases [General function prediction only]; Region: Iap; COG2234 228405005860 PA/protease or protease-like domain interface [polypeptide binding]; other site 228405005861 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_1; cd05660 228405005862 metal binding site [ion binding]; metal-binding site 228405005863 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 228405005864 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 228405005865 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 228405005866 active site 228405005867 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 228405005868 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405005869 active site 228405005870 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405005871 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 228405005872 FAD binding site [chemical binding]; other site 228405005873 substrate binding site [chemical binding]; other site 228405005874 catalytic base [active] 228405005875 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 228405005876 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 228405005877 putative dimer interface [polypeptide binding]; other site 228405005878 active site pocket [active] 228405005879 putative cataytic base [active] 228405005880 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 228405005881 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 228405005882 catalytic motif [active] 228405005883 Catalytic residue [active] 228405005884 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 228405005885 domain interfaces; other site 228405005886 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 228405005887 active site 228405005888 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 228405005889 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405005890 metal binding site [ion binding]; metal-binding site 228405005891 active site 228405005892 I-site; other site 228405005893 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405005894 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 228405005895 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 228405005896 substrate binding pocket [chemical binding]; other site 228405005897 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 228405005898 B12 binding site [chemical binding]; other site 228405005899 cobalt ligand [ion binding]; other site 228405005900 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 228405005901 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 228405005902 dimerization interface [polypeptide binding]; other site 228405005903 putative active site pocket [active] 228405005904 putative catalytic residue [active] 228405005905 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 228405005906 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 228405005907 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 228405005908 FAD binding site [chemical binding]; other site 228405005909 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 228405005910 dimerization interface [polypeptide binding]; other site 228405005911 putative DNA binding site [nucleotide binding]; other site 228405005912 putative Zn2+ binding site [ion binding]; other site 228405005913 Methyltransferase domain; Region: Methyltransf_23; pfam13489 228405005914 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 228405005915 S-adenosylmethionine binding site [chemical binding]; other site 228405005916 VacJ like lipoprotein; Region: VacJ; cl01073 228405005917 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 228405005918 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 228405005919 AbgT putative transporter family; Region: ABG_transport; cl17431 228405005920 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405005921 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405005922 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405005923 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 228405005924 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 228405005925 HlyD family secretion protein; Region: HlyD_2; pfam12700 228405005926 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405005927 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405005928 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405005929 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405005930 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 228405005931 Heme-dependent peroxidases similar to plant peroxidases; Region: plant_peroxidase_like; cl00196 228405005932 heme binding site [chemical binding]; other site 228405005933 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 228405005934 catecholate siderophore receptor Fiu; Provisional; Region: PRK09840 228405005935 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 228405005936 N-terminal plug; other site 228405005937 ligand-binding site [chemical binding]; other site 228405005938 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 228405005939 Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate...; Region: alpha_hydroxyacid_oxid_FMN; cd02809 228405005940 FMN-dependent dehydrogenase; Region: FMN_dh; pfam01070 228405005941 active site 228405005942 substrate binding site [chemical binding]; other site 228405005943 FMN binding site [chemical binding]; other site 228405005944 putative catalytic residues [active] 228405005945 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 228405005946 Benzyl alcohol dehydrogenase; Region: benzyl_alcohol_DH; cd08278 228405005947 catalytic Zn binding site [ion binding]; other site 228405005948 NAD binding site [chemical binding]; other site 228405005949 structural Zn binding site [ion binding]; other site 228405005950 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405005951 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405005952 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405005953 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 228405005954 N-terminal plug; other site 228405005955 ligand-binding site [chemical binding]; other site 228405005956 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 228405005957 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; cl00896 228405005958 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 228405005959 uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB; Region: LamB_YcsF_like_1; cd10801 228405005960 putative active site [active] 228405005961 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 228405005962 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 228405005963 Protein of unknown function (DUF2891); Region: DUF2891; pfam11199 228405005964 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405005965 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 228405005966 N-terminal plug; other site 228405005967 ligand-binding site [chemical binding]; other site 228405005968 MFS/sugar transport protein; Region: MFS_2; pfam13347 228405005969 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 228405005970 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405005971 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405005972 Transcriptional regulator [Transcription]; Region: IclR; COG1414 228405005973 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 228405005974 Bacterial transcriptional regulator; Region: IclR; pfam01614 228405005975 Domain of unknown function (DUF718); Region: DUF718; pfam05336 228405005976 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily [Cell envelope biogenesis, outer membrane / General function prediction only]; Region: COG4948 228405005977 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 228405005978 metal binding site [ion binding]; metal-binding site 228405005979 substrate binding pocket [chemical binding]; other site 228405005980 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 228405005981 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405005982 active site 228405005983 catalytic tetrad [active] 228405005984 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 228405005985 Amidohydrolase; Region: Amidohydro_2; pfam04909 228405005986 active site 228405005987 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405005988 human DHRS6-like, classical (c) SDRs; Region: DHRS6_like_SDR_c; cd05368 228405005989 NAD binding site [chemical binding]; other site 228405005990 homotetramer interface [polypeptide binding]; other site 228405005991 homodimer interface [polypeptide binding]; other site 228405005992 active site 228405005993 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 228405005994 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 228405005995 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 228405005996 von Willebrand factor type A domain; Region: VWA_2; pfam13519 228405005997 metal ion-dependent adhesion site (MIDAS); other site 228405005998 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 228405005999 trimer interface [polypeptide binding]; other site 228405006000 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 228405006001 trimer interface [polypeptide binding]; other site 228405006002 YadA-like C-terminal region; Region: YadA; pfam03895 228405006003 RNA polymerase sigma factor, TIGR02999 family; Region: Sig-70_X6 228405006004 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 228405006005 DNA binding residues [nucleotide binding] 228405006006 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 228405006007 Catalytic domain of Protein Kinases; Region: PKc; cd00180 228405006008 active site 228405006009 ATP binding site [chemical binding]; other site 228405006010 substrate binding site [chemical binding]; other site 228405006011 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 228405006012 activation loop (A-loop); other site 228405006013 activation loop (A-loop); other site 228405006014 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 228405006015 TPR motif; other site 228405006016 binding surface 228405006017 Tetratricopeptide repeat; Region: TPR_12; pfam13424 228405006018 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 228405006019 binding surface 228405006020 TPR motif; other site 228405006021 Tetratricopeptide repeat; Region: TPR_12; pfam13424 228405006022 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 228405006023 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405006024 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 228405006025 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 228405006026 DNA protecting protein DprA; Region: dprA; TIGR00732 228405006027 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 228405006028 Organic solvent tolerance protein; Region: OstA_C; pfam04453 228405006029 SurA N-terminal domain; Region: SurA_N; pfam09312 228405006030 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 228405006031 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 228405006032 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 228405006033 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 228405006034 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 228405006035 S-adenosylmethionine binding site [chemical binding]; other site 228405006036 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 228405006037 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 228405006038 catalytic site [active] 228405006039 G-X2-G-X-G-K; other site 228405006040 hypothetical protein; Provisional; Region: PRK11820 228405006041 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 228405006042 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 228405006043 YceG-like family; Region: YceG; pfam02618 228405006044 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 228405006045 dimerization interface [polypeptide binding]; other site 228405006046 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 228405006047 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 228405006048 dimer interface [polypeptide binding]; other site 228405006049 active site 228405006050 acyl carrier protein; Provisional; Region: acpP; PRK00982 228405006051 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 228405006052 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 228405006053 NAD(P) binding site [chemical binding]; other site 228405006054 homotetramer interface [polypeptide binding]; other site 228405006055 homodimer interface [polypeptide binding]; other site 228405006056 active site 228405006057 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 228405006058 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 228405006059 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 228405006060 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 228405006061 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 228405006062 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 228405006063 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 228405006064 replicative DNA helicase; Provisional; Region: PRK09165 228405006065 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 228405006066 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 228405006067 Walker A motif; other site 228405006068 ATP binding site [chemical binding]; other site 228405006069 Walker B motif; other site 228405006070 DNA binding loops [nucleotide binding] 228405006071 Competence-damaged protein; Region: CinA; pfam02464 228405006072 enoyl-CoA hydratase; Provisional; Region: PRK08260 228405006073 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 228405006074 substrate binding site [chemical binding]; other site 228405006075 oxyanion hole (OAH) forming residues; other site 228405006076 trimer interface [polypeptide binding]; other site 228405006077 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 228405006078 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 228405006079 Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_A; cd01299 228405006080 active site 228405006081 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 228405006082 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 228405006083 cobyric acid synthase; Provisional; Region: PRK00784 228405006084 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 228405006085 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 228405006086 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 228405006087 catalytic triad [active] 228405006088 Protein of unknown function (DUF1636); Region: DUF1636; pfam07845 228405006089 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 228405006090 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 228405006091 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 228405006092 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405006093 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 228405006094 N-terminal plug; other site 228405006095 ligand-binding site [chemical binding]; other site 228405006096 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 228405006097 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 228405006098 tetrameric interface [polypeptide binding]; other site 228405006099 NAD binding site [chemical binding]; other site 228405006100 catalytic residues [active] 228405006101 putative transporter; Provisional; Region: PRK10484 228405006102 uncharacterized SLC5 subfamily, Escherichia coli YidK-like; solute binding domain; Region: SLC5sbd_YidK; cd10328 228405006103 Na binding site [ion binding]; other site 228405006104 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 228405006105 Sulfatase; Region: Sulfatase; pfam00884 228405006106 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006107 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 228405006108 N-terminal plug; other site 228405006109 ligand-binding site [chemical binding]; other site 228405006110 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 228405006111 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 228405006112 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 228405006113 putative active site [active] 228405006114 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 228405006115 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 228405006116 substrate binding site [chemical binding]; other site 228405006117 ATP binding site [chemical binding]; other site 228405006118 Uncharacterized protein conserved in bacteria (DUF2090); Region: DUF2090; pfam09863 228405006119 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3892 228405006120 Acetolactate synthase [Amino acid transport and metabolism]; Region: COG3962 228405006121 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 228405006122 PYR/PP interface [polypeptide binding]; other site 228405006123 dimer interface [polypeptide binding]; other site 228405006124 TPP binding site [chemical binding]; other site 228405006125 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 228405006126 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 228405006127 TPP-binding site [chemical binding]; other site 228405006128 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 228405006129 Uncharacterized enzyme involved in inositol metabolism [Carbohydrate transport and metabolism]; Region: IolB; COG3718 228405006130 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 228405006131 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 228405006132 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 228405006133 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 228405006134 heavy metal response regulator; Region: cztR_silR_copR; TIGR01387 228405006135 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 228405006136 active site 228405006137 phosphorylation site [posttranslational modification] 228405006138 intermolecular recognition site; other site 228405006139 dimerization interface [polypeptide binding]; other site 228405006140 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 228405006141 DNA binding site [nucleotide binding] 228405006142 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 228405006143 HAMP domain; Region: HAMP; pfam00672 228405006144 dimerization interface [polypeptide binding]; other site 228405006145 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 228405006146 dimer interface [polypeptide binding]; other site 228405006147 phosphorylation site [posttranslational modification] 228405006148 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 228405006149 ATP binding site [chemical binding]; other site 228405006150 Mg2+ binding site [ion binding]; other site 228405006151 G-X-G motif; other site 228405006152 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 228405006153 Protein export membrane protein; Region: SecD_SecF; cl14618 228405006154 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 228405006155 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405006156 short chain dehydrogenase; Provisional; Region: PRK05854 228405006157 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 228405006158 putative NAD(P) binding site [chemical binding]; other site 228405006159 active site 228405006160 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 228405006161 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 228405006162 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405006163 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405006164 NAD(P) binding site [chemical binding]; other site 228405006165 active site 228405006166 Predicted membrane protein [Function unknown]; Region: COG2259 228405006167 short chain dehydrogenase; Provisional; Region: PRK05854 228405006168 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405006169 NAD(P) binding site [chemical binding]; other site 228405006170 active site 228405006171 Flagellin N-methylase; Region: FliB; cl00497 228405006172 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 228405006173 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 228405006174 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 228405006175 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006176 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006177 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 228405006178 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 228405006179 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 228405006180 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 228405006181 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 228405006182 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 228405006183 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 228405006184 Sulfatase; Region: Sulfatase; cl17466 228405006185 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 228405006186 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405006187 active site 228405006188 catalytic tetrad [active] 228405006189 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 228405006190 short chain dehydrogenase; Provisional; Region: PRK12937 228405006191 NADP binding site [chemical binding]; other site 228405006192 homodimer interface [polypeptide binding]; other site 228405006193 active site 228405006194 substrate binding site [chemical binding]; other site 228405006195 Transcriptional regulators [Transcription]; Region: GntR; COG1802 228405006196 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405006197 DNA-binding site [nucleotide binding]; DNA binding site 228405006198 FCD domain; Region: FCD; pfam07729 228405006199 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405006200 Cytochrome P450; Region: p450; cl12078 228405006201 hypothetical protein; Provisional; Region: PRK06126 228405006202 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 228405006203 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405006204 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405006205 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006206 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 228405006207 N-terminal plug; other site 228405006208 ligand-binding site [chemical binding]; other site 228405006209 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 228405006210 Sulfatase; Region: Sulfatase; pfam00884 228405006211 Phosphotransferase enzyme family; Region: APH; pfam01636 228405006212 Ecdysteroid kinase; Region: EcKinase; cl17738 228405006213 hypothetical protein; Validated; Region: PRK07586 228405006214 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 228405006215 PYR/PP interface [polypeptide binding]; other site 228405006216 dimer interface [polypeptide binding]; other site 228405006217 TPP binding site [chemical binding]; other site 228405006218 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 228405006219 TPP-binding site [chemical binding]; other site 228405006220 dimer interface [polypeptide binding]; other site 228405006221 SnoaL-like domain; Region: SnoaL_4; pfam13577 228405006222 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 228405006223 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405006224 putative substrate translocation pore; other site 228405006225 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405006226 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405006227 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 228405006228 dimerization interface [polypeptide binding]; other site 228405006229 Domain of unknown function (DUF2437); Region: DUF2437; pfam10370 228405006230 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 228405006231 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 228405006232 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 228405006233 active site 228405006234 metal binding site [ion binding]; metal-binding site 228405006235 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405006236 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 228405006237 Nocardioides 2-carboxybenzaldehyde dehydrogenase, PhdK-like; Region: ALDH_PhdK-like; cd07107 228405006238 NAD(P) binding site [chemical binding]; other site 228405006239 catalytic residues [active] 228405006240 catalytic residues [active] 228405006241 Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases [Carbohydrate transport and metabolism]; Region: AraD; COG0235 228405006242 intersubunit interface [polypeptide binding]; other site 228405006243 active site 228405006244 Zn2+ binding site [ion binding]; other site 228405006245 short chain dehydrogenase; Provisional; Region: PRK06197 228405006246 retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs; Region: retinol-DH_like_SDR_c_like; cd05327 228405006247 putative NAD(P) binding site [chemical binding]; other site 228405006248 active site 228405006249 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 228405006250 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 228405006251 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006252 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006253 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 228405006254 putative substrate translocation pore; other site 228405006255 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405006256 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 228405006257 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 228405006258 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405006259 active site 228405006260 catalytic tetrad [active] 228405006261 AraC-type transcriptional regulator N-terminus; Region: AraC_N; pfam06719 228405006262 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006263 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 228405006264 atypical (a) SDRs, subgroup 7; Region: SDR_a7; cd05262 228405006265 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 228405006266 putative NAD(P) binding site [chemical binding]; other site 228405006267 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 228405006268 salt bridge; other site 228405006269 non-specific DNA binding site [nucleotide binding]; other site 228405006270 conjugal transfer protein TrbA; Provisional; Region: PRK13890 228405006271 sequence-specific DNA binding site [nucleotide binding]; other site 228405006272 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 228405006273 active site 228405006274 SAM binding site [chemical binding]; other site 228405006275 homodimer interface [polypeptide binding]; other site 228405006276 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 228405006277 NMT1-like family; Region: NMT1_2; pfam13379 228405006278 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 228405006279 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 228405006280 active site 228405006281 phosphorylation site [posttranslational modification] 228405006282 intermolecular recognition site; other site 228405006283 ANTAR domain; Region: ANTAR; pfam03861 228405006284 NAD(P)H-nitrite reductase [Energy production and conversion]; Region: NirB; COG1251 228405006285 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405006286 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 228405006287 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 228405006288 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 228405006289 Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain...; Region: Rieske_NirD_small_Bacillus; cd03530 228405006290 [2Fe-2S] cluster binding site [ion binding]; other site 228405006291 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 228405006292 Serine/threonine protein phosphatase [Signal transduction mechanisms]; Region: PTC1; COG0631 228405006293 active site 228405006294 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 228405006295 Catalytic domain of Protein Kinases; Region: PKc; cd00180 228405006296 active site 228405006297 ATP binding site [chemical binding]; other site 228405006298 substrate binding site [chemical binding]; other site 228405006299 activation loop (A-loop); other site 228405006300 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 228405006301 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 228405006302 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 228405006303 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 228405006304 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 228405006305 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 228405006306 inhibitor-cofactor binding pocket; inhibition site 228405006307 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405006308 catalytic residue [active] 228405006309 multifunctional aminopeptidase A; Provisional; Region: PRK00913 228405006310 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 228405006311 interface (dimer of trimers) [polypeptide binding]; other site 228405006312 Substrate-binding/catalytic site; other site 228405006313 Zn-binding sites [ion binding]; other site 228405006314 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 228405006315 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 228405006316 motif II; other site 228405006317 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 228405006318 ThiS interaction site; other site 228405006319 putative active site [active] 228405006320 tetramer interface [polypeptide binding]; other site 228405006321 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 228405006322 thiS-thiF/thiG interaction site; other site 228405006323 Dehydroquinase class II; Region: DHquinase_II; pfam01220 228405006324 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 228405006325 trimer interface [polypeptide binding]; other site 228405006326 active site 228405006327 dimer interface [polypeptide binding]; other site 228405006328 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 228405006329 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 228405006330 carboxyltransferase (CT) interaction site; other site 228405006331 biotinylation site [posttranslational modification]; other site 228405006332 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 228405006333 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 228405006334 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 228405006335 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 228405006336 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 228405006337 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; pfam09923 228405006338 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 228405006339 mce related protein; Region: MCE; pfam02470 228405006340 NADH dehydrogenase; Validated; Region: PRK08183 228405006341 TSCPD domain; Region: TSCPD; pfam12637 228405006342 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 228405006343 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 228405006344 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 228405006345 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 228405006346 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 228405006347 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 228405006348 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 228405006349 dimer interface [polypeptide binding]; other site 228405006350 anticodon binding site; other site 228405006351 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 228405006352 homodimer interface [polypeptide binding]; other site 228405006353 motif 1; other site 228405006354 active site 228405006355 motif 2; other site 228405006356 GAD domain; Region: GAD; pfam02938 228405006357 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 228405006358 active site 228405006359 motif 3; other site 228405006360 ribonuclease D; Region: rnd; TIGR01388 228405006361 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 228405006362 catalytic site [active] 228405006363 putative active site [active] 228405006364 putative substrate binding site [chemical binding]; other site 228405006365 HRDC domain; Region: HRDC; pfam00570 228405006366 exopolyphosphatase; Region: exo_poly_only; TIGR03706 228405006367 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 228405006368 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 228405006369 polyphosphate kinase 1; Region: poly_P_kin; TIGR03705 228405006370 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 228405006371 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 228405006372 putative domain interface [polypeptide binding]; other site 228405006373 putative active site [active] 228405006374 catalytic site [active] 228405006375 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 228405006376 putative domain interface [polypeptide binding]; other site 228405006377 putative active site [active] 228405006378 catalytic site [active] 228405006379 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 228405006380 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 228405006381 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 228405006382 dimerization interface [polypeptide binding]; other site 228405006383 putative ATP binding site [chemical binding]; other site 228405006384 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 228405006385 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 228405006386 active site 228405006387 substrate binding site [chemical binding]; other site 228405006388 cosubstrate binding site; other site 228405006389 catalytic site [active] 228405006390 Predicted acetyltransferase [General function prediction only]; Region: COG2388 228405006391 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 228405006392 Prostaglandin dehydrogenases; Region: PGDH; cd05288 228405006393 NAD(P) binding site [chemical binding]; other site 228405006394 substrate binding site [chemical binding]; other site 228405006395 dimer interface [polypeptide binding]; other site 228405006396 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 228405006397 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 228405006398 active site 228405006399 multimer interface [polypeptide binding]; other site 228405006400 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 228405006401 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 228405006402 PhnA protein; Region: PhnA; pfam03831 228405006403 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 228405006404 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405006405 Coenzyme A binding pocket [chemical binding]; other site 228405006406 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 228405006407 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 228405006408 multifunctional aminopeptidase A; Provisional; Region: PRK00913 228405006409 interface (dimer of trimers) [polypeptide binding]; other site 228405006410 Substrate-binding/catalytic site; other site 228405006411 Zn-binding sites [ion binding]; other site 228405006412 Predicted permeases [General function prediction only]; Region: COG0795 228405006413 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 228405006414 Predicted permeases [General function prediction only]; Region: COG0795 228405006415 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 228405006416 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 228405006417 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 228405006418 active site 228405006419 interdomain interaction site; other site 228405006420 putative metal-binding site [ion binding]; other site 228405006421 nucleotide binding site [chemical binding]; other site 228405006422 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 228405006423 domain I; other site 228405006424 DNA binding groove [nucleotide binding] 228405006425 phosphate binding site [ion binding]; other site 228405006426 domain II; other site 228405006427 domain III; other site 228405006428 nucleotide binding site [chemical binding]; other site 228405006429 catalytic site [active] 228405006430 domain IV; other site 228405006431 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 228405006432 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 228405006433 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 228405006434 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 228405006435 ribonuclease R; Region: RNase_R; TIGR02063 228405006436 RNB domain; Region: RNB; pfam00773 228405006437 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 228405006438 RNA binding site [nucleotide binding]; other site 228405006439 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 228405006440 nudix motif; other site 228405006441 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 228405006442 enterobactin exporter EntS; Provisional; Region: PRK10489 228405006443 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 228405006444 putative substrate translocation pore; other site 228405006445 response regulator PleD; Reviewed; Region: pleD; PRK09581 228405006446 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 228405006447 active site 228405006448 phosphorylation site [posttranslational modification] 228405006449 intermolecular recognition site; other site 228405006450 dimerization interface [polypeptide binding]; other site 228405006451 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 228405006452 active site 228405006453 phosphorylation site [posttranslational modification] 228405006454 intermolecular recognition site; other site 228405006455 dimerization interface [polypeptide binding]; other site 228405006456 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405006457 metal binding site [ion binding]; metal-binding site 228405006458 active site 228405006459 I-site; other site 228405006460 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 228405006461 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 228405006462 active site 228405006463 phosphorylation site [posttranslational modification] 228405006464 intermolecular recognition site; other site 228405006465 dimerization interface [polypeptide binding]; other site 228405006466 DNA polymerase IV; Provisional; Region: PRK02794 228405006467 Putative regulatory protein; Region: CxxC_CXXC_SSSS; smart00834 228405006468 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 228405006469 active site 228405006470 DNA binding site [nucleotide binding] 228405006471 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 228405006472 homotrimer interaction site [polypeptide binding]; other site 228405006473 putative active site [active] 228405006474 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases; Region: GDPD_like_3; cd08585 228405006475 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 228405006476 putative active site [active] 228405006477 catalytic site [active] 228405006478 putative metal binding site [ion binding]; other site 228405006479 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3146 228405006480 Protein of unknown function, DUF482; Region: DUF482; pfam04339 228405006481 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 228405006482 HIT family signature motif; other site 228405006483 catalytic residue [active] 228405006484 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 228405006485 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 228405006486 GatB domain; Region: GatB_Yqey; smart00845 228405006487 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 228405006488 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 228405006489 SET domain; Region: SET; pfam00856 228405006490 2-enoyl thioester reductase (ETR) like proteins, child 1; Region: ETR_like_1; cd08291 228405006491 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 228405006492 NADP binding site [chemical binding]; other site 228405006493 dimer interface [polypeptide binding]; other site 228405006494 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 228405006495 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 228405006496 Predicted permeases [General function prediction only]; Region: COG0679 228405006497 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 228405006498 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 228405006499 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 228405006500 dihydroorotase; Validated; Region: PRK09059 228405006501 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 228405006502 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 228405006503 active site 228405006504 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 228405006505 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 228405006506 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 228405006507 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 228405006508 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405006509 Coenzyme A binding pocket [chemical binding]; other site 228405006510 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 228405006511 PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic...; Region: PA_M28_1_1; cd04820 228405006512 PA/protease or protease-like domain interface [polypeptide binding]; other site 228405006513 M28 Zn-Peptidases containing a PA domain insert; Region: M28_like_PA_2; cd05661 228405006514 Peptidase family M28; Region: Peptidase_M28; pfam04389 228405006515 metal binding site [ion binding]; metal-binding site 228405006516 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405006517 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 228405006518 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 228405006519 acyl-activating enzyme (AAE) consensus motif; other site 228405006520 putative AMP binding site [chemical binding]; other site 228405006521 putative active site [active] 228405006522 acyl-activating enzyme (AAE) consensus motif; other site 228405006523 putative CoA binding site [chemical binding]; other site 228405006524 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 228405006525 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 228405006526 putative active site [active] 228405006527 homoserine dehydrogenase; Provisional; Region: PRK06349 228405006528 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 228405006529 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 228405006530 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 228405006531 aminotransferase; Validated; Region: PRK09148 228405006532 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 228405006533 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405006534 homodimer interface [polypeptide binding]; other site 228405006535 catalytic residue [active] 228405006536 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 228405006537 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 228405006538 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 228405006539 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 228405006540 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 228405006541 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 228405006542 23S rRNA interface [nucleotide binding]; other site 228405006543 L3 interface [polypeptide binding]; other site 228405006544 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 228405006545 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 228405006546 Protein of unknown function (DUF2842); Region: DUF2842; pfam11003 228405006547 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405006548 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405006549 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 228405006550 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 228405006551 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405006552 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405006553 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405006554 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 228405006555 CoA-transferase family III; Region: CoA_transf_3; pfam02515 228405006556 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 228405006557 CoenzymeA binding site [chemical binding]; other site 228405006558 subunit interaction site [polypeptide binding]; other site 228405006559 PHB binding site; other site 228405006560 succinic semialdehyde dehydrogenase; Region: PLN02278 228405006561 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 228405006562 tetramerization interface [polypeptide binding]; other site 228405006563 NAD(P) binding site [chemical binding]; other site 228405006564 catalytic residues [active] 228405006565 Cupin domain; Region: Cupin_2; cl17218 228405006566 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006567 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 228405006568 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405006569 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 228405006570 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 228405006571 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 228405006572 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 228405006573 ferrichrome outer membrane transporter; Provisional; Region: PRK10044 228405006574 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 228405006575 N-terminal plug; other site 228405006576 ligand-binding site [chemical binding]; other site 228405006577 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 228405006578 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 228405006579 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 228405006580 Putative FMN-binding domain; Region: FMN_bind_2; cl17803 228405006581 Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH families 4 and 17; Region: ALDH_F4-17_P5CDH; cd07123 228405006582 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1; Region: D1pyr5carbox1; TIGR01236 228405006583 Glutamate binding site [chemical binding]; other site 228405006584 NAD binding site [chemical binding]; other site 228405006585 catalytic residues [active] 228405006586 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 228405006587 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 228405006588 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 228405006589 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like; Region: ALDH_AldA-AAD23400; cd07106 228405006590 NAD(P) binding site [chemical binding]; other site 228405006591 catalytic residues [active] 228405006592 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 228405006593 Bacillus subtilis YydB and related proteins, metallophosphatase domain; Region: MPP_YydB; cd07400 228405006594 putative active site [active] 228405006595 putative metal binding site [ion binding]; other site 228405006596 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 228405006597 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 228405006598 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 228405006599 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 228405006600 Histidine kinase; Region: HisKA_2; pfam07568 228405006601 RNA polymerase sigma factor; Provisional; Region: PRK12547 228405006602 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405006603 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 228405006604 DNA binding residues [nucleotide binding] 228405006605 two-component response regulator; Provisional; Region: PRK09191 228405006606 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 228405006607 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 228405006608 active site 228405006609 phosphorylation site [posttranslational modification] 228405006610 intermolecular recognition site; other site 228405006611 dimerization interface [polypeptide binding]; other site 228405006612 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 228405006613 transmembrane helices; other site 228405006614 TrkA-C domain; Region: TrkA_C; pfam02080 228405006615 TrkA-C domain; Region: TrkA_C; pfam02080 228405006616 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 228405006617 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 228405006618 CsbD-like; Region: CsbD; pfam05532 228405006619 PAS fold; Region: PAS_4; pfam08448 228405006620 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405006621 putative active site [active] 228405006622 heme pocket [chemical binding]; other site 228405006623 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 228405006624 HWE histidine kinase; Region: HWE_HK; smart00911 228405006625 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 228405006626 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 228405006627 Predicted transcriptional regulators [Transcription]; Region: COG1733 228405006628 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 228405006629 classical (c) SDR, subgroup 10; Region: SDR_c10; cd05373 228405006630 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 228405006631 putative NAD(P) binding site [chemical binding]; other site 228405006632 active site 228405006633 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 228405006634 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 228405006635 putative catalytic residue [active] 228405006636 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006637 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006638 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 228405006639 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 228405006640 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 228405006641 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405006642 homodimer interface [polypeptide binding]; other site 228405006643 catalytic residue [active] 228405006644 GAF domain; Region: GAF; pfam01590 228405006645 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405006646 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405006647 metal binding site [ion binding]; metal-binding site 228405006648 active site 228405006649 I-site; other site 228405006650 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 228405006651 Predicted membrane protein [Function unknown]; Region: COG3212 228405006652 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 228405006653 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405006654 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 228405006655 active site 228405006656 phosphorylation site [posttranslational modification] 228405006657 intermolecular recognition site; other site 228405006658 dimerization interface [polypeptide binding]; other site 228405006659 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 228405006660 DNA binding site [nucleotide binding] 228405006661 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405006662 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 228405006663 ATP binding site [chemical binding]; other site 228405006664 G-X-G motif; other site 228405006665 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 228405006666 catalytic center binding site [active] 228405006667 ATP binding site [chemical binding]; other site 228405006668 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 228405006669 homooctamer interface [polypeptide binding]; other site 228405006670 active site 228405006671 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 228405006672 dihydropteroate synthase; Region: DHPS; TIGR01496 228405006673 substrate binding pocket [chemical binding]; other site 228405006674 dimer interface [polypeptide binding]; other site 228405006675 inhibitor binding site; inhibition site 228405006676 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 228405006677 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 228405006678 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405006679 catalytic residue [active] 228405006680 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 228405006681 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 228405006682 glutamine binding [chemical binding]; other site 228405006683 catalytic triad [active] 228405006684 Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]; Region: TrpE; COG0147 228405006685 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 228405006686 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 228405006687 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 228405006688 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405006689 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 228405006690 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 228405006691 YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgH_like; cd02198 228405006692 homotrimer interaction site [polypeptide binding]; other site 228405006693 putative active site [active] 228405006694 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 228405006695 Ligand binding site; other site 228405006696 Glycosyl transferase family 21; Region: Glyco_transf_21; pfam13506 228405006697 DXD motif; other site 228405006698 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 228405006699 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 228405006700 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 228405006701 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 228405006702 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 228405006703 Protein export membrane protein; Region: SecD_SecF; pfam02355 228405006704 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07204 228405006705 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 228405006706 dimer interface [polypeptide binding]; other site 228405006707 active site 228405006708 CoA binding pocket [chemical binding]; other site 228405006709 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405006710 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405006711 NAD(P) binding site [chemical binding]; other site 228405006712 active site 228405006713 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 228405006714 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405006715 putative adenylate-forming enzyme; Region: aden_form_hyp; TIGR02304 228405006716 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 228405006717 This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the...; Region: GT1_Gtf_like; cd03784 228405006718 homodimer interface [polypeptide binding]; other site 228405006719 Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]; Region: COG1819 228405006720 active site 228405006721 TDP-binding site; other site 228405006722 acceptor substrate-binding pocket; other site 228405006723 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 228405006724 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 228405006725 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 228405006726 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 228405006727 RNA binding site [nucleotide binding]; other site 228405006728 Transcriptional regulators [Transcription]; Region: MarR; COG1846 228405006729 MarR family; Region: MarR; pfam01047 228405006730 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 228405006731 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006732 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 228405006733 N-terminal plug; other site 228405006734 ligand-binding site [chemical binding]; other site 228405006735 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 228405006736 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405006737 putative substrate translocation pore; other site 228405006738 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 228405006739 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405006740 C-terminal domain interface [polypeptide binding]; other site 228405006741 GSH binding site (G-site) [chemical binding]; other site 228405006742 dimer interface [polypeptide binding]; other site 228405006743 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 228405006744 N-terminal domain interface [polypeptide binding]; other site 228405006745 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 228405006746 DNA-binding site [nucleotide binding]; DNA binding site 228405006747 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 228405006748 UTRA domain; Region: UTRA; pfam07702 228405006749 N-formimino-L-glutamate deiminase; Validated; Region: PRK09229 228405006750 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 228405006751 active site 228405006752 imidazolonepropionase; Validated; Region: PRK09356 228405006753 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 228405006754 active site 228405006755 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 228405006756 active sites [active] 228405006757 tetramer interface [polypeptide binding]; other site 228405006758 N-formylglutamate amidohydrolase; Region: FGase; cl01522 228405006759 urocanate hydratase; Provisional; Region: PRK05414 228405006760 Lipocalin-like domain; Region: Lipocalin_2; pfam08212 228405006761 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 228405006762 pyrimidine utilization regulatory protein R; Region: RutR; TIGR03613 228405006763 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405006764 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 228405006765 Cytochrome c; Region: Cytochrom_C; pfam00034 228405006766 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 228405006767 HlyD family secretion protein; Region: HlyD; pfam00529 228405006768 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405006769 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405006770 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 228405006771 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 228405006772 putative substrate translocation pore; other site 228405006773 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 228405006774 Predicted methyltransferase [General function prediction only]; Region: COG3897 228405006775 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 228405006776 S-adenosylmethionine binding site [chemical binding]; other site 228405006777 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006778 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006779 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006780 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006781 glycerophosphodiester phosphodiesterase; Provisional; Region: glpQ; PRK11143 228405006782 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 228405006783 active site 228405006784 catalytic site [active] 228405006785 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 228405006786 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 228405006787 active site 228405006788 putative substrate binding pocket [chemical binding]; other site 228405006789 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 228405006790 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405006791 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405006792 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 228405006793 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 228405006794 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405006795 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405006796 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 228405006797 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405006798 hydroxyglutarate oxidase; Provisional; Region: PRK11728 228405006799 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 228405006800 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 228405006801 active site 228405006802 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 228405006803 dimer interface [polypeptide binding]; other site 228405006804 substrate binding site [chemical binding]; other site 228405006805 catalytic residues [active] 228405006806 Glutamate-1-semialdehyde aminotransferase [Coenzyme metabolism]; Region: HemL; COG0001 228405006807 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 228405006808 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405006809 catalytic residue [active] 228405006810 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 228405006811 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 228405006812 substrate binding site [chemical binding]; other site 228405006813 ATP binding site [chemical binding]; other site 228405006814 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 228405006815 intersubunit interface [polypeptide binding]; other site 228405006816 active site 228405006817 Zn2+ binding site [ion binding]; other site 228405006818 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 228405006819 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006820 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 228405006821 N-terminal plug; other site 228405006822 ligand-binding site [chemical binding]; other site 228405006823 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405006824 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405006825 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 228405006826 thioredoxin 2; Provisional; Region: PRK10996 228405006827 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 228405006828 catalytic residues [active] 228405006829 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 228405006830 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 228405006831 active site residue [active] 228405006832 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 228405006833 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 228405006834 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405006835 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 228405006836 Protein export membrane protein; Region: SecD_SecF; cl14618 228405006837 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 228405006838 putative DNA binding site [nucleotide binding]; other site 228405006839 putative Zn2+ binding site [ion binding]; other site 228405006840 Transmembrane secretion effector; Region: MFS_3; pfam05977 228405006841 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 228405006842 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 228405006843 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 228405006844 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 228405006845 NAD(P) binding site [chemical binding]; other site 228405006846 Heme NO binding; Region: HNOB; pfam07700 228405006847 Heme NO binding associated; Region: HNOBA; pfam07701 228405006848 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405006849 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405006850 metal binding site [ion binding]; metal-binding site 228405006851 active site 228405006852 I-site; other site 228405006853 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405006854 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 228405006855 Predicted flavoprotein [General function prediction only]; Region: COG0431 228405006856 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 228405006857 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 228405006858 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405006859 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405006860 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 228405006861 FAD binding site [chemical binding]; other site 228405006862 substrate binding site [chemical binding]; other site 228405006863 catalytic base [active] 228405006864 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405006865 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405006866 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 228405006867 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 228405006868 substrate binding site [chemical binding]; other site 228405006869 oxyanion hole (OAH) forming residues; other site 228405006870 trimer interface [polypeptide binding]; other site 228405006871 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 228405006872 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405006873 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 228405006874 acyl-activating enzyme (AAE) consensus motif; other site 228405006875 acyl-activating enzyme (AAE) consensus motif; other site 228405006876 putative AMP binding site [chemical binding]; other site 228405006877 putative active site [active] 228405006878 putative CoA binding site [chemical binding]; other site 228405006879 MFS/sugar transport protein; Region: MFS_2; pfam13347 228405006880 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 228405006881 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 228405006882 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 228405006883 PA14 domain; Region: PA14; cl08459 228405006884 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 228405006885 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405006886 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405006887 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006888 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 228405006889 N-terminal plug; other site 228405006890 ligand-binding site [chemical binding]; other site 228405006891 Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]; Region: AslA; COG3119 228405006892 Sulfatase; Region: Sulfatase; pfam00884 228405006893 Cna protein B-type domain; Region: Cna_B_2; pfam13715 228405006894 TonB-dependent receptor; Region: TonB-Xanth-Caul; TIGR01782 228405006895 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006896 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006897 Predicted phosphatase [General function prediction only]; Region: PhoX; COG3211 228405006898 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405006899 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 228405006900 ligand binding site [chemical binding]; other site 228405006901 PhoD-like phosphatase; Region: PhoD; pfam09423 228405006902 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 228405006903 putative active site [active] 228405006904 putative metal binding site [ion binding]; other site 228405006905 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 228405006906 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405006907 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006908 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405006909 Haloacid Dehalogenase Superfamily Class (subfamily) IIA; Region: HAD-SF-IIA; TIGR01460 228405006910 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 228405006911 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 228405006912 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 228405006913 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 228405006914 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 228405006915 putative active site [active] 228405006916 phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein; Region: 3A0109s03R; TIGR01098 228405006917 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 228405006918 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 228405006919 ATP-binding cassette domain of the binding protein-dependent phosphonate transport system; Region: ABC_PhnC_transporter; cd03256 228405006920 Walker A/P-loop; other site 228405006921 ATP binding site [chemical binding]; other site 228405006922 Q-loop/lid; other site 228405006923 ABC transporter signature motif; other site 228405006924 Walker B; other site 228405006925 D-loop; other site 228405006926 H-loop/switch region; other site 228405006927 phosphonate ABC transporter, permease protein PhnE; Region: PhnE; TIGR01097 228405006928 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 228405006929 dimer interface [polypeptide binding]; other site 228405006930 conserved gate region; other site 228405006931 ABC-ATPase subunit interface; other site 228405006932 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 228405006933 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405006934 Uncharacterized conserved protein [Function unknown]; Region: COG4544 228405006935 DNA Polymerase Y-family; Region: PolY_like; cd03468 228405006936 active site 228405006937 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 228405006938 DNA binding site [nucleotide binding] 228405006939 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 228405006940 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 228405006941 putative active site [active] 228405006942 putative PHP Thumb interface [polypeptide binding]; other site 228405006943 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 228405006944 generic binding surface I; other site 228405006945 generic binding surface II; other site 228405006946 hydroperoxidase II; Provisional; Region: katE; PRK11249 228405006947 Catalase-like heme-binding proteins and protein domains; Region: catalase_like; cl09506 228405006948 heme binding pocket [chemical binding]; other site 228405006949 Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases; Region: GATase1_catalase; cd03132 228405006950 domain interactions; other site 228405006951 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 228405006952 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 228405006953 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 228405006954 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 228405006955 IHF dimer interface [polypeptide binding]; other site 228405006956 IHF - DNA interface [nucleotide binding]; other site 228405006957 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 228405006958 Prostaglandin dehydrogenases; Region: PGDH; cd05288 228405006959 NAD(P) binding site [chemical binding]; other site 228405006960 substrate binding site [chemical binding]; other site 228405006961 dimer interface [polypeptide binding]; other site 228405006962 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 228405006963 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405006964 DNA binding residues [nucleotide binding] 228405006965 dimerization interface [polypeptide binding]; other site 228405006966 CopC domain; Region: CopC; cl01012 228405006967 Cytochrome c [Energy production and conversion]; Region: COG3258 228405006968 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 228405006969 sulfur oxidation protein SoxY; Provisional; Region: PRK07474 228405006970 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 228405006971 Cytochrome c; Region: Cytochrom_C; pfam00034 228405006972 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 228405006973 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 228405006974 Cytochrome c; Region: Cytochrom_C; cl11414 228405006975 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 228405006976 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 228405006977 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 228405006978 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 228405006979 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 228405006980 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 228405006981 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 228405006982 catalytic loop [active] 228405006983 iron binding site [ion binding]; other site 228405006984 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 228405006985 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 228405006986 catalytic residues [active] 228405006987 Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]; Region: SelB; COG3276 228405006988 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 228405006989 G1 box; other site 228405006990 GTP/Mg2+ binding site [chemical binding]; other site 228405006991 G2 box; other site 228405006992 Switch I region; other site 228405006993 G3 box; other site 228405006994 Switch II region; other site 228405006995 G4 box; other site 228405006996 G5 box; other site 228405006997 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 228405006998 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 228405006999 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 228405007000 seryl-tRNA(sec) selenium transferase; Region: selA; TIGR00474 228405007001 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 228405007002 pyridine nucleotide-disulfide oxidoreductase family protein; Region: Nterm_to_SelD; TIGR03169 228405007003 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405007004 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 228405007005 selenophosphate synthetase; Provisional; Region: PRK00943 228405007006 dimerization interface [polypeptide binding]; other site 228405007007 putative ATP binding site [chemical binding]; other site 228405007008 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 228405007009 tRNA 2-selenouridine synthase; Region: tRNA_sel_U_synt; TIGR03167 228405007010 active site residue [active] 228405007011 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 228405007012 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 228405007013 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 228405007014 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 228405007015 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 228405007016 Uncharacterized ALDH ( RL0313) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1; Region: ALDH_RL0313; cd07148 228405007017 NAD(P) binding site [chemical binding]; other site 228405007018 catalytic residues [active] 228405007019 acetolactate synthase; Reviewed; Region: PRK08322 228405007020 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 228405007021 PYR/PP interface [polypeptide binding]; other site 228405007022 dimer interface [polypeptide binding]; other site 228405007023 TPP binding site [chemical binding]; other site 228405007024 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 228405007025 Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2...; Region: TPP_ALS; cd02010 228405007026 TPP-binding site [chemical binding]; other site 228405007027 dimer interface [polypeptide binding]; other site 228405007028 ATP-dependent transcriptional regulator [Transcription]; Region: MalT; COG2909 228405007029 AAA ATPase domain; Region: AAA_16; pfam13191 228405007030 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 228405007031 DNA binding residues [nucleotide binding] 228405007032 dimerization interface [polypeptide binding]; other site 228405007033 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 228405007034 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 228405007035 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 228405007036 Protein of unknown function (DUF917); Region: DUF917; pfam06032 228405007037 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405007038 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 228405007039 N-terminal plug; other site 228405007040 ligand-binding site [chemical binding]; other site 228405007041 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 228405007042 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 228405007043 active site 228405007044 catalytic site [active] 228405007045 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 228405007046 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 228405007047 homodimer interface [polypeptide binding]; other site 228405007048 substrate-cofactor binding pocket; other site 228405007049 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405007050 catalytic residue [active] 228405007051 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405007052 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405007053 hypothetical protein; Provisional; Region: PRK11019 228405007054 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3316 228405007055 Integrase core domain; Region: rve; pfam00665 228405007056 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 228405007057 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 228405007058 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 228405007059 type II secretion system protein D; Region: type_II_gspD; TIGR02517 228405007060 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 228405007061 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 228405007062 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 228405007063 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 228405007064 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 228405007065 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 228405007066 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 228405007067 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 228405007068 Walker A motif; other site 228405007069 ATP binding site [chemical binding]; other site 228405007070 Walker B motif; other site 228405007071 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 228405007072 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405007073 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405007074 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 228405007075 RHS Repeat; Region: RHS_repeat; pfam05593 228405007076 Rhs family protein [Cell envelope biogenesis, outer membrane]; Region: RhsA; COG3209 228405007077 RHS Repeat; Region: RHS_repeat; cl11982 228405007078 RHS repeat-associated core domain; Region: Rhs_assc_core; TIGR03696 228405007079 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 228405007080 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 228405007081 catalytic residues [active] 228405007082 catalytic nucleophile [active] 228405007083 Recombinase; Region: Recombinase; pfam07508 228405007084 ParB-like nuclease domain; Region: ParBc; pfam02195 228405007085 RepB plasmid partitioning protein; Region: RepB; pfam07506 228405007086 ParB-like nuclease domain; Region: ParB; smart00470 228405007087 RepB plasmid partitioning protein; Region: RepB; pfam07506 228405007088 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 228405007089 active site 228405007090 catalytic site [active] 228405007091 substrate binding site [chemical binding]; other site 228405007092 Superfamily II DNA helicase [DNA replication, recombination, and repair]; Region: RecQ; COG0514 228405007093 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 228405007094 ATP binding site [chemical binding]; other site 228405007095 putative Mg++ binding site [ion binding]; other site 228405007096 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 228405007097 nucleotide binding region [chemical binding]; other site 228405007098 ATP-binding site [chemical binding]; other site 228405007099 Part of AAA domain; Region: AAA_19; pfam13245 228405007100 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 228405007101 Family description; Region: UvrD_C_2; pfam13538 228405007102 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405007103 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 228405007104 non-specific DNA binding site [nucleotide binding]; other site 228405007105 salt bridge; other site 228405007106 sequence-specific DNA binding site [nucleotide binding]; other site 228405007107 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 228405007108 Ligand Binding Site [chemical binding]; other site 228405007109 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 228405007110 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: HsdR; COG4096 228405007111 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 228405007112 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 228405007113 ATP binding site [chemical binding]; other site 228405007114 putative Mg++ binding site [ion binding]; other site 228405007115 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 228405007116 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 228405007117 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 228405007118 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 228405007119 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 228405007120 HsdM N-terminal domain; Region: HsdM_N; pfam12161 228405007121 Methyltransferase domain; Region: Methyltransf_26; pfam13659 228405007122 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 228405007123 non-specific DNA binding site [nucleotide binding]; other site 228405007124 salt bridge; other site 228405007125 sequence-specific DNA binding site [nucleotide binding]; other site 228405007126 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 228405007127 ParB-like nuclease domain; Region: ParBc; pfam02195 228405007128 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 228405007129 DNA methylase; Region: N6_N4_Mtase; pfam01555 228405007130 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 228405007131 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 228405007132 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 228405007133 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 228405007134 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 228405007135 ATP binding site [chemical binding]; other site 228405007136 substrate interface [chemical binding]; other site 228405007137 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 228405007138 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 228405007139 Prokaryotic E2 family E; Region: Prok-E2_E; pfam14462 228405007140 Domain of unknown function (DUF955); Region: DUF955; cl01076 228405007141 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 228405007142 Part of AAA domain; Region: AAA_19; pfam13245 228405007143 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 228405007144 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 228405007145 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 228405007146 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 228405007147 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 228405007148 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 228405007149 catalytic residues [active] 228405007150 catalytic nucleophile [active] 228405007151 Presynaptic Site I dimer interface [polypeptide binding]; other site 228405007152 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 228405007153 Synaptic Flat tetramer interface [polypeptide binding]; other site 228405007154 Synaptic Site I dimer interface [polypeptide binding]; other site 228405007155 DNA binding site [nucleotide binding] 228405007156 Recombinase; Region: Recombinase; pfam07508 228405007157 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405007158 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405007159 metal binding site [ion binding]; metal-binding site 228405007160 active site 228405007161 I-site; other site 228405007162 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 228405007163 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 228405007164 Uncharacterized conserved protein [Function unknown]; Region: COG3743 228405007165 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 228405007166 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 228405007167 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 228405007168 GTPase CgtA; Reviewed; Region: obgE; PRK12299 228405007169 GTP1/OBG; Region: GTP1_OBG; pfam01018 228405007170 Obg GTPase; Region: Obg; cd01898 228405007171 G1 box; other site 228405007172 GTP/Mg2+ binding site [chemical binding]; other site 228405007173 Switch I region; other site 228405007174 G2 box; other site 228405007175 G3 box; other site 228405007176 Switch II region; other site 228405007177 G4 box; other site 228405007178 G5 box; other site 228405007179 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 228405007180 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 228405007181 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; cl17355 228405007182 DNA binding site [nucleotide binding] 228405007183 Predicted integral membrane protein [Function unknown]; Region: COG5616 228405007184 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 228405007185 TPR motif; other site 228405007186 TPR repeat; Region: TPR_11; pfam13414 228405007187 binding surface 228405007188 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 228405007189 binding surface 228405007190 Tetratricopeptide repeat; Region: TPR_16; pfam13432 228405007191 TPR motif; other site 228405007192 Tetratricopeptide repeat; Region: TPR_16; pfam13432 228405007193 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405007194 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 228405007195 putative C-terminal domain interface [polypeptide binding]; other site 228405007196 putative GSH binding site (G-site) [chemical binding]; other site 228405007197 putative dimer interface [polypeptide binding]; other site 228405007198 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405007199 N-terminal domain interface [polypeptide binding]; other site 228405007200 dimer interface [polypeptide binding]; other site 228405007201 substrate binding pocket (H-site) [chemical binding]; other site 228405007202 gamma-glutamyl kinase; Provisional; Region: PRK05429 228405007203 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 228405007204 nucleotide binding site [chemical binding]; other site 228405007205 homotetrameric interface [polypeptide binding]; other site 228405007206 putative phosphate binding site [ion binding]; other site 228405007207 putative allosteric binding site; other site 228405007208 PUA domain; Region: PUA; pfam01472 228405007209 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 228405007210 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405007211 Coenzyme A binding pocket [chemical binding]; other site 228405007212 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 228405007213 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 228405007214 ATP-grasp domain; Region: ATP-grasp_4; cl17255 228405007215 long-chain-acyl-CoA synthetase; Validated; Region: PRK08279 228405007216 Fatty acid transport proteins (FATP) play dual roles as fatty acid transporters and its activation enzymes; Region: FATP_FACS; cd05940 228405007217 acyl-activating enzyme (AAE) consensus motif; other site 228405007218 putative AMP binding site [chemical binding]; other site 228405007219 putative active site [active] 228405007220 putative CoA binding site [chemical binding]; other site 228405007221 Acyl-CoA thioesterase [Lipid metabolism]; Region: TesB; COG1946 228405007222 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat2; cd03445 228405007223 active site 228405007224 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP)...; Region: Thioesterase_II_repeat1; cd03444 228405007225 catalytic triad [active] 228405007226 dimer interface [polypeptide binding]; other site 228405007227 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 228405007228 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 228405007229 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 228405007230 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 228405007231 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405007232 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405007233 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405007234 NAD synthetase; Provisional; Region: PRK13981 228405007235 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 228405007236 multimer interface [polypeptide binding]; other site 228405007237 active site 228405007238 catalytic triad [active] 228405007239 protein interface 1 [polypeptide binding]; other site 228405007240 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 228405007241 homodimer interface [polypeptide binding]; other site 228405007242 NAD binding pocket [chemical binding]; other site 228405007243 ATP binding pocket [chemical binding]; other site 228405007244 Mg binding site [ion binding]; other site 228405007245 active-site loop [active] 228405007246 dihydroxyacetone kinase subunit DhaK; Provisional; Region: PRK14481; cl10557 228405007247 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 228405007248 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405007249 active site 228405007250 HIGH motif; other site 228405007251 nucleotide binding site [chemical binding]; other site 228405007252 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 228405007253 active site 228405007254 KMSKS motif; other site 228405007255 Pectinacetylesterase; Region: PAE; pfam03283 228405007256 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 228405007257 apolar tunnel; other site 228405007258 heme binding site [chemical binding]; other site 228405007259 dimerization interface [polypeptide binding]; other site 228405007260 Protein of unknown function (DUF3034); Region: DUF3034; pfam11231 228405007261 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 228405007262 dimerization interface [polypeptide binding]; other site 228405007263 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405007264 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405007265 active site 228405007266 I-site; other site 228405007267 metal binding site [ion binding]; metal-binding site 228405007268 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 228405007269 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 228405007270 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 228405007271 putative DNA binding site [nucleotide binding]; other site 228405007272 putative Zn2+ binding site [ion binding]; other site 228405007273 AsnC family; Region: AsnC_trans_reg; pfam01037 228405007274 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 228405007275 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 228405007276 Amidohydrolase; Region: Amidohydro_4; pfam13147 228405007277 active site 228405007278 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 228405007279 homotrimer interaction site [polypeptide binding]; other site 228405007280 putative active site [active] 228405007281 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 228405007282 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 228405007283 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 228405007284 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 228405007285 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405007286 catalytic residue [active] 228405007287 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 228405007288 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 228405007289 Predicted ornithine cyclodeaminase, mu-crystallin homolog [Amino acid transport and metabolism]; Region: COG2423 228405007290 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 228405007291 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 228405007292 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 228405007293 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405007294 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 228405007295 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405007296 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405007297 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405007298 amino acid transporter; Region: 2A0306; TIGR00909 228405007299 aspartate aminotransferase; Provisional; Region: PRK06108 228405007300 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 228405007301 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405007302 homodimer interface [polypeptide binding]; other site 228405007303 catalytic residue [active] 228405007304 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 228405007305 Zn binding site [ion binding]; other site 228405007306 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 228405007307 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 228405007308 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405007309 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405007310 acyl-activating enzyme (AAE) consensus motif; other site 228405007311 acyl-activating enzyme (AAE) consensus motif; other site 228405007312 AMP binding site [chemical binding]; other site 228405007313 active site 228405007314 CoA binding site [chemical binding]; other site 228405007315 Predicted transcriptional regulators [Transcription]; Region: COG1733 228405007316 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 228405007317 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4246 228405007318 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 228405007319 lichenase, member of glycosyl hydrolase family 16; Region: GH16_lichenase; cd02175 228405007320 active site 228405007321 active site 228405007322 catalytic residues [active] 228405007323 Domain of unknown function (DUF1476); Region: DUF1476; pfam07345 228405007324 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 228405007325 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 228405007326 ATP binding site [chemical binding]; other site 228405007327 active site 228405007328 substrate binding site [chemical binding]; other site 228405007329 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; pfam02700 228405007330 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405007331 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405007332 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 228405007333 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 228405007334 putative acyl-acceptor binding pocket; other site 228405007335 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 228405007336 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 228405007337 putative active site [active] 228405007338 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 228405007339 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 228405007340 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 228405007341 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 228405007342 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405007343 catalytic residue [active] 228405007344 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 228405007345 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 228405007346 FeS assembly ATPase SufC; Region: sufC; TIGR01978 228405007347 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 228405007348 Walker A/P-loop; other site 228405007349 ATP binding site [chemical binding]; other site 228405007350 Q-loop/lid; other site 228405007351 ABC transporter signature motif; other site 228405007352 Walker B; other site 228405007353 D-loop; other site 228405007354 H-loop/switch region; other site 228405007355 Family description; Region: VCBS; pfam13517 228405007356 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 228405007357 putative ABC transporter; Region: ycf24; CHL00085 228405007358 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 228405007359 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 228405007360 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405007361 catalytic residue [active] 228405007362 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 228405007363 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 228405007364 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 228405007365 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405007366 Coenzyme A binding pocket [chemical binding]; other site 228405007367 Helix-turn-helix domain; Region: HTH_28; pfam13518 228405007368 Winged helix-turn helix; Region: HTH_29; pfam13551 228405007369 Homeodomain-like domain; Region: HTH_32; pfam13565 228405007370 Integrase core domain; Region: rve; pfam00665 228405007371 Integrase core domain; Region: rve_3; pfam13683 228405007372 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 228405007373 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 228405007374 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 228405007375 active site 228405007376 HIGH motif; other site 228405007377 dimer interface [polypeptide binding]; other site 228405007378 KMSKS motif; other site 228405007379 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 228405007380 RNA binding surface [nucleotide binding]; other site 228405007381 Protein of unknown function; Region: DUF3971; pfam13116 228405007382 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 228405007383 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 228405007384 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 228405007385 catalytic triad [active] 228405007386 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 228405007387 Peptidase family M23; Region: Peptidase_M23; pfam01551 228405007388 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 228405007389 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 228405007390 TPR motif; other site 228405007391 binding surface 228405007392 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 228405007393 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 228405007394 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 228405007395 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 228405007396 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 228405007397 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 228405007398 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 228405007399 Protein of unknown function (DUF3450); Region: DUF3450; pfam11932 228405007400 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 228405007401 tandem repeat interface [polypeptide binding]; other site 228405007402 oligomer interface [polypeptide binding]; other site 228405007403 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 228405007404 active site residues [active] 228405007405 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 228405007406 tandem repeat interface [polypeptide binding]; other site 228405007407 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 228405007408 oligomer interface [polypeptide binding]; other site 228405007409 active site residues [active] 228405007410 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405007411 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405007412 NAD(P) binding site [chemical binding]; other site 228405007413 active site 228405007414 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 228405007415 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 228405007416 active site 228405007417 Uncharacterized bacterial proteins with similarity to Aminoglycoside 3'-phosphotransferase (APH) and Choline kinase (ChoK) family members. The APH/ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases; Region: APH_ChoK_like_1; cd05155 228405007418 Phosphotransferase enzyme family; Region: APH; pfam01636 228405007419 putative active site [active] 228405007420 putative substrate binding site [chemical binding]; other site 228405007421 ATP binding site [chemical binding]; other site 228405007422 recombination factor protein RarA; Reviewed; Region: PRK13342 228405007423 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 228405007424 Walker A motif; other site 228405007425 ATP binding site [chemical binding]; other site 228405007426 Walker B motif; other site 228405007427 arginine finger; other site 228405007428 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 228405007429 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 228405007430 Taurine catabolism dioxygenase TauD, TfdA family; Region: TauD; pfam02668 228405007431 active site 228405007432 iron coordination sites [ion binding]; other site 228405007433 substrate binding pocket [chemical binding]; other site 228405007434 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 228405007435 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 228405007436 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 228405007437 protein binding site [polypeptide binding]; other site 228405007438 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 228405007439 protein binding site [polypeptide binding]; other site 228405007440 melibiose:sodium symporter; Provisional; Region: PRK10429; cl15392 228405007441 MFS/sugar transport protein; Region: MFS_2; pfam13347 228405007442 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405007443 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405007444 active site 228405007445 Uncharacterized conserved protein [Function unknown]; Region: COG1359 228405007446 ExoA is involved in the biosynthesis of succinoglycan; Region: Succinoglycan_BP_ExoA; cd02525 228405007447 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 228405007448 Ligand binding site; other site 228405007449 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 228405007450 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 228405007451 active site 228405007452 metal binding site [ion binding]; metal-binding site 228405007453 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 228405007454 putative polysaccharide export protein, PEP-CTERM sytem-associated; Region: pepcterm_export; TIGR03027 228405007455 SLBB domain; Region: SLBB; pfam10531 228405007456 Bacterial sugar transferase; Region: Bac_transf; pfam02397 228405007457 lichenase, member of glycosyl hydrolase family 16; Region: GH16_lichenase; cd02175 228405007458 active site 228405007459 active site 228405007460 catalytic residues [active] 228405007461 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 228405007462 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 228405007463 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_10; cd04623 228405007464 FOG: CBS domain [General function prediction only]; Region: COG0517 228405007465 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405007466 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405007467 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405007468 PAS domain; Region: PAS_5; pfam07310 228405007469 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 228405007470 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 228405007471 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 228405007472 non-specific DNA binding site [nucleotide binding]; other site 228405007473 salt bridge; other site 228405007474 sequence-specific DNA binding site [nucleotide binding]; other site 228405007475 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 228405007476 choline dehydrogenase; Validated; Region: PRK02106 228405007477 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 228405007478 PilZ domain; Region: PilZ; pfam07238 228405007479 PilZ domain; Region: PilZ; pfam07238 228405007480 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 228405007481 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 228405007482 trimer interface [polypeptide binding]; other site 228405007483 putative metal binding site [ion binding]; other site 228405007484 PhoH-like protein; Region: PhoH; pfam02562 228405007485 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 228405007486 O-succinylhomoserine sulfhydrylase; Reviewed; Region: PRK07504 228405007487 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 228405007488 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405007489 catalytic residue [active] 228405007490 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 228405007491 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 228405007492 trimer interface [polypeptide binding]; other site 228405007493 active site 228405007494 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 228405007495 amino acid transporter; Region: 2A0306; TIGR00909 228405007496 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic); Region: Peptidase_C39_like; cl00296 228405007497 putative active site [active] 228405007498 Protein of unknown function, DUF481; Region: DUF481; pfam04338 228405007499 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 228405007500 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 228405007501 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 228405007502 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 228405007503 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 228405007504 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 228405007505 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 228405007506 Uncharacterized conserved protein [Function unknown]; Region: COG2308 228405007507 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 228405007508 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 228405007509 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 228405007510 TrkA-C domain; Region: TrkA_C; pfam02080 228405007511 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 228405007512 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 228405007513 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405007514 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 228405007515 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 228405007516 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 228405007517 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405007518 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405007519 active site 228405007520 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 228405007521 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 228405007522 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 228405007523 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 228405007524 dimer interface [polypeptide binding]; other site 228405007525 conserved gate region; other site 228405007526 ABC-ATPase subunit interface; other site 228405007527 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 228405007528 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 228405007529 Walker A/P-loop; other site 228405007530 ATP binding site [chemical binding]; other site 228405007531 Q-loop/lid; other site 228405007532 ABC transporter signature motif; other site 228405007533 Walker B; other site 228405007534 D-loop; other site 228405007535 H-loop/switch region; other site 228405007536 Peptidase family M48; Region: Peptidase_M48; cl12018 228405007537 TPR repeat; Region: TPR_11; pfam13414 228405007538 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 228405007539 TPR motif; other site 228405007540 binding surface 228405007541 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 228405007542 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 228405007543 catalytic residues [active] 228405007544 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405007545 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 228405007546 NAD binding site [chemical binding]; other site 228405007547 putative substrate binding site 2 [chemical binding]; other site 228405007548 putative substrate binding site 1 [chemical binding]; other site 228405007549 active site 228405007550 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 228405007551 hypothetical protein; Provisional; Region: PRK09256 228405007552 Domain of unknown function (DUF3315); Region: DUF3315; cl02275 228405007553 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 228405007554 nudix motif; other site 228405007555 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 228405007556 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 228405007557 Surface antigen; Region: Bac_surface_Ag; pfam01103 228405007558 Phosphoenolpyruvate carboxykinase; Region: PEPCK_ATP; pfam01293 228405007559 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 228405007560 active site 228405007561 substrate-binding site [chemical binding]; other site 228405007562 metal-binding site [ion binding] 228405007563 ATP binding site [chemical binding]; other site 228405007564 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 228405007565 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 228405007566 dimer interface [polypeptide binding]; other site 228405007567 active site 228405007568 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 228405007569 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 228405007570 catalytic residues [active] 228405007571 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 228405007572 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 228405007573 active site residue [active] 228405007574 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 228405007575 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 228405007576 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 228405007577 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 228405007578 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 228405007579 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 228405007580 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 228405007581 active site 228405007582 HIGH motif; other site 228405007583 KMSK motif region; other site 228405007584 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 228405007585 tRNA binding surface [nucleotide binding]; other site 228405007586 anticodon binding site; other site 228405007587 Domain of unknown function (DUF697); Region: DUF697; pfam05128 228405007588 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 228405007589 putative phosphate binding site [ion binding]; other site 228405007590 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 228405007591 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 228405007592 tetramer interface [polypeptide binding]; other site 228405007593 active site 228405007594 Mg2+/Mn2+ binding site [ion binding]; other site 228405007595 glycine cleavage system aminomethyltransferase T; Provisional; Region: gcvT; PRK13579 228405007596 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 228405007597 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 228405007598 lipoyl attachment site [posttranslational modification]; other site 228405007599 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 228405007600 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 228405007601 tetramer interface [polypeptide binding]; other site 228405007602 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405007603 catalytic residue [active] 228405007604 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 228405007605 tetramer interface [polypeptide binding]; other site 228405007606 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405007607 catalytic residue [active] 228405007608 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 228405007609 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 228405007610 Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_C; cd01309 228405007611 active site 228405007612 Imidazolonepropionase and related amidohydrolases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: HutI; COG1228 228405007613 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 228405007614 active site 228405007615 Protein of unknown function (DUF1489); Region: DUF1489; pfam07370 228405007616 Cupin domain; Region: Cupin_2; cl17218 228405007617 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 228405007618 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 228405007619 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 228405007620 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 228405007621 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 228405007622 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 228405007623 NAD binding site [chemical binding]; other site 228405007624 Phe binding site; other site 228405007625 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 228405007626 Ligand Binding Site [chemical binding]; other site 228405007627 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 228405007628 Rrf2 family protein; Region: rrf2_super; TIGR00738 228405007629 Transcriptional regulator; Region: Rrf2; pfam02082 228405007630 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 228405007631 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 228405007632 motif 1; other site 228405007633 active site 228405007634 motif 2; other site 228405007635 motif 3; other site 228405007636 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 228405007637 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 228405007638 recombinase A; Provisional; Region: recA; PRK09354 228405007639 hexamer interface [polypeptide binding]; other site 228405007640 Walker A motif; other site 228405007641 ATP binding site [chemical binding]; other site 228405007642 Walker B motif; other site 228405007643 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; pfam09866 228405007644 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 228405007645 PAN domain; Region: PAN_4; pfam14295 228405007646 PAN domain; Region: PAN_4; pfam14295 228405007647 PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins, plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech...; Region: PAN_APPLE; cl00112 228405007648 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 228405007649 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 228405007650 NADP binding site [chemical binding]; other site 228405007651 dimer interface [polypeptide binding]; other site 228405007652 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 228405007653 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405007654 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 228405007655 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 228405007656 substrate binding site [chemical binding]; other site 228405007657 oxyanion hole (OAH) forming residues; other site 228405007658 trimer interface [polypeptide binding]; other site 228405007659 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 228405007660 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405007661 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 228405007662 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405007663 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405007664 NAD(P) binding site [chemical binding]; other site 228405007665 active site 228405007666 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 228405007667 RNA/DNA hybrid binding site [nucleotide binding]; other site 228405007668 active site 228405007669 GIY-YIG catalytic domain; Region: GIY-YIG; pfam01541 228405007670 GIY-YIG motif/motif A; other site 228405007671 active site 228405007672 catalytic site [active] 228405007673 metal binding site [ion binding]; metal-binding site 228405007674 Queuosine biosynthesis protein; Region: Queuosine_synth; pfam02547 228405007675 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 228405007676 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 228405007677 active site 228405007678 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 228405007679 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 228405007680 active site 228405007681 (T/H)XGH motif; other site 228405007682 DNA gyrase subunit A; Validated; Region: PRK05560 228405007683 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 228405007684 CAP-like domain; other site 228405007685 active site 228405007686 primary dimer interface [polypeptide binding]; other site 228405007687 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 228405007688 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 228405007689 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 228405007690 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 228405007691 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 228405007692 Galactose oxidase, central domain; Region: Kelch_3; cl02701 228405007693 Galactose oxidase, central domain; Region: Kelch_3; cl02701 228405007694 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405007695 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 228405007696 C-terminal domain interface [polypeptide binding]; other site 228405007697 GSH binding site (G-site) [chemical binding]; other site 228405007698 dimer interface [polypeptide binding]; other site 228405007699 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 228405007700 N-terminal domain interface [polypeptide binding]; other site 228405007701 dimer interface [polypeptide binding]; other site 228405007702 substrate binding pocket (H-site) [chemical binding]; other site 228405007703 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 228405007704 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 228405007705 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 228405007706 dimer interface [polypeptide binding]; other site 228405007707 ssDNA binding site [nucleotide binding]; other site 228405007708 tetramer (dimer of dimers) interface [polypeptide binding]; other site 228405007709 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 228405007710 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 228405007711 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 228405007712 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 228405007713 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 228405007714 Glucose inhibited division protein A; Region: GIDA; pfam01134 228405007715 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 228405007716 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 228405007717 Ligand Binding Site [chemical binding]; other site 228405007718 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405007719 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405007720 active site 228405007721 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 228405007722 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 228405007723 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405007724 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405007725 active site 228405007726 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 228405007727 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405007728 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 228405007729 substrate binding pocket [chemical binding]; other site 228405007730 dimerization interface [polypeptide binding]; other site 228405007731 putative cation:proton antiport protein; Provisional; Region: PRK10669 228405007732 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 228405007733 TrkA-N domain; Region: TrkA_N; pfam02254 228405007734 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 228405007735 nucleoside/Zn binding site; other site 228405007736 dimer interface [polypeptide binding]; other site 228405007737 catalytic motif [active] 228405007738 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 228405007739 substrate binding site [chemical binding]; other site 228405007740 oxyanion hole (OAH) forming residues; other site 228405007741 trimer interface [polypeptide binding]; other site 228405007742 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 228405007743 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 228405007744 S-adenosylmethionine binding site [chemical binding]; other site 228405007745 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 228405007746 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 228405007747 active site 228405007748 nucleophile elbow; other site 228405007749 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 228405007750 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_15; cd04673 228405007751 nudix motif; other site 228405007752 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405007753 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405007754 NAD(P) binding site [chemical binding]; other site 228405007755 active site 228405007756 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 228405007757 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 228405007758 FMN binding site [chemical binding]; other site 228405007759 substrate binding site [chemical binding]; other site 228405007760 putative catalytic residue [active] 228405007761 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 228405007762 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 228405007763 Cl binding site [ion binding]; other site 228405007764 oligomer interface [polypeptide binding]; other site 228405007765 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 228405007766 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 228405007767 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 228405007768 Putative D-isomer specific 2-hydroxyacid dehydrogenase; Region: 2-Hacid_dh_1; cd05300 228405007769 NAD binding site [chemical binding]; other site 228405007770 ligand binding site [chemical binding]; other site 228405007771 catalytic site [active] 228405007772 Protein of unknown function (DUF2385); Region: DUF2385; cl11490 228405007773 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 228405007774 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 228405007775 Family-5 Uracil-DNA glycosylases (UDG), found in thermophilic organisms; Region: UDG_F5_TTUDGB_like; cd10031 228405007776 Fe-S cluster binding site [ion binding]; other site 228405007777 DNA binding site [nucleotide binding] 228405007778 active site 228405007779 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405007780 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 228405007781 putative active site [active] 228405007782 putative substrate binding site [chemical binding]; other site 228405007783 ATP binding site [chemical binding]; other site 228405007784 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405007785 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405007786 active site 228405007787 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 2; Region: FDH_like_2; cd08284 228405007788 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 228405007789 catalytic Zn binding site [ion binding]; other site 228405007790 NAD(P) binding site [chemical binding]; other site 228405007791 structural Zn binding site [ion binding]; other site 228405007792 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405007793 Cytochrome P450; Region: p450; cl12078 228405007794 NLI interacting factor-like phosphatase; Region: NIF; pfam03031 228405007795 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 228405007796 SmpB-tmRNA interface; other site 228405007797 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 228405007798 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 228405007799 dimer interface [polypeptide binding]; other site 228405007800 active site 228405007801 catalytic residue [active] 228405007802 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 228405007803 N-acetyl-D-glucosamine binding site [chemical binding]; other site 228405007804 catalytic residue [active] 228405007805 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 228405007806 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 228405007807 NAD(P) binding site [chemical binding]; other site 228405007808 catalytic residues [active] 228405007809 enoyl-CoA hydratase; Provisional; Region: PRK05981 228405007810 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 228405007811 substrate binding site [chemical binding]; other site 228405007812 oxyanion hole (OAH) forming residues; other site 228405007813 trimer interface [polypeptide binding]; other site 228405007814 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 228405007815 Domain of unknown function (DUF3291); Region: DUF3291; pfam11695 228405007816 TfoX N-terminal domain; Region: TfoX_N; pfam04993 228405007817 Protein of unknown function (DUF3253); Region: DUF3253; pfam11625 228405007818 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405007819 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405007820 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405007821 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405007822 active site 228405007823 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 228405007824 CoenzymeA binding site [chemical binding]; other site 228405007825 subunit interaction site [polypeptide binding]; other site 228405007826 PHB binding site; other site 228405007827 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405007828 classical (c) SDRs; Region: SDR_c; cd05233 228405007829 NAD(P) binding site [chemical binding]; other site 228405007830 active site 228405007831 Peptidase family M1; Region: Peptidase_M1; pfam01433 228405007832 Peptidase M1 Aminopeptidase N family incudes tricorn interacting factor F3, Endoplasmic reticulum aminopeptidase 1 (ERAP1), Aminopeptidase Q (APQ); Region: M1_APN_2; cd09601 228405007833 Zn binding site [ion binding]; other site 228405007834 Domain of unknown function (DUF3358); Region: DUF3358; pfam11838 228405007835 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405007836 GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing...; Region: GST_N_GTT2_like; cd03051 228405007837 putative C-terminal domain interface [polypeptide binding]; other site 228405007838 putative GSH binding site (G-site) [chemical binding]; other site 228405007839 putative dimer interface [polypeptide binding]; other site 228405007840 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405007841 N-terminal domain interface [polypeptide binding]; other site 228405007842 dimer interface [polypeptide binding]; other site 228405007843 substrate binding pocket (H-site) [chemical binding]; other site 228405007844 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405007845 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 228405007846 N-terminal plug; other site 228405007847 ligand-binding site [chemical binding]; other site 228405007848 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 228405007849 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 228405007850 Nucleoside recognition; Region: Gate; pfam07670 228405007851 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 228405007852 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 228405007853 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 228405007854 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_19; cd07262 228405007855 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405007856 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405007857 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 228405007858 NAD(P) binding site [chemical binding]; other site 228405007859 active site 228405007860 Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the...; Region: KAZAL_FS; cd00104 228405007861 Predicted HD phosphohydrolase [General function prediction only]; Region: COG4341; cl17564 228405007862 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 228405007863 active site 228405007864 metal binding site [ion binding]; metal-binding site 228405007865 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 228405007866 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 228405007867 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 228405007868 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 228405007869 alphaNTD - beta interaction site [polypeptide binding]; other site 228405007870 alphaNTD homodimer interface [polypeptide binding]; other site 228405007871 alphaNTD - beta' interaction site [polypeptide binding]; other site 228405007872 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 228405007873 30S ribosomal protein S11; Validated; Region: PRK05309 228405007874 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 228405007875 30S ribosomal protein S13; Region: bact_S13; TIGR03631 228405007876 adenylate kinase; Provisional; Region: PRK14532 228405007877 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 228405007878 AMP-binding site [chemical binding]; other site 228405007879 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 228405007880 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 228405007881 SecY translocase; Region: SecY; pfam00344 228405007882 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 228405007883 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 228405007884 23S rRNA binding site [nucleotide binding]; other site 228405007885 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 228405007886 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 228405007887 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 228405007888 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 228405007889 23S rRNA interface [nucleotide binding]; other site 228405007890 L21e interface [polypeptide binding]; other site 228405007891 5S rRNA interface [nucleotide binding]; other site 228405007892 L27 interface [polypeptide binding]; other site 228405007893 L5 interface [polypeptide binding]; other site 228405007894 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 228405007895 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 228405007896 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 228405007897 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 228405007898 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 228405007899 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 228405007900 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 228405007901 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 228405007902 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 228405007903 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 228405007904 RNA binding site [nucleotide binding]; other site 228405007905 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 228405007906 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 228405007907 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 228405007908 23S rRNA interface [nucleotide binding]; other site 228405007909 putative translocon interaction site; other site 228405007910 signal recognition particle (SRP54) interaction site; other site 228405007911 L23 interface [polypeptide binding]; other site 228405007912 trigger factor interaction site; other site 228405007913 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 228405007914 23S rRNA interface [nucleotide binding]; other site 228405007915 5S rRNA interface [nucleotide binding]; other site 228405007916 putative antibiotic binding site [chemical binding]; other site 228405007917 L25 interface [polypeptide binding]; other site 228405007918 L27 interface [polypeptide binding]; other site 228405007919 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 228405007920 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 228405007921 G-X-X-G motif; other site 228405007922 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 228405007923 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 228405007924 putative translocon binding site; other site 228405007925 protein-rRNA interface [nucleotide binding]; other site 228405007926 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 228405007927 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 228405007928 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 228405007929 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 228405007930 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 228405007931 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 228405007932 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 228405007933 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 228405007934 elongation factor Tu; Reviewed; Region: PRK00049 228405007935 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 228405007936 G1 box; other site 228405007937 GEF interaction site [polypeptide binding]; other site 228405007938 GTP/Mg2+ binding site [chemical binding]; other site 228405007939 Switch I region; other site 228405007940 G2 box; other site 228405007941 G3 box; other site 228405007942 Switch II region; other site 228405007943 G4 box; other site 228405007944 G5 box; other site 228405007945 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 228405007946 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 228405007947 Antibiotic Binding Site [chemical binding]; other site 228405007948 elongation factor G; Reviewed; Region: PRK00007 228405007949 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 228405007950 G1 box; other site 228405007951 putative GEF interaction site [polypeptide binding]; other site 228405007952 GTP/Mg2+ binding site [chemical binding]; other site 228405007953 Switch I region; other site 228405007954 G2 box; other site 228405007955 G3 box; other site 228405007956 Switch II region; other site 228405007957 G4 box; other site 228405007958 G5 box; other site 228405007959 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 228405007960 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 228405007961 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 228405007962 30S ribosomal protein S7; Validated; Region: PRK05302 228405007963 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 228405007964 S17 interaction site [polypeptide binding]; other site 228405007965 S8 interaction site; other site 228405007966 16S rRNA interaction site [nucleotide binding]; other site 228405007967 streptomycin interaction site [chemical binding]; other site 228405007968 23S rRNA interaction site [nucleotide binding]; other site 228405007969 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 228405007970 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 228405007971 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 228405007972 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 228405007973 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 228405007974 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 228405007975 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 228405007976 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 228405007977 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 228405007978 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 228405007979 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 228405007980 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 228405007981 DNA binding site [nucleotide binding] 228405007982 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 228405007983 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 228405007984 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 228405007985 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 228405007986 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 228405007987 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 228405007988 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 228405007989 RPB3 interaction site [polypeptide binding]; other site 228405007990 RPB1 interaction site [polypeptide binding]; other site 228405007991 RPB11 interaction site [polypeptide binding]; other site 228405007992 RPB10 interaction site [polypeptide binding]; other site 228405007993 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 228405007994 L11 interface [polypeptide binding]; other site 228405007995 putative EF-Tu interaction site [polypeptide binding]; other site 228405007996 putative EF-G interaction site [polypeptide binding]; other site 228405007997 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 228405007998 23S rRNA interface [nucleotide binding]; other site 228405007999 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 228405008000 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 228405008001 mRNA/rRNA interface [nucleotide binding]; other site 228405008002 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 228405008003 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 228405008004 23S rRNA interface [nucleotide binding]; other site 228405008005 L7/L12 interface [polypeptide binding]; other site 228405008006 putative thiostrepton binding site; other site 228405008007 L25 interface [polypeptide binding]; other site 228405008008 Peptidase family M48; Region: Peptidase_M48; pfam01435 228405008009 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 228405008010 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 228405008011 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 228405008012 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 228405008013 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 228405008014 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 228405008015 S-adenosylmethionine binding site [chemical binding]; other site 228405008016 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405008017 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405008018 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 228405008019 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 228405008020 peptide binding site [polypeptide binding]; other site 228405008021 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405008022 Putative phosphatase (DUF442); Region: DUF442; cl17385 228405008023 oligopeptide transporter permease; Reviewed; Region: oppB; PRK09471 228405008024 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 228405008025 dimer interface [polypeptide binding]; other site 228405008026 conserved gate region; other site 228405008027 putative PBP binding loops; other site 228405008028 ABC-ATPase subunit interface; other site 228405008029 oligopeptide ABC transporter permease OppC; Provisional; Region: PRK15406 228405008030 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 228405008031 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 228405008032 dimer interface [polypeptide binding]; other site 228405008033 conserved gate region; other site 228405008034 putative PBP binding loops; other site 228405008035 ABC-ATPase subunit interface; other site 228405008036 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405008037 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405008038 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405008039 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 228405008040 active site 228405008041 metal binding site [ion binding]; metal-binding site 228405008042 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 228405008043 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 228405008044 Predicted metalloprotease [General function prediction only]; Region: COG2321 228405008045 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 228405008046 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 228405008047 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 228405008048 homodimer interface [polypeptide binding]; other site 228405008049 substrate-cofactor binding pocket; other site 228405008050 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405008051 catalytic residue [active] 228405008052 Protein of unknown function DUF72; Region: DUF72; pfam01904 228405008053 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 228405008054 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 228405008055 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 228405008056 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 228405008057 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405008058 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 228405008059 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 228405008060 DNA binding residues [nucleotide binding] 228405008061 DNA primase; Validated; Region: dnaG; PRK05667 228405008062 CHC2 zinc finger; Region: zf-CHC2; pfam01807 228405008063 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 228405008064 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 228405008065 active site 228405008066 metal binding site [ion binding]; metal-binding site 228405008067 interdomain interaction site; other site 228405008068 Yqey-like protein; Region: YqeY; cl17540 228405008069 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 228405008070 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 228405008071 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 228405008072 catalytic site [active] 228405008073 subunit interface [polypeptide binding]; other site 228405008074 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 228405008075 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 228405008076 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 228405008077 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 228405008078 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 228405008079 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405008080 Zn binding site [ion binding]; other site 228405008081 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 228405008082 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 228405008083 dimer interface [polypeptide binding]; other site 228405008084 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 228405008085 active site 228405008086 Fe binding site [ion binding]; other site 228405008087 Transcriptional regulators [Transcription]; Region: MarR; COG1846 228405008088 MarR family; Region: MarR_2; pfam12802 228405008089 MarR family; Region: MarR_2; cl17246 228405008090 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405008091 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405008092 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 228405008093 catalytic site [active] 228405008094 Penicillinase repressor; Region: Pencillinase_R; pfam03965 228405008095 BlaR1 peptidase M56; Region: Peptidase_M56; pfam05569 228405008096 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 228405008097 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 228405008098 Ligand binding site; other site 228405008099 oligomer interface; other site 228405008100 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 228405008101 catalytic core [active] 228405008102 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 228405008103 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405008104 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 228405008105 dimer interface [polypeptide binding]; other site 228405008106 phosphorylation site [posttranslational modification] 228405008107 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 228405008108 ATP binding site [chemical binding]; other site 228405008109 Mg2+ binding site [ion binding]; other site 228405008110 G-X-G motif; other site 228405008111 aminopeptidase N; Provisional; Region: pepN; PRK14015 228405008112 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 228405008113 Zn binding site [ion binding]; other site 228405008114 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405008115 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 228405008116 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405008117 active site 228405008118 Protein of unknown function (DUF796); Region: DUF796; cl01226 228405008119 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405008120 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 228405008121 FAD binding site [chemical binding]; other site 228405008122 substrate binding site [chemical binding]; other site 228405008123 catalytic base [active] 228405008124 Protein of unknown function (DUF330); Region: DUF330; cl01135 228405008125 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 228405008126 mce related protein; Region: MCE; pfam02470 228405008127 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 228405008128 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 228405008129 Walker A/P-loop; other site 228405008130 ATP binding site [chemical binding]; other site 228405008131 Q-loop/lid; other site 228405008132 ABC transporter signature motif; other site 228405008133 Walker B; other site 228405008134 D-loop; other site 228405008135 H-loop/switch region; other site 228405008136 STAS domain; Region: STAS_2; pfam13466 228405008137 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 228405008138 Permease; Region: Permease; pfam02405 228405008139 L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of...; Region: L-Ala-DL-Glu_epimerase; cd03319 228405008140 active site 228405008141 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 228405008142 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405008143 Walker A/P-loop; other site 228405008144 ATP binding site [chemical binding]; other site 228405008145 Q-loop/lid; other site 228405008146 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405008147 ABC transporter; Region: ABC_tran_2; pfam12848 228405008148 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 228405008149 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 228405008150 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 228405008151 Coenzyme A binding pocket [chemical binding]; other site 228405008152 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 228405008153 CoenzymeA binding site [chemical binding]; other site 228405008154 subunit interaction site [polypeptide binding]; other site 228405008155 PHB binding site; other site 228405008156 Uncharacterized small membrane protein [Function unknown]; Region: COG2363 228405008157 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 228405008158 Alpha/beta hydrolase of unknown function (DUF1057); Region: DUF1057; pfam06342 228405008159 TAP-like protein; Region: Abhydrolase_4; pfam08386 228405008160 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 228405008161 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 228405008162 Na2 binding site [ion binding]; other site 228405008163 putative substrate binding site 1 [chemical binding]; other site 228405008164 Na binding site 1 [ion binding]; other site 228405008165 putative substrate binding site 2 [chemical binding]; other site 228405008166 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 228405008167 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 228405008168 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 228405008169 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 228405008170 rod shape-determining protein MreC; Provisional; Region: PRK13922 228405008171 rod shape-determining protein MreC; Region: MreC; pfam04085 228405008172 rod shape-determining protein MreB; Provisional; Region: PRK13927 228405008173 MreB and similar proteins; Region: MreB_like; cd10225 228405008174 nucleotide binding site [chemical binding]; other site 228405008175 Mg binding site [ion binding]; other site 228405008176 putative protofilament interaction site [polypeptide binding]; other site 228405008177 RodZ interaction site [polypeptide binding]; other site 228405008178 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 228405008179 Part of AAA domain; Region: AAA_19; pfam13245 228405008180 Family description; Region: UvrD_C_2; pfam13538 228405008181 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 228405008182 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 228405008183 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 228405008184 Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_5_FMN; cd04747 228405008185 putative active site [active] 228405008186 putative FMN binding site [chemical binding]; other site 228405008187 putative substrate binding site [chemical binding]; other site 228405008188 putative catalytic residue [active] 228405008189 Domain of unknown function (DUF4169); Region: DUF4169; pfam13770 228405008190 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 228405008191 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 228405008192 fumarate hydratase; Reviewed; Region: fumC; PRK00485 228405008193 Class II fumarases; Region: Fumarase_classII; cd01362 228405008194 active site 228405008195 tetramer interface [polypeptide binding]; other site 228405008196 Endodeoxyribonuclease RusA; Region: RusA; cl01885 228405008197 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 228405008198 Cytochrome P450; Region: p450; cl12078 228405008199 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 228405008200 Thioesterase-like superfamily; Region: 4HBT_3; pfam13622 228405008201 CoenzymeA binding site [chemical binding]; other site 228405008202 subunit interaction site [polypeptide binding]; other site 228405008203 PHB binding site; other site 228405008204 Stringent starvation protein B; Region: SspB; pfam04386 228405008205 Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; Region: GadB; COG0076 228405008206 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405008207 catalytic residue [active] 228405008208 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 228405008209 phosphonoacetate hydrolase; Region: hydr_PhnA; TIGR02335 228405008210 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 228405008211 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405008212 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405008213 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 228405008214 putative C-terminal domain interface [polypeptide binding]; other site 228405008215 putative GSH binding site (G-site) [chemical binding]; other site 228405008216 putative dimer interface [polypeptide binding]; other site 228405008217 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405008218 N-terminal domain interface [polypeptide binding]; other site 228405008219 dimer interface [polypeptide binding]; other site 228405008220 substrate binding pocket (H-site) [chemical binding]; other site 228405008221 short chain dehydrogenase; Provisional; Region: PRK06914 228405008222 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 228405008223 NADP binding site [chemical binding]; other site 228405008224 active site 228405008225 steroid binding site; other site 228405008226 Zinc dependent phospholipase C/S1-P1 nuclease; Region: ZnPC_S1P1; cl16915 228405008227 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405008228 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405008229 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 228405008230 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 228405008231 GIY-YIG motif/motif A; other site 228405008232 active site 228405008233 catalytic site [active] 228405008234 putative DNA binding site [nucleotide binding]; other site 228405008235 metal binding site [ion binding]; metal-binding site 228405008236 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 228405008237 aspartate aminotransferase; Provisional; Region: PRK05764 228405008238 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 228405008239 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405008240 homodimer interface [polypeptide binding]; other site 228405008241 catalytic residue [active] 228405008242 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 228405008243 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 228405008244 dimerization interface [polypeptide binding]; other site 228405008245 DPS ferroxidase diiron center [ion binding]; other site 228405008246 ion pore; other site 228405008247 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 228405008248 Transcriptional regulator [Transcription]; Region: LysR; COG0583 228405008249 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405008250 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 228405008251 putative effector binding pocket; other site 228405008252 dimerization interface [polypeptide binding]; other site 228405008253 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 228405008254 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405008255 NAD(P) binding site [chemical binding]; other site 228405008256 active site 228405008257 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 228405008258 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 228405008259 NAD(P) binding site [chemical binding]; other site 228405008260 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 228405008261 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405008262 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405008263 Predicted membrane protein [Function unknown]; Region: COG2860 228405008264 UPF0126 domain; Region: UPF0126; pfam03458 228405008265 UPF0126 domain; Region: UPF0126; pfam03458 228405008266 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 228405008267 Predicted P-loop ATPase [General function prediction only]; Region: COG4928 228405008268 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 228405008269 Peptidase family M23; Region: Peptidase_M23; pfam01551 228405008270 Flavin-binding monooxygenase-like; Region: FMO-like; pfam00743 228405008271 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 228405008272 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 228405008273 CoenzymeA binding site [chemical binding]; other site 228405008274 subunit interaction site [polypeptide binding]; other site 228405008275 PHB binding site; other site 228405008276 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 228405008277 CoenzymeA binding site [chemical binding]; other site 228405008278 subunit interaction site [polypeptide binding]; other site 228405008279 PHB binding site; other site 228405008280 Domain of unknown function (DUF4163); Region: DUF4163; pfam13739 228405008281 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 228405008282 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 228405008283 Proline dehydrogenase; Region: Pro_dh; pfam01619 228405008284 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 228405008285 Glutamate binding site [chemical binding]; other site 228405008286 NAD binding site [chemical binding]; other site 228405008287 catalytic residues [active] 228405008288 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 228405008289 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 228405008290 PBP superfamily domain; Region: PBP_like_2; cl17296 228405008291 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 228405008292 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase; Region: PLPDE_III_ODC; cd00622 228405008293 dimer interface [polypeptide binding]; other site 228405008294 active site 228405008295 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 228405008296 catalytic residues [active] 228405008297 substrate binding site [chemical binding]; other site 228405008298 glutamate racemase; Provisional; Region: PRK00865 228405008299 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 228405008300 SnoaL-like domain; Region: SnoaL_2; pfam12680 228405008301 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 228405008302 TPP-binding site [chemical binding]; other site 228405008303 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 228405008304 PYR/PP interface [polypeptide binding]; other site 228405008305 dimer interface [polypeptide binding]; other site 228405008306 TPP binding site [chemical binding]; other site 228405008307 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 228405008308 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 228405008309 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405008310 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405008311 metal binding site [ion binding]; metal-binding site 228405008312 active site 228405008313 I-site; other site 228405008314 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 228405008315 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 228405008316 putative active site; other site 228405008317 catalytic triad [active] 228405008318 putative dimer interface [polypeptide binding]; other site 228405008319 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 228405008320 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 228405008321 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 228405008322 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405008323 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 228405008324 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; pfam13231 228405008325 Peptide methionine sulfoxide reductase; Region: PMSR; pfam01625 228405008326 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 228405008327 Transglycosylase; Region: Transgly; pfam00912 228405008328 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 228405008329 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 228405008330 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 228405008331 MG2 domain; Region: A2M_N; pfam01835 228405008332 Alpha-2-macroglobulin family; Region: A2M; pfam00207 228405008333 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 228405008334 surface patch; other site 228405008335 thioester region; other site 228405008336 specificity defining residues; other site 228405008337 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 228405008338 putative NAD(P) binding site [chemical binding]; other site 228405008339 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405008340 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 228405008341 binding surface 228405008342 TPR motif; other site 228405008343 TPR repeat; Region: TPR_11; pfam13414 228405008344 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 228405008345 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 228405008346 interface (dimer of trimers) [polypeptide binding]; other site 228405008347 Substrate-binding/catalytic site; other site 228405008348 Zn-binding sites [ion binding]; other site 228405008349 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 228405008350 binding surface 228405008351 TPR motif; other site 228405008352 TPR repeat; Region: TPR_11; pfam13414 228405008353 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 228405008354 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405008355 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 228405008356 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 228405008357 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 228405008358 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 228405008359 Walker A motif; other site 228405008360 hexamer interface [polypeptide binding]; other site 228405008361 ATP binding site [chemical binding]; other site 228405008362 Walker B motif; other site 228405008363 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 228405008364 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 228405008365 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 228405008366 Type IV pili component [Cell motility and secretion]; Region: COG5461 228405008367 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 228405008368 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 228405008369 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 228405008370 BON domain; Region: BON; pfam04972 228405008371 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 228405008372 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 228405008373 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 228405008374 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 228405008375 Flp/Fap pilin component; Region: Flp_Fap; cl01585 228405008376 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 228405008377 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 228405008378 TadE-like protein; Region: TadE; pfam07811 228405008379 Vacuole effluxer Atg22 like; Region: ATG22; pfam11700 228405008380 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 228405008381 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 228405008382 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 228405008383 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 228405008384 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 228405008385 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 228405008386 active site 228405008387 homodimer interface [polypeptide binding]; other site 228405008388 cell division protein FtsW; Region: ftsW; TIGR02614 228405008389 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 228405008390 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 228405008391 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 228405008392 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 228405008393 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 228405008394 Mg++ binding site [ion binding]; other site 228405008395 putative catalytic motif [active] 228405008396 putative substrate binding site [chemical binding]; other site 228405008397 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 228405008398 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 228405008399 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 228405008400 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 228405008401 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 228405008402 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 228405008403 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 228405008404 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 228405008405 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 228405008406 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 228405008407 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 228405008408 Cell division protein FtsL; Region: FtsL; cl11433 228405008409 MraW methylase family; Region: Methyltransf_5; cl17771 228405008410 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 228405008411 cell division protein MraZ; Reviewed; Region: PRK00326 228405008412 MraZ protein; Region: MraZ; pfam02381 228405008413 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 228405008414 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 228405008415 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 228405008416 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 228405008417 dimer interface [polypeptide binding]; other site 228405008418 decamer (pentamer of dimers) interface [polypeptide binding]; other site 228405008419 catalytic triad [active] 228405008420 peroxidatic and resolving cysteines [active] 228405008421 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 228405008422 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 228405008423 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 228405008424 dimerization interface [polypeptide binding]; other site 228405008425 phenyl proprionate permease family protein; Region: 2A0127; TIGR00902 228405008426 Transcriptional regulators [Transcription]; Region: MarR; COG1846 228405008427 MarR family; Region: MarR_2; pfam12802 228405008428 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 228405008429 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 228405008430 Coenzyme A binding pocket [chemical binding]; other site 228405008431 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 228405008432 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 228405008433 active site 228405008434 phosphorylation site [posttranslational modification] 228405008435 intermolecular recognition site; other site 228405008436 dimerization interface [polypeptide binding]; other site 228405008437 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 228405008438 Walker A motif; other site 228405008439 ATP binding site [chemical binding]; other site 228405008440 Walker B motif; other site 228405008441 arginine finger; other site 228405008442 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 228405008443 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 228405008444 Glycerate kinase family; Region: Gly_kinase; cl00841 228405008445 Uncharacterized protein conserved in bacteria (DUF2200); Region: DUF2200; pfam09966 228405008446 excinuclease ABC subunit B; Provisional; Region: PRK05298 228405008447 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 228405008448 ATP binding site [chemical binding]; other site 228405008449 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 228405008450 nucleotide binding region [chemical binding]; other site 228405008451 ATP-binding site [chemical binding]; other site 228405008452 Ultra-violet resistance protein B; Region: UvrB; pfam12344 228405008453 UvrB/uvrC motif; Region: UVR; pfam02151 228405008454 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 228405008455 active site 228405008456 NTP binding site [chemical binding]; other site 228405008457 metal binding triad [ion binding]; metal-binding site 228405008458 antibiotic binding site [chemical binding]; other site 228405008459 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 228405008460 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405008461 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 228405008462 N-terminal plug; other site 228405008463 ligand-binding site [chemical binding]; other site 228405008464 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 228405008465 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 228405008466 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405008467 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 228405008468 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 228405008469 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405008470 putative substrate translocation pore; other site 228405008471 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 228405008472 CoenzymeA binding site [chemical binding]; other site 228405008473 subunit interaction site [polypeptide binding]; other site 228405008474 PHB binding site; other site 228405008475 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 228405008476 ABC-2 type transporter; Region: ABC2_membrane; cl17235 228405008477 GcrA cell cycle regulator; Region: GcrA; cl11564 228405008478 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 228405008479 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 228405008480 dimer interface [polypeptide binding]; other site 228405008481 phosphorylation site [posttranslational modification] 228405008482 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 228405008483 ATP binding site [chemical binding]; other site 228405008484 Mg2+ binding site [ion binding]; other site 228405008485 G-X-G motif; other site 228405008486 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 228405008487 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 228405008488 HlyD family secretion protein; Region: HlyD_3; pfam13437 228405008489 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 228405008490 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 228405008491 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 228405008492 active site 228405008493 Zn binding site [ion binding]; other site 228405008494 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 228405008495 catalytic residues [active] 228405008496 dimer interface [polypeptide binding]; other site 228405008497 putative acyltransferase; Provisional; Region: PRK05790 228405008498 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 228405008499 dimer interface [polypeptide binding]; other site 228405008500 active site 228405008501 Uncharacterized protein conserved in bacteria (DUF2332); Region: DUF2332; pfam10094 228405008502 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405008503 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405008504 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 228405008505 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 228405008506 putative DNA binding site [nucleotide binding]; other site 228405008507 putative Zn2+ binding site [ion binding]; other site 228405008508 AsnC family; Region: AsnC_trans_reg; pfam01037 228405008509 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 228405008510 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 228405008511 dimer interface [polypeptide binding]; other site 228405008512 PYR/PP interface [polypeptide binding]; other site 228405008513 TPP binding site [chemical binding]; other site 228405008514 substrate binding site [chemical binding]; other site 228405008515 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 228405008516 TPP-binding site; other site 228405008517 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 228405008518 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 228405008519 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405008520 active site 228405008521 nucleotide binding site [chemical binding]; other site 228405008522 HIGH motif; other site 228405008523 KMSKS motif; other site 228405008524 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 228405008525 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 228405008526 non-specific DNA binding site [nucleotide binding]; other site 228405008527 salt bridge; other site 228405008528 sequence-specific DNA binding site [nucleotide binding]; other site 228405008529 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 228405008530 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 228405008531 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 228405008532 heme binding site [chemical binding]; other site 228405008533 ferroxidase pore; other site 228405008534 ferroxidase diiron center [ion binding]; other site 228405008535 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 228405008536 Protein of unknown function (DUF2853); Region: DUF2853; pfam11015 228405008537 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405008538 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405008539 active site 228405008540 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405008541 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405008542 active site 228405008543 photolyase PhrII; Region: phr2; TIGR00591 228405008544 DNA photolyase; Region: DNA_photolyase; pfam00875 228405008545 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 228405008546 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 228405008547 catalytic core [active] 228405008548 two-component response regulator; Provisional; Region: PRK09191 228405008549 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 228405008550 active site 228405008551 phosphorylation site [posttranslational modification] 228405008552 intermolecular recognition site; other site 228405008553 dimerization interface [polypeptide binding]; other site 228405008554 PAS fold; Region: PAS_4; pfam08448 228405008555 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405008556 putative active site [active] 228405008557 heme pocket [chemical binding]; other site 228405008558 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 228405008559 HWE histidine kinase; Region: HWE_HK; smart00911 228405008560 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 228405008561 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 228405008562 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 228405008563 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 228405008564 EamA-like transporter family; Region: EamA; pfam00892 228405008565 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405008566 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 228405008567 Walker A/P-loop; other site 228405008568 ATP binding site [chemical binding]; other site 228405008569 Q-loop/lid; other site 228405008570 ABC transporter signature motif; other site 228405008571 Walker B; other site 228405008572 D-loop; other site 228405008573 H-loop/switch region; other site 228405008574 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 228405008575 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 228405008576 homodimer interface [polypeptide binding]; other site 228405008577 substrate-cofactor binding pocket; other site 228405008578 catalytic residue [active] 228405008579 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 228405008580 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 228405008581 putative DNA binding site [nucleotide binding]; other site 228405008582 putative Zn2+ binding site [ion binding]; other site 228405008583 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405008584 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 228405008585 active site 228405008586 phosphorylation site [posttranslational modification] 228405008587 intermolecular recognition site; other site 228405008588 dimerization interface [polypeptide binding]; other site 228405008589 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 228405008590 DNA binding site [nucleotide binding] 228405008591 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405008592 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 228405008593 ATP binding site [chemical binding]; other site 228405008594 Mg2+ binding site [ion binding]; other site 228405008595 G-X-G motif; other site 228405008596 Predicted amidohydrolase [General function prediction only]; Region: COG0388 228405008597 Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases); Region: nitrilase_Rim1_like; cd07574 228405008598 putative active site [active] 228405008599 catalytic triad [active] 228405008600 putative dimer interface [polypeptide binding]; other site 228405008601 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 228405008602 aromatic arch; other site 228405008603 DCoH dimer interaction site [polypeptide binding]; other site 228405008604 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 228405008605 DCoH tetramer interaction site [polypeptide binding]; other site 228405008606 substrate binding site [chemical binding]; other site 228405008607 epoxide hydrolase N-terminal domain-like phosphatase; Region: HAD-1A3-hyp; TIGR02247 228405008608 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 228405008609 motif II; other site 228405008610 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405008611 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 228405008612 NAD(P) binding site [chemical binding]; other site 228405008613 active site 228405008614 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405008615 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405008616 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405008617 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 228405008618 Transglycosylase; Region: Transgly; cl17702 228405008619 epoxyqueuosine reductase; Region: TIGR00276 228405008620 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 228405008621 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405008622 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 228405008623 C-terminal domain interface [polypeptide binding]; other site 228405008624 GSH binding site (G-site) [chemical binding]; other site 228405008625 dimer interface [polypeptide binding]; other site 228405008626 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 228405008627 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 228405008628 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 228405008629 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 228405008630 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 228405008631 NAD binding site [chemical binding]; other site 228405008632 catalytic residues [active] 228405008633 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 228405008634 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405008635 putative C-terminal domain interface [polypeptide binding]; other site 228405008636 putative GSH binding site (G-site) [chemical binding]; other site 228405008637 putative dimer interface [polypeptide binding]; other site 228405008638 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 228405008639 N-terminal domain interface [polypeptide binding]; other site 228405008640 dimer interface [polypeptide binding]; other site 228405008641 substrate binding pocket (H-site) [chemical binding]; other site 228405008642 Dystroglycan-type cadherin-like domains; Region: CADG; smart00736 228405008643 Cadherin tandem repeat domain; Region: Cadherin_repeat; cd11304 228405008644 Ca2+ binding site [ion binding]; other site 228405008645 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 228405008646 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 228405008647 putative substrate translocation pore; other site 228405008648 ribosomal protein S6 modification protein; Provisional; Region: PRK10446 228405008649 ATP-grasp domain; Region: ATP-grasp_4; cl17255 228405008650 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 228405008651 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 228405008652 B12 binding site [chemical binding]; other site 228405008653 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 228405008654 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 228405008655 homodimer interface [polypeptide binding]; other site 228405008656 substrate-cofactor binding pocket; other site 228405008657 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405008658 catalytic residue [active] 228405008659 crotonyl-CoA reductase; Region: crotonyl_coA_red; cd08246 228405008660 crotonyl-CoA reductase; Region: crot-CoA-red; TIGR01751 228405008661 putative NAD(P) binding site [chemical binding]; other site 228405008662 SnoaL-like domain; Region: SnoaL_2; pfam12680 228405008663 AAA domain; Region: AAA_17; pfam13207 228405008664 AAA domain; Region: AAA_18; pfam13238 228405008665 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 228405008666 MarR family; Region: MarR_2; pfam12802 228405008667 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 228405008668 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 228405008669 GDP-binding site [chemical binding]; other site 228405008670 ACT binding site; other site 228405008671 IMP binding site; other site 228405008672 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 228405008673 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 228405008674 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 228405008675 ligand binding site [chemical binding]; other site 228405008676 NAD binding site [chemical binding]; other site 228405008677 dimerization interface [polypeptide binding]; other site 228405008678 catalytic site [active] 228405008679 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 228405008680 putative L-serine binding site [chemical binding]; other site 228405008681 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 228405008682 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 228405008683 Coenzyme A binding pocket [chemical binding]; other site 228405008684 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cd01494 228405008685 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 228405008686 catalytic residue [active] 228405008687 YhhN-like protein; Region: YhhN; pfam07947 228405008688 Uncharacterized conserved protein [Function unknown]; Region: COG3339 228405008689 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405008690 NAD(P) binding site [chemical binding]; other site 228405008691 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 228405008692 active site 228405008693 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 228405008694 putative FMN binding site [chemical binding]; other site 228405008695 acetyl-CoA acetyltransferase; Provisional; Region: PRK06504 228405008696 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 228405008697 dimer interface [polypeptide binding]; other site 228405008698 active site 228405008699 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 228405008700 putative active site [active] 228405008701 putative catalytic site [active] 228405008702 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 228405008703 metal ion-dependent adhesion site (MIDAS); other site 228405008704 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 228405008705 Fatty acid desaturase; Region: FA_desaturase; pfam00487 228405008706 Di-iron ligands [ion binding]; other site 228405008707 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 228405008708 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 228405008709 FeS/SAM binding site; other site 228405008710 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 228405008711 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 228405008712 motif 1; other site 228405008713 dimer interface [polypeptide binding]; other site 228405008714 active site 228405008715 motif 2; other site 228405008716 motif 3; other site 228405008717 elongation factor P; Validated; Region: PRK00529 228405008718 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 228405008719 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 228405008720 RNA binding site [nucleotide binding]; other site 228405008721 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 228405008722 RNA binding site [nucleotide binding]; other site 228405008723 PilZ domain; Region: PilZ; pfam07238 228405008724 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405008725 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 228405008726 active site 228405008727 phosphorylation site [posttranslational modification] 228405008728 intermolecular recognition site; other site 228405008729 dimerization interface [polypeptide binding]; other site 228405008730 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 228405008731 DNA binding site [nucleotide binding] 228405008732 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405008733 PAS fold; Region: PAS_3; pfam08447 228405008734 putative active site [active] 228405008735 heme pocket [chemical binding]; other site 228405008736 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405008737 PAS domain; Region: PAS_9; pfam13426 228405008738 putative active site [active] 228405008739 heme pocket [chemical binding]; other site 228405008740 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 228405008741 PAS fold; Region: PAS_3; pfam08447 228405008742 putative active site [active] 228405008743 heme pocket [chemical binding]; other site 228405008744 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405008745 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 228405008746 dimer interface [polypeptide binding]; other site 228405008747 phosphorylation site [posttranslational modification] 228405008748 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 228405008749 ATP binding site [chemical binding]; other site 228405008750 Mg2+ binding site [ion binding]; other site 228405008751 G-X-G motif; other site 228405008752 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 228405008753 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 228405008754 active site 228405008755 phosphorylation site [posttranslational modification] 228405008756 intermolecular recognition site; other site 228405008757 dimerization interface [polypeptide binding]; other site 228405008758 two-component response regulator; Provisional; Region: PRK09191 228405008759 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; cd00190 228405008760 active site 228405008761 substrate binding sites [chemical binding]; other site 228405008762 nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of...; Region: nylC_like; cd02252 228405008763 putative active site pocket [active] 228405008764 cleavage site 228405008765 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 228405008766 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 228405008767 thymidine kinase; Provisional; Region: PRK04296 228405008768 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 228405008769 active site residue [active] 228405008770 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 228405008771 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 228405008772 FAD binding pocket [chemical binding]; other site 228405008773 FAD binding motif [chemical binding]; other site 228405008774 phosphate binding motif [ion binding]; other site 228405008775 beta-alpha-beta structure motif; other site 228405008776 NAD binding pocket [chemical binding]; other site 228405008777 Ion transport protein; Region: Ion_trans; pfam00520 228405008778 TPR/MLP1/MLP2-like protein; Region: TPR_MLP1_2; pfam07926 228405008779 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 228405008780 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 228405008781 putative catalytic residue [active] 228405008782 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 228405008783 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 228405008784 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 228405008785 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 228405008786 DsbD alpha interface [polypeptide binding]; other site 228405008787 catalytic residues [active] 228405008788 SapC; Region: SapC; pfam07277 228405008789 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 228405008790 Protein of unknown function (DUF2794); Region: DUF2794; pfam10984 228405008791 rpsU-divergently transcribed protein; Region: diverge_rpsU; TIGR02396 228405008792 COQ9; Region: COQ9; pfam08511 228405008793 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 228405008794 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 228405008795 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 228405008796 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405008797 Walker A/P-loop; other site 228405008798 ATP binding site [chemical binding]; other site 228405008799 Q-loop/lid; other site 228405008800 ABC transporter signature motif; other site 228405008801 Walker B; other site 228405008802 D-loop; other site 228405008803 H-loop/switch region; other site 228405008804 Bacterial aa3 type cytochrome c oxidase subunit IV; Region: COX4_pro_2; pfam07835 228405008805 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 228405008806 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 228405008807 GSH binding site [chemical binding]; other site 228405008808 catalytic residues [active] 228405008809 comF family protein; Region: comF; TIGR00201 228405008810 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 228405008811 active site 228405008812 Methyltransferase domain; Region: Methyltransf_11; pfam08241 228405008813 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 228405008814 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 228405008815 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 228405008816 active site 228405008817 8-oxo-dGMP binding site [chemical binding]; other site 228405008818 nudix motif; other site 228405008819 metal binding site [ion binding]; metal-binding site 228405008820 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 228405008821 heterotetramer interface [polypeptide binding]; other site 228405008822 active site pocket [active] 228405008823 cleavage site 228405008824 SurA N-terminal domain; Region: SurA_N_3; cl07813 228405008825 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 228405008826 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 228405008827 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 228405008828 SEC-C motif; Region: SEC-C; pfam02810 228405008829 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 228405008830 EamA-like transporter family; Region: EamA; pfam00892 228405008831 EamA-like transporter family; Region: EamA; pfam00892 228405008832 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 228405008833 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 228405008834 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 228405008835 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 228405008836 Phosphoglycerate kinase; Region: PGK; pfam00162 228405008837 substrate binding site [chemical binding]; other site 228405008838 hinge regions; other site 228405008839 ADP binding site [chemical binding]; other site 228405008840 catalytic site [active] 228405008841 fructose-1,6-bisphosphate aldolase; Reviewed; Region: PRK05377 228405008842 catalytic residue [active] 228405008843 Transcription factor zinc-finger; Region: zf-TFIIB; cl01565 228405008844 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3813 228405008845 Protein of unknown function (DUF1272); Region: DUF1272; pfam06906 228405008846 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 228405008847 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 228405008848 thiamine phosphate binding site [chemical binding]; other site 228405008849 active site 228405008850 pyrophosphate binding site [ion binding]; other site 228405008851 Domain of unknown function (DUF4282); Region: DUF4282; pfam14110 228405008852 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 228405008853 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 228405008854 active site 228405008855 dimerization interface [polypeptide binding]; other site 228405008856 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 228405008857 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 228405008858 Helix-turn-helix domain; Region: HTH_28; pfam13518 228405008859 Winged helix-turn helix; Region: HTH_29; pfam13551 228405008860 Homeodomain-like domain; Region: HTH_32; pfam13565 228405008861 Integrase core domain; Region: rve; pfam00665 228405008862 Integrase core domain; Region: rve_3; pfam13683 228405008863 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 228405008864 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 228405008865 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405008866 Walker A/P-loop; other site 228405008867 ATP binding site [chemical binding]; other site 228405008868 Q-loop/lid; other site 228405008869 ABC transporter signature motif; other site 228405008870 Walker B; other site 228405008871 D-loop; other site 228405008872 H-loop/switch region; other site 228405008873 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 228405008874 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 228405008875 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 228405008876 Probable Catalytic site; other site 228405008877 metal-binding site 228405008878 O-Antigen ligase; Region: Wzy_C; pfam04932 228405008879 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 228405008880 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 228405008881 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 228405008882 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 228405008883 active site 228405008884 dimer interface [polypeptide binding]; other site 228405008885 motif 1; other site 228405008886 motif 2; other site 228405008887 motif 3; other site 228405008888 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 228405008889 anticodon binding site; other site 228405008890 hypothetical protein; Validated; Region: PRK00041 228405008891 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 228405008892 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 228405008893 trimerization site [polypeptide binding]; other site 228405008894 active site 228405008895 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 228405008896 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 228405008897 catalytic core [active] 228405008898 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 228405008899 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405008900 active site 228405008901 HIGH motif; other site 228405008902 nucleotide binding site [chemical binding]; other site 228405008903 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 228405008904 KMSKS motif; other site 228405008905 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 228405008906 tRNA binding surface [nucleotide binding]; other site 228405008907 anticodon binding site; other site 228405008908 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 228405008909 GTP cyclohydrolase I; Provisional; Region: PLN03044 228405008910 active site 228405008911 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 228405008912 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 228405008913 homodimer interface [polypeptide binding]; other site 228405008914 substrate-cofactor binding pocket; other site 228405008915 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405008916 catalytic residue [active] 228405008917 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405008918 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 228405008919 putative active site [active] 228405008920 Ap4A binding site [chemical binding]; other site 228405008921 nudix motif; other site 228405008922 putative metal binding site [ion binding]; other site 228405008923 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 228405008924 NodB motif; other site 228405008925 putative active site [active] 228405008926 putative catalytic site [active] 228405008927 Zn binding site [ion binding]; other site 228405008928 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 228405008929 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 228405008930 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 228405008931 protein binding site [polypeptide binding]; other site 228405008932 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 228405008933 Catalytic dyad [active] 228405008934 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 228405008935 Peptidase family M23; Region: Peptidase_M23; pfam01551 228405008936 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 228405008937 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 228405008938 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 228405008939 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 228405008940 Uncharacterized conserved protein [Function unknown]; Region: COG1359 228405008941 malate dehydrogenase; Reviewed; Region: PRK06223 228405008942 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 228405008943 NAD(P) binding site [chemical binding]; other site 228405008944 dimer interface [polypeptide binding]; other site 228405008945 tetramer (dimer of dimers) interface [polypeptide binding]; other site 228405008946 substrate binding site [chemical binding]; other site 228405008947 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 228405008948 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 228405008949 Protein of unknown function (DUF2853); Region: DUF2853; pfam11015 228405008950 2'-5' RNA ligase; Region: 2_5_ligase; TIGR02258 228405008951 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 228405008952 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 228405008953 Exopolysaccharide synthesis, ExoD; Region: ExoD; pfam06055 228405008954 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 228405008955 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 228405008956 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405008957 active site 228405008958 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 228405008959 porphobilinogen deaminase; Region: hemC; TIGR00212 228405008960 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 228405008961 domain interfaces; other site 228405008962 active site 228405008963 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 228405008964 active site 228405008965 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 228405008966 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 228405008967 C factor cell-cell signaling protein; Provisional; Region: PRK09009 228405008968 NADP binding site [chemical binding]; other site 228405008969 homodimer interface [polypeptide binding]; other site 228405008970 active site 228405008971 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 228405008972 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 228405008973 dimer interface [polypeptide binding]; other site 228405008974 substrate binding site [chemical binding]; other site 228405008975 ATP binding site [chemical binding]; other site 228405008976 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 228405008977 active site 228405008978 intersubunit interactions; other site 228405008979 catalytic residue [active] 228405008980 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 228405008981 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 228405008982 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 228405008983 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 228405008984 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405008985 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 228405008986 putative C-terminal domain interface [polypeptide binding]; other site 228405008987 putative GSH binding site (G-site) [chemical binding]; other site 228405008988 putative dimer interface [polypeptide binding]; other site 228405008989 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 228405008990 dimer interface [polypeptide binding]; other site 228405008991 N-terminal domain interface [polypeptide binding]; other site 228405008992 putative substrate binding pocket (H-site) [chemical binding]; other site 228405008993 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 228405008994 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 228405008995 active site 228405008996 substrate binding site [chemical binding]; other site 228405008997 metal binding site [ion binding]; metal-binding site 228405008998 Surface antigen; Region: Surface_Ag_2; pfam01617 228405008999 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 228405009000 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 228405009001 catalytic triad [active] 228405009002 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 228405009003 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 228405009004 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 228405009005 Walker A/P-loop; other site 228405009006 ATP binding site [chemical binding]; other site 228405009007 Q-loop/lid; other site 228405009008 ABC transporter signature motif; other site 228405009009 Walker B; other site 228405009010 D-loop; other site 228405009011 H-loop/switch region; other site 228405009012 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 228405009013 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 228405009014 Iron-sulfur protein interface; other site 228405009015 proximal quinone binding site [chemical binding]; other site 228405009016 SdhD (CybS) interface [polypeptide binding]; other site 228405009017 proximal heme binding site [chemical binding]; other site 228405009018 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 228405009019 putative SdhC subunit interface [polypeptide binding]; other site 228405009020 putative proximal heme binding site [chemical binding]; other site 228405009021 putative Iron-sulfur protein interface [polypeptide binding]; other site 228405009022 putative proximal quinone binding site; other site 228405009023 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 228405009024 L-aspartate oxidase; Provisional; Region: PRK06175 228405009025 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 228405009026 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 228405009027 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 228405009028 catalytic loop [active] 228405009029 iron binding site [ion binding]; other site 228405009030 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405009031 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405009032 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405009033 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 228405009034 active site 228405009035 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14190 228405009036 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 228405009037 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 228405009038 homodimer interface [polypeptide binding]; other site 228405009039 NADP binding site [chemical binding]; other site 228405009040 substrate binding site [chemical binding]; other site 228405009041 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 228405009042 YGGT family; Region: YGGT; pfam02325 228405009043 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 228405009044 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405009045 putative substrate translocation pore; other site 228405009046 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 228405009047 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405009048 putative substrate translocation pore; other site 228405009049 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405009050 short chain dehydrogenase; Validated; Region: PRK07069 228405009051 NAD(P) binding site [chemical binding]; other site 228405009052 active site 228405009053 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06115 228405009054 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 228405009055 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 228405009056 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 228405009057 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 228405009058 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405009059 Coenzyme A binding pocket [chemical binding]; other site 228405009060 PIF1-like helicase; Region: PIF1; pfam05970 228405009061 AAA domain; Region: AAA_30; pfam13604 228405009062 Family description; Region: UvrD_C_2; pfam13538 228405009063 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 228405009064 trimer interface [polypeptide binding]; other site 228405009065 active site 228405009066 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 228405009067 Flavoprotein; Region: Flavoprotein; pfam02441 228405009068 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 228405009069 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405009070 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 228405009071 ABC1 family; Region: ABC1; cl17513 228405009072 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 228405009073 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 228405009074 S-adenosylmethionine binding site [chemical binding]; other site 228405009075 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 228405009076 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 228405009077 DNA binding site [nucleotide binding] 228405009078 catalytic residue [active] 228405009079 H2TH interface [polypeptide binding]; other site 228405009080 putative catalytic residues [active] 228405009081 turnover-facilitating residue; other site 228405009082 intercalation triad [nucleotide binding]; other site 228405009083 8OG recognition residue [nucleotide binding]; other site 228405009084 putative reading head residues; other site 228405009085 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 228405009086 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 228405009087 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 228405009088 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 228405009089 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 228405009090 catalytic motif [active] 228405009091 Catalytic residue [active] 228405009092 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405009093 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405009094 active site 228405009095 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 228405009096 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 228405009097 active site 228405009098 Protein of unknown function (DUF419); Region: DUF419; pfam04237 228405009099 Protein of unknown function (DUF3667); Region: DUF3667; pfam12412 228405009100 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924; Region: LPLAT_ACT14924-like; cd07986 228405009101 putative acyl-acceptor binding pocket; other site 228405009102 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405009103 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 228405009104 active site 228405009105 Homoserine O-succinyltransferase; Region: HTS; pfam04204 228405009106 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 228405009107 proposed active site lysine [active] 228405009108 conserved cys residue [active] 228405009109 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 228405009110 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 228405009111 substrate binding site [chemical binding]; other site 228405009112 oxyanion hole (OAH) forming residues; other site 228405009113 trimer interface [polypeptide binding]; other site 228405009114 Uncharacterized ABC-type transport system, permease components [General function prediction only]; Region: COG3932 228405009115 Protein of unknown function (DUF3088); Region: DUF3088; pfam11287 228405009116 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 228405009117 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 228405009118 FMN binding site [chemical binding]; other site 228405009119 substrate binding site [chemical binding]; other site 228405009120 putative catalytic residue [active] 228405009121 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 228405009122 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 228405009123 active site 228405009124 Zn binding site [ion binding]; other site 228405009125 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 228405009126 active site 228405009127 phosphorylation site [posttranslational modification] 228405009128 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 228405009129 30S subunit binding site; other site 228405009130 Tetratricopeptide repeat; Region: TPR_12; pfam13424 228405009131 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 228405009132 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 228405009133 Walker A motif; other site 228405009134 ATP binding site [chemical binding]; other site 228405009135 Walker B motif; other site 228405009136 arginine finger; other site 228405009137 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 228405009138 phage shock protein A; Region: phageshock_pspA; TIGR02977 228405009139 phage shock protein B; Region: phageshock_pspB; TIGR02976 228405009140 phage shock protein C; Region: phageshock_pspC; TIGR02978 228405009141 PspC domain; Region: PspC; pfam04024 228405009142 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 228405009143 Uncharacterized conserved protein [Function unknown]; Region: COG4121 228405009144 Predicted acetyltransferase [General function prediction only]; Region: COG2388 228405009145 Predicted acetyltransferase [General function prediction only]; Region: COG2388 228405009146 hypothetical protein; Provisional; Region: PRK05170 228405009147 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 228405009148 dimerization interface [polypeptide binding]; other site 228405009149 putative DNA binding site [nucleotide binding]; other site 228405009150 putative Zn2+ binding site [ion binding]; other site 228405009151 Uncharacterized conserved protein [Function unknown]; Region: COG5649 228405009152 Uncharacterized conserved protein [Function unknown]; Region: COG5649 228405009153 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 228405009154 putative hydrophobic ligand binding site [chemical binding]; other site 228405009155 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 228405009156 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 228405009157 active site 228405009158 DNA binding site [nucleotide binding] 228405009159 Int/Topo IB signature motif; other site 228405009160 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 228405009161 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 228405009162 FeS/SAM binding site; other site 228405009163 HemN C-terminal domain; Region: HemN_C; pfam06969 228405009164 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 228405009165 active site 228405009166 dimerization interface [polypeptide binding]; other site 228405009167 Predicted transcriptional regulator [Transcription]; Region: COG3655 228405009168 non-specific DNA binding site [nucleotide binding]; other site 228405009169 salt bridge; other site 228405009170 sequence-specific DNA binding site [nucleotide binding]; other site 228405009171 ribonuclease PH; Reviewed; Region: rph; PRK00173 228405009172 Ribonuclease PH; Region: RNase_PH_bact; cd11362 228405009173 hexamer interface [polypeptide binding]; other site 228405009174 active site 228405009175 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 228405009176 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 228405009177 Potassium binding sites [ion binding]; other site 228405009178 Cesium cation binding sites [ion binding]; other site 228405009179 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 228405009180 GrpE; Region: GrpE; pfam01025 228405009181 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 228405009182 dimer interface [polypeptide binding]; other site 228405009183 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 228405009184 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 228405009185 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 228405009186 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 228405009187 nucleotide binding site [chemical binding]; other site 228405009188 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 228405009189 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 228405009190 NAD(P) binding site [chemical binding]; other site 228405009191 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 228405009192 catalytic nucleophile [active] 228405009193 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 228405009194 anti-sigma factor, putative, ChrR family; Region: anti_sig_ChrR; TIGR02451 228405009195 ChrR Cupin-like domain; Region: Cupin_7; pfam12973 228405009196 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 228405009197 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405009198 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 228405009199 DNA binding residues [nucleotide binding] 228405009200 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 228405009201 ligand binding site [chemical binding]; other site 228405009202 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 228405009203 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 228405009204 FeS/SAM binding site; other site 228405009205 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 228405009206 Predicted periplasmic protein [Function unknown]; Region: COG3698 228405009207 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 228405009208 Uncharacterized conserved protein (DUF2164); Region: DUF2164; cl02278 228405009209 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 228405009210 ArsC family; Region: ArsC; pfam03960 228405009211 Domain of unknown function (DU1801); Region: DUF1801; cl17490 228405009212 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 228405009213 ThiC-associated domain; Region: ThiC-associated; pfam13667 228405009214 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 228405009215 This domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised; Region: FRG; smart00901 228405009216 Flagellin N-methylase; Region: FliB; cl00497 228405009217 Domain of unknown function (DUF4168); Region: DUF4168; pfam13767 228405009218 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 228405009219 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 228405009220 putative active site [active] 228405009221 metal binding site [ion binding]; metal-binding site 228405009222 homodimer binding site [polypeptide binding]; other site 228405009223 Protein of unknown function DUF45; Region: DUF45; pfam01863 228405009224 flagellar motor stator protein MotA; Region: MotA1; TIGR03818 228405009225 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 228405009226 Major Facilitator Superfamily; Region: MFS_1; pfam07690 228405009227 putative substrate translocation pore; other site 228405009228 Transglycosylase SLT domain; Region: SLT_2; pfam13406 228405009229 murein hydrolase B; Provisional; Region: PRK10760; cl17906 228405009230 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 228405009231 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 228405009232 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 228405009233 ?-D-glucose-1-phosphatase; Provisional; Region: PRK09456 228405009234 TPR repeat; Region: TPR_11; pfam13414 228405009235 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 228405009236 TPR motif; other site 228405009237 binding surface 228405009238 TPR repeat; Region: TPR_11; pfam13414 228405009239 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405009240 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 228405009241 catalytic site [active] 228405009242 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; pfam10073 228405009243 short chain dehydrogenase; Validated; Region: PRK06182 228405009244 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405009245 NAD(P) binding site [chemical binding]; other site 228405009246 active site 228405009247 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 228405009248 classical (c) SDRs; Region: SDR_c; cd05233 228405009249 NAD(P) binding site [chemical binding]; other site 228405009250 active site 228405009251 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 228405009252 EamA-like transporter family; Region: EamA; pfam00892 228405009253 EamA-like transporter family; Region: EamA; pfam00892 228405009254 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 228405009255 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405009256 NAD(P) binding site [chemical binding]; other site 228405009257 active site 228405009258 Transcriptional regulators [Transcription]; Region: MarR; COG1846 228405009259 MarR family; Region: MarR_2; cl17246 228405009260 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405009261 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 228405009262 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 228405009263 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 228405009264 heat shock protein HtpX; Provisional; Region: PRK01345 228405009265 NusB family; Region: NusB; pfam01029 228405009266 putative RNA binding site [nucleotide binding]; other site 228405009267 16S rRNA methyltransferase B; Provisional; Region: PRK10901 228405009268 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 228405009269 S-adenosylmethionine binding site [chemical binding]; other site 228405009270 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 228405009271 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 228405009272 substrate binding site [chemical binding]; other site 228405009273 hexamer interface [polypeptide binding]; other site 228405009274 metal binding site [ion binding]; metal-binding site 228405009275 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 228405009276 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 228405009277 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 228405009278 purine monophosphate binding site [chemical binding]; other site 228405009279 dimer interface [polypeptide binding]; other site 228405009280 putative catalytic residues [active] 228405009281 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 228405009282 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 228405009283 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 228405009284 active site 228405009285 catalytic residues [active] 228405009286 metal binding site [ion binding]; metal-binding site 228405009287 enoyl-CoA hydratase; Provisional; Region: PRK06210 228405009288 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 228405009289 substrate binding site [chemical binding]; other site 228405009290 oxyanion hole (OAH) forming residues; other site 228405009291 trimer interface [polypeptide binding]; other site 228405009292 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 228405009293 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405009294 Domain of unknown function (DUF389); Region: DUF389; pfam04087 228405009295 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 228405009296 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 228405009297 active site 228405009298 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 228405009299 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405009300 NAD(P) binding site [chemical binding]; other site 228405009301 active site 228405009302 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 228405009303 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 228405009304 N-terminal plug; other site 228405009305 ligand-binding site [chemical binding]; other site 228405009306 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405009307 PGAP1-like protein; Region: PGAP1; pfam07819 228405009308 TAP-like protein; Region: Abhydrolase_4; pfam08386 228405009309 Putative cyclase; Region: Cyclase; pfam04199 228405009310 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 228405009311 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 228405009312 C-terminal domain interface [polypeptide binding]; other site 228405009313 GSH binding site (G-site) [chemical binding]; other site 228405009314 dimer interface [polypeptide binding]; other site 228405009315 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 228405009316 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 228405009317 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 228405009318 DNA binding site [nucleotide binding] 228405009319 active site 228405009320 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 228405009321 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405009322 dimer interface [polypeptide binding]; other site 228405009323 active site 228405009324 metal binding site [ion binding]; metal-binding site 228405009325 glutathione binding site [chemical binding]; other site 228405009326 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 228405009327 active site 228405009328 zinc-ribbon domain; Region: zinc_ribbon_5; pfam13719 228405009329 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 228405009330 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 228405009331 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 228405009332 Walker A/P-loop; other site 228405009333 ATP binding site [chemical binding]; other site 228405009334 Q-loop/lid; other site 228405009335 ABC transporter signature motif; other site 228405009336 Walker B; other site 228405009337 D-loop; other site 228405009338 H-loop/switch region; other site 228405009339 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 228405009340 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 228405009341 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 228405009342 putative acyl-acceptor binding pocket; other site 228405009343 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 228405009344 endonuclease III; Region: ENDO3c; smart00478 228405009345 minor groove reading motif; other site 228405009346 helix-hairpin-helix signature motif; other site 228405009347 substrate binding pocket [chemical binding]; other site 228405009348 active site 228405009349 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 228405009350 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 228405009351 active site 228405009352 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 228405009353 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 228405009354 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 228405009355 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 228405009356 active site 228405009357 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 228405009358 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 228405009359 Cu(I) binding site [ion binding]; other site 228405009360 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 228405009361 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 228405009362 dimer interface [polypeptide binding]; other site 228405009363 phosphorylation site [posttranslational modification] 228405009364 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 228405009365 ATP binding site [chemical binding]; other site 228405009366 Mg2+ binding site [ion binding]; other site 228405009367 G-X-G motif; other site 228405009368 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 228405009369 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 228405009370 active site 228405009371 phosphorylation site [posttranslational modification] 228405009372 intermolecular recognition site; other site 228405009373 dimerization interface [polypeptide binding]; other site 228405009374 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 228405009375 cyclohexadienyl dehydrogenase; Validated; Region: PRK07502 228405009376 prephenate dehydrogenase; Validated; Region: PRK08507 228405009377 Protein of unknown function (DUF983); Region: DUF983; cl02211 228405009378 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 228405009379 polyhydroxyalkanoate synthesis repressor PhaR; Region: PHA_reg_PhaR; TIGR01848 228405009380 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 228405009381 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 228405009382 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 228405009383 NAD(P) binding site [chemical binding]; other site 228405009384 homotetramer interface [polypeptide binding]; other site 228405009385 homodimer interface [polypeptide binding]; other site 228405009386 active site 228405009387 Cupin superfamily (DUF985); Region: Cupin_5; pfam06172 228405009388 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 228405009389 Methyltransferase domain; Region: Methyltransf_11; pfam08241 228405009390 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 228405009391 Nitrogen regulatory protein P-II; Region: P-II; smart00938 228405009392 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 228405009393 Peptidase family M23; Region: Peptidase_M23; pfam01551 228405009394 Subtilisin-like serine proteases [Posttranslational modification, protein turnover, chaperones]; Region: AprE; COG1404 228405009395 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 228405009396 active site 228405009397 catalytic triad [active] 228405009398 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 228405009399 homodimer interaction site [polypeptide binding]; other site 228405009400 cofactor binding site; other site 228405009401 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 228405009402 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 228405009403 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 228405009404 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 228405009405 ATP binding site [chemical binding]; other site 228405009406 putative Mg++ binding site [ion binding]; other site 228405009407 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 228405009408 nucleotide binding region [chemical binding]; other site 228405009409 ATP-binding site [chemical binding]; other site 228405009410 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 228405009411 RNA binding surface [nucleotide binding]; other site 228405009412 tellurium resistance terB-like protein, subgroup 2; Region: terB_like_2; cd07313 228405009413 putative metal binding site [ion binding]; other site 228405009414 Ferredoxin [Energy production and conversion]; Region: COG1146 228405009415 4Fe-4S binding domain; Region: Fer4; pfam00037 228405009416 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 228405009417 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 228405009418 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405009419 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 228405009420 Sel1 repeat; Region: Sel1; cl02723 228405009421 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405009422 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 228405009423 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 228405009424 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 228405009425 active site 228405009426 Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator; Region: HTH_SoxR; cd01110 228405009427 redox-sensitive transcriptional activator SoxR; Region: SoxR; TIGR01950 228405009428 DNA binding residues [nucleotide binding] 228405009429 dimer interface [polypeptide binding]; other site 228405009430 [2Fe-2S] cluster binding site [ion binding]; other site 228405009431 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 228405009432 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 228405009433 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 228405009434 acyl-activating enzyme (AAE) consensus motif; other site 228405009435 acyl-activating enzyme (AAE) consensus motif; other site 228405009436 putative AMP binding site [chemical binding]; other site 228405009437 putative active site [active] 228405009438 putative CoA binding site [chemical binding]; other site 228405009439 Protein of unknown function (DUF2785); Region: DUF2785; pfam10978 228405009440 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 228405009441 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 228405009442 putative catalytic cysteine [active] 228405009443 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 228405009444 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 228405009445 active site 228405009446 (T/H)XGH motif; other site 228405009447 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 228405009448 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 228405009449 ATP binding site [chemical binding]; other site 228405009450 substrate interface [chemical binding]; other site 228405009451 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 228405009452 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 228405009453 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 228405009454 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 228405009455 dimerization interface [polypeptide binding]; other site 228405009456 ligand binding site [chemical binding]; other site 228405009457 NADP binding site [chemical binding]; other site 228405009458 catalytic site [active] 228405009459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 228405009460 Bacterial SH3 domain; Region: SH3_4; pfam06347 228405009461 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 228405009462 active site 1 [active] 228405009463 dimer interface [polypeptide binding]; other site 228405009464 active site 2 [active] 228405009465 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 228405009466 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 228405009467 NAD binding site [chemical binding]; other site 228405009468 homotetramer interface [polypeptide binding]; other site 228405009469 homodimer interface [polypeptide binding]; other site 228405009470 substrate binding site [chemical binding]; other site 228405009471 active site 228405009472 hypothetical protein; Provisional; Region: PRK13687 228405009473 Uncharacterized conserved protein [Function unknown]; Region: COG3791 228405009474 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 228405009475 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 228405009476 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 228405009477 active site 228405009478 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 228405009479 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 228405009480 RNase E interface [polypeptide binding]; other site 228405009481 trimer interface [polypeptide binding]; other site 228405009482 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 228405009483 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 228405009484 RNase E interface [polypeptide binding]; other site 228405009485 trimer interface [polypeptide binding]; other site 228405009486 active site 228405009487 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 228405009488 putative nucleic acid binding region [nucleotide binding]; other site 228405009489 G-X-X-G motif; other site 228405009490 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 228405009491 RNA binding site [nucleotide binding]; other site 228405009492 domain interface; other site 228405009493 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 228405009494 16S/18S rRNA binding site [nucleotide binding]; other site 228405009495 S13e-L30e interaction site [polypeptide binding]; other site 228405009496 25S rRNA binding site [nucleotide binding]; other site 228405009497 Protein of unknown function (DUF808); Region: DUF808; cl01002 228405009498 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 228405009499 Transposase; Region: DEDD_Tnp_IS110; pfam01548 228405009500 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 228405009501 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 228405009502 methionine gamma-lyase; Validated; Region: PRK07049 228405009503 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 228405009504 homodimer interface [polypeptide binding]; other site 228405009505 substrate-cofactor binding pocket; other site 228405009506 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405009507 catalytic residue [active] 228405009508 Staphylococcal nuclease homologues; Region: SNc; smart00318 228405009509 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 228405009510 Catalytic site; other site 228405009511 RNA polymerase factor sigma-32; Reviewed; Region: rpoH2; PRK07500 228405009512 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 228405009513 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 228405009514 DNA binding residues [nucleotide binding] 228405009515 Protein of unknown function (DUF1052); Region: DUF1052; cl02197 228405009516 Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the...; Region: BsCS-I_like; cd06109 228405009517 dimer interface [polypeptide binding]; other site 228405009518 Citrate synthase; Region: Citrate_synt; pfam00285 228405009519 active site 228405009520 citrylCoA binding site [chemical binding]; other site 228405009521 oxalacetate/citrate binding site [chemical binding]; other site 228405009522 coenzyme A binding site [chemical binding]; other site 228405009523 catalytic triad [active] 228405009524 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 228405009525 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_2; cd06102 228405009526 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 228405009527 dimer interface [polypeptide binding]; other site 228405009528 active site 228405009529 oxalacetate/citrate binding site [chemical binding]; other site 228405009530 citrylCoA binding site [chemical binding]; other site 228405009531 coenzyme A binding site [chemical binding]; other site 228405009532 catalytic triad [active] 228405009533 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 228405009534 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 228405009535 TPP-binding site [chemical binding]; other site 228405009536 dimer interface [polypeptide binding]; other site 228405009537 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 228405009538 PYR/PP interface [polypeptide binding]; other site 228405009539 dimer interface [polypeptide binding]; other site 228405009540 TPP binding site [chemical binding]; other site 228405009541 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 228405009542 Domain of unknown function (DUF4164); Region: DUF4164; pfam13747 228405009543 Cell division protein ZapA; Region: ZapA; pfam05164 228405009544 Etoposide-induced protein 2.4 (EI24); Region: EI24; cl01126 228405009545 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 228405009546 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 228405009547 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 228405009548 diaminopimelate decarboxylase; Region: lysA; TIGR01048 228405009549 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 228405009550 active site 228405009551 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 228405009552 substrate binding site [chemical binding]; other site 228405009553 catalytic residues [active] 228405009554 dimer interface [polypeptide binding]; other site 228405009555 argininosuccinate lyase; Provisional; Region: PRK00855 228405009556 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 228405009557 active sites [active] 228405009558 tetramer interface [polypeptide binding]; other site 228405009559 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 228405009560 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 228405009561 catalytic residues [active] 228405009562 Micrococcal nuclease (thermonuclease) homologs [DNA replication, recombination, and repair]; Region: COG1525 228405009563 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 228405009564 Catalytic site; other site 228405009565 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK07530 228405009566 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 228405009567 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 228405009568 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 228405009569 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 228405009570 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 228405009571 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 228405009572 Ligand binding site [chemical binding]; other site 228405009573 Electron transfer flavoprotein domain; Region: ETF; pfam01012 228405009574 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 228405009575 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 228405009576 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 228405009577 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 228405009578 substrate binding site [chemical binding]; other site 228405009579 active site 228405009580 catalytic residues [active] 228405009581 heterodimer interface [polypeptide binding]; other site 228405009582 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 228405009583 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 228405009584 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 228405009585 pyridoxal 5'-phosphate binding site [chemical binding]; other site 228405009586 catalytic residue [active] 228405009587 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 228405009588 active site 228405009589 methionine sulfoxide reductase A; Provisional; Region: PRK00058 228405009590 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 228405009591 active site 228405009592 HIGH motif; other site 228405009593 nucleotide binding site [chemical binding]; other site 228405009594 active site 228405009595 KMSKS motif; other site 228405009596 EamA-like transporter family; Region: EamA; pfam00892 228405009597 EamA-like transporter family; Region: EamA; pfam00892 228405009598 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 228405009599 Alkaline phosphatase homologues; Region: alkPPc; smart00098 228405009600 active site 228405009601 dimer interface [polypeptide binding]; other site 228405009602 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 228405009603 non-specific DNA binding site [nucleotide binding]; other site 228405009604 salt bridge; other site 228405009605 sequence-specific DNA binding site [nucleotide binding]; other site 228405009606 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 228405009607 Class III alcohol dehydrogenase; Region: Zn_ADH_class_III; cd08279 228405009608 NAD binding site [chemical binding]; other site 228405009609 catalytic Zn binding site [ion binding]; other site 228405009610 substrate binding site [chemical binding]; other site 228405009611 structural Zn binding site [ion binding]; other site 228405009612 Methyltransferase domain; Region: Methyltransf_24; pfam13578 228405009613 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 228405009614 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 228405009615 quinone interaction residues [chemical binding]; other site 228405009616 active site 228405009617 catalytic residues [active] 228405009618 FMN binding site [chemical binding]; other site 228405009619 substrate binding site [chemical binding]; other site 228405009620 Protein of unknown function (DUF952); Region: DUF952; pfam06108 228405009621 argininosuccinate synthase; Provisional; Region: PRK13820 228405009622 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 228405009623 ANP binding site [chemical binding]; other site 228405009624 Substrate Binding Site II [chemical binding]; other site 228405009625 Substrate Binding Site I [chemical binding]; other site 228405009626 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 228405009627 cobaltochelatase, CobT subunit; Region: CobT; TIGR01651 228405009628 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 228405009629 metal ion-dependent adhesion site (MIDAS); other site 228405009630 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 228405009631 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 228405009632 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 228405009633 CbbQ/NirQ/NorQ C-terminal; Region: CbbQ_C; pfam08406 228405009634 Peptide methionine sulfoxide reductase; Region: PMSR; pfam01625 228405009635 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 228405009636 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 228405009637 active site 228405009638 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 228405009639 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 228405009640 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 228405009641 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 228405009642 RNA binding surface [nucleotide binding]; other site 228405009643 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 228405009644 active site 228405009645 PhoD-like phosphatase; Region: PhoD; pfam09423 228405009646 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 228405009647 putative active site [active] 228405009648 putative metal binding site [ion binding]; other site 228405009649 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 228405009650 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 228405009651 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 228405009652 NAD(P) binding site [chemical binding]; other site 228405009653 active site 228405009654 Protein of unknown function (DUF465); Region: DUF465; cl01070 228405009655 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 228405009656 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 228405009657 metal binding site [ion binding]; metal-binding site 228405009658 active site 228405009659 I-site; other site 228405009660 AIR carboxylase; Region: AIRC; pfam00731 228405009661 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 228405009662 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 228405009663 NAD binding site [chemical binding]; other site 228405009664 ATP-grasp domain; Region: ATP-grasp; pfam02222 228405009665 Creatinine amidohydrolase; Region: Creatininase; pfam02633 228405009666 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 228405009667 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 228405009668 Walker A/P-loop; other site 228405009669 ATP binding site [chemical binding]; other site 228405009670 Q-loop/lid; other site 228405009671 ABC transporter signature motif; other site 228405009672 Walker B; other site 228405009673 D-loop; other site 228405009674 H-loop/switch region; other site 228405009675 gliding motility-associated ABC transporter permease protein GldF; Region: ABC_perm_GldF; TIGR03518 228405009676 ABC-type uncharacterized transport system; Region: ABC_transp_aux; pfam09822 228405009677 Domain of unknown function (DUF4340); Region: DUF4340; pfam14238 228405009678 Protein of unknown function (DUF1223); Region: DUF1223; pfam06764 228405009679 aconitate hydratase; Validated; Region: PRK09277 228405009680 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 228405009681 substrate binding site [chemical binding]; other site 228405009682 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 228405009683 ligand binding site [chemical binding]; other site 228405009684 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 228405009685 substrate binding site [chemical binding]; other site 228405009686 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 228405009687 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 228405009688 Walker A/P-loop; other site 228405009689 ATP binding site [chemical binding]; other site 228405009690 Q-loop/lid; other site 228405009691 ABC transporter signature motif; other site 228405009692 Walker B; other site 228405009693 D-loop; other site 228405009694 H-loop/switch region; other site 228405009695 CcmB protein; Region: CcmB; cl17444 228405009696 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 228405009697 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; Region: dsbE; TIGR00385 228405009698 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 228405009699 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 228405009700 MarR family; Region: MarR_2; pfam12802 228405009701 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 228405009702 nudix motif; other site 228405009703 Intracellular septation protein A; Region: IspA; cl01098 228405009704 EamA-like transporter family; Region: EamA; pfam00892 228405009705 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 228405009706 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 228405009707 active site 228405009708 putative substrate binding pocket [chemical binding]; other site 228405009709 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 228405009710 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 228405009711 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 228405009712 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 228405009713 P loop; other site 228405009714 GTP binding site [chemical binding]; other site 228405009715 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 228405009716 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 228405009717 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 228405009718 FeS/SAM binding site; other site 228405009719 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 228405009720 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 228405009721 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 228405009722 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 228405009723 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 228405009724 putative active site [active] 228405009725 putative catalytic site [active] 228405009726 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal...; Region: FkbR2; cd03451 228405009727 putative active site [active] 228405009728 putative catalytic site [active] 228405009729 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 228405009730 ArsC family; Region: ArsC; pfam03960 228405009731 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 228405009732 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 228405009733 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 228405009734 Coenzyme A binding pocket [chemical binding]; other site 228405009735 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 228405009736 Beta-lactamase; Region: Beta-lactamase; pfam00144 228405009737 Predicted permeases [General function prediction only]; Region: RarD; COG2962 228405009738 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 228405009739 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 228405009740 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 228405009741 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 228405009742 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 228405009743 active site 228405009744 catalytic tetrad [active] 228405009745 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 228405009746 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 228405009747 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 228405009748 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 228405009749 probable ammonium transporter, marine subtype; Region: marine_trans_1; TIGR03644 228405009750 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 228405009751 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 228405009752 Protein of unknown function (DUF971); Region: DUF971; pfam06155 228405009753 Uncharacterized conserved protein [Function unknown]; Region: COG2835 228405009754 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 228405009755 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 228405009756 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 228405009757 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 228405009758 TPR motif; other site 228405009759 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 228405009760 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 228405009761 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 228405009762 putative catalytic site [active] 228405009763 putative phosphate binding site [ion binding]; other site 228405009764 active site 228405009765 metal binding site A [ion binding]; metal-binding site 228405009766 DNA binding site [nucleotide binding] 228405009767 putative AP binding site [nucleotide binding]; other site 228405009768 putative metal binding site B [ion binding]; other site 228405009769 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 228405009770 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 228405009771 active site 228405009772 phosphorylation site [posttranslational modification] 228405009773 intermolecular recognition site; other site 228405009774 dimerization interface [polypeptide binding]; other site 228405009775 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 228405009776 DNA binding site [nucleotide binding] 228405009777 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3786 228405009778 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 228405009779 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 228405009780 catalytic residue [active] 228405009781 Thiamine monophosphate synthase/TENI; Region: TMP-TENI; cl17228 228405009782 Gram-negative porin; Region: Porin_4; pfam13609 228405009783 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 228405009784 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 228405009785 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 228405009786 HIGH motif; other site 228405009787 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 228405009788 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 228405009789 active site 228405009790 KMSKS motif; other site 228405009791 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 228405009792 tRNA binding surface [nucleotide binding]; other site 228405009793 Lipopolysaccharide-assembly; Region: LptE; pfam04390 228405009794 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 228405009795 nucleoid occlusion protein; Region: nucleoid_noc; TIGR04285 228405009796 ParB-like nuclease domain; Region: ParB; smart00470 228405009797 KorB domain; Region: KorB; pfam08535 228405009798 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 228405009799 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405009800 P-loop; other site 228405009801 Magnesium ion binding site [ion binding]; other site 228405009802 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 228405009803 Magnesium ion binding site [ion binding]; other site 228405009804 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 228405009805 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 228405009806 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 228405009807 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 228405009808 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 228405009809 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 228405009810 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 228405009811 trmE is a tRNA modification GTPase; Region: trmE; cd04164 228405009812 G1 box; other site 228405009813 GTP/Mg2+ binding site [chemical binding]; other site 228405009814 Switch I region; other site 228405009815 G2 box; other site 228405009816 Switch II region; other site 228405009817 G3 box; other site 228405009818 G4 box; other site 228405009819 G5 box; other site 228405009820 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 228405009821 transcription termination factor Rho; Provisional; Region: rho; PRK09376 228405009822 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 228405009823 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 228405009824 RNA binding site [nucleotide binding]; other site 228405009825 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 228405009826 multimer interface [polypeptide binding]; other site 228405009827 Walker A motif; other site 228405009828 ATP binding site [chemical binding]; other site 228405009829 Walker B motif; other site 228405009830 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 228405009831 Ferrochelatase; Region: Ferrochelatase; pfam00762 228405009832 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 228405009833 C-terminal domain interface [polypeptide binding]; other site 228405009834 active site 228405009835 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 228405009836 active site 228405009837 N-terminal domain interface [polypeptide binding]; other site 228405009838 uroporphyrinogen decarboxylase; Validated; Region: hemE; PRK00115