-- dump date 20140619_093540 -- class Genbank::misc_feature -- table misc_feature_note -- id note 546269000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 546269000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 546269000003 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 546269000004 Walker A motif; other site 546269000005 ATP binding site [chemical binding]; other site 546269000006 Walker B motif; other site 546269000007 arginine finger; other site 546269000008 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 546269000009 DnaA box-binding interface [nucleotide binding]; other site 546269000010 DNA polymerase III subunit beta; Validated; Region: PRK05643 546269000011 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 546269000012 putative DNA binding surface [nucleotide binding]; other site 546269000013 dimer interface [polypeptide binding]; other site 546269000014 beta-clamp/clamp loader binding surface; other site 546269000015 beta-clamp/translesion DNA polymerase binding surface; other site 546269000016 Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Region: PGDH_2; cd05303 546269000017 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 546269000018 putative ligand binding site [chemical binding]; other site 546269000019 NAD binding site [chemical binding]; other site 546269000020 dimerization interface [polypeptide binding]; other site 546269000021 catalytic site [active] 546269000022 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 546269000023 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 546269000024 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 546269000025 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3580 546269000026 2-hydroxyglutaryl-CoA dehydratase, D-component; Region: HGD-D; pfam06050 546269000027 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3581 546269000028 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269000029 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269000030 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 546269000031 Walker A/P-loop; other site 546269000032 ATP binding site [chemical binding]; other site 546269000033 Q-loop/lid; other site 546269000034 ABC transporter signature motif; other site 546269000035 Walker B; other site 546269000036 D-loop; other site 546269000037 H-loop/switch region; other site 546269000038 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 546269000039 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269000040 FtsX-like permease family; Region: FtsX; pfam02687 546269000041 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 546269000042 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269000043 FtsX-like permease family; Region: FtsX; pfam02687 546269000044 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 546269000045 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 546269000046 HlyD family secretion protein; Region: HlyD_3; pfam13437 546269000047 S4 domain; Region: S4_2; pfam13275 546269000048 recombination protein F; Reviewed; Region: recF; PRK00064 546269000049 ATP-binding cassette domain of RecF; Region: ABC_RecF; cd03242 546269000050 Walker A/P-loop; other site 546269000051 ATP binding site [chemical binding]; other site 546269000052 Q-loop/lid; other site 546269000053 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269000054 ABC transporter signature motif; other site 546269000055 Walker B; other site 546269000056 D-loop; other site 546269000057 H-loop/switch region; other site 546269000058 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 546269000059 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 546269000060 Mg2+ binding site [ion binding]; other site 546269000061 G-X-G motif; other site 546269000062 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 546269000063 anchoring element; other site 546269000064 dimer interface [polypeptide binding]; other site 546269000065 ATP binding site [chemical binding]; other site 546269000066 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 546269000067 active site 546269000068 putative metal-binding site [ion binding]; other site 546269000069 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 546269000070 DNA gyrase subunit A; Validated; Region: PRK05560 546269000071 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 546269000072 CAP-like domain; other site 546269000073 active site 546269000074 primary dimer interface [polypeptide binding]; other site 546269000075 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 546269000076 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 546269000077 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 546269000078 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 546269000079 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 546269000080 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 546269000081 YtxH-like protein; Region: YtxH; pfam12732 546269000082 Bacterial protein of unknown function (DUF948); Region: DUF948; cl01972 546269000083 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 546269000084 anti sigma factor interaction site; other site 546269000085 regulatory phosphorylation site [posttranslational modification]; other site 546269000086 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 546269000087 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 546269000088 ATP binding site [chemical binding]; other site 546269000089 Mg2+ binding site [ion binding]; other site 546269000090 G-X-G motif; other site 546269000091 RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; Region: SigBFG; TIGR02980 546269000092 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 546269000093 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 546269000094 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 546269000095 DNA binding residues [nucleotide binding] 546269000096 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 546269000097 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 546269000098 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 546269000099 active site 546269000100 metal binding site [ion binding]; metal-binding site 546269000101 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 546269000102 putative FMN binding site [chemical binding]; other site 546269000103 NADPH bind site [chemical binding]; other site 546269000104 prolyl-tRNA synthetase; Provisional; Region: PRK09194 546269000105 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 546269000106 dimer interface [polypeptide binding]; other site 546269000107 motif 1; other site 546269000108 active site 546269000109 motif 2; other site 546269000110 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 546269000111 putative deacylase active site [active] 546269000112 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 546269000113 active site 546269000114 motif 3; other site 546269000115 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 546269000116 anticodon binding site; other site 546269000117 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14190 546269000118 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 546269000119 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 546269000120 homodimer interface [polypeptide binding]; other site 546269000121 NADP binding site [chemical binding]; other site 546269000122 substrate binding site [chemical binding]; other site 546269000123 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 546269000124 CRISPR/Cas system-associated protein Cas3'' Region: Cas3''_I; cd09641 546269000125 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 546269000126 CRISPR-associated protein (Cas_Cas5); Region: Cas_Cas5d; pfam09704 546269000127 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I; cl12040 546269000128 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cl12004 546269000129 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 546269000130 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 546269000131 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-C; cd09721 546269000132 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 546269000133 Protein of unknown function (DUF4241); Region: DUF4241; pfam14025 546269000134 Domain of unknown function (DUF4261); Region: DUF4261; pfam14080 546269000135 Domain of unknown function (DUF1877); Region: DUF1877; pfam08974 546269000136 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 546269000137 additional DNA contacts [nucleotide binding]; other site 546269000138 mismatch recognition site; other site 546269000139 active site 546269000140 zinc binding site [ion binding]; other site 546269000141 DNA intercalation site [nucleotide binding]; other site 546269000142 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 546269000143 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 546269000144 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 546269000145 cofactor binding site; other site 546269000146 DNA binding site [nucleotide binding] 546269000147 substrate interaction site [chemical binding]; other site 546269000148 Beta propeller domain; Region: Beta_propel; pfam09826 546269000149 QueT transporter; Region: QueT; pfam06177 546269000150 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 546269000151 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 546269000152 active site 546269000153 HIGH motif; other site 546269000154 dimer interface [polypeptide binding]; other site 546269000155 KMSKS motif; other site 546269000156 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 546269000157 Putative rRNA methylase; Region: rRNA_methylase; pfam06962 546269000158 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 546269000159 EamA-like transporter family; Region: EamA; pfam00892 546269000160 EamA-like transporter family; Region: EamA; pfam00892 546269000161 S-layer homology domain; Region: SLH; pfam00395 546269000162 S-layer homology domain; Region: SLH; pfam00395 546269000163 S-layer homology domain; Region: SLH; pfam00395 546269000164 Caspase domain; Region: Peptidase_C14; pfam00656 546269000165 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 546269000166 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 546269000167 G1 box; other site 546269000168 GTP/Mg2+ binding site [chemical binding]; other site 546269000169 Switch I region; other site 546269000170 G2 box; other site 546269000171 Switch II region; other site 546269000172 G3 box; other site 546269000173 G4 box; other site 546269000174 G5 box; other site 546269000175 [FeFe] hydrogenase H-cluster radical SAM maturase HydG; Region: rSAM_HydG; TIGR03955 546269000176 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 546269000177 FeS/SAM binding site; other site 546269000178 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 546269000179 biotin synthase; Provisional; Region: PRK07094 546269000180 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cl15377 546269000181 FeS/SAM binding site; other site 546269000182 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 546269000183 putative iron-only hydrogenase system regulator; Region: hyd_TM1266; TIGR03959 546269000184 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 546269000185 Domain of unknown function (DUF4304); Region: DUF4304; pfam14137 546269000186 CTP synthetase; Validated; Region: pyrG; PRK05380 546269000187 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 546269000188 Catalytic site [active] 546269000189 active site 546269000190 UTP binding site [chemical binding]; other site 546269000191 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 546269000192 active site 546269000193 putative oxyanion hole; other site 546269000194 catalytic triad [active] 546269000195 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 546269000196 4Fe-4S binding domain; Region: Fer4; pfam00037 546269000197 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 546269000198 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 546269000199 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 546269000200 motif II; other site 546269000201 Predicted membrane protein [Function unknown]; Region: COG2860 546269000202 UPF0126 domain; Region: UPF0126; pfam03458 546269000203 UPF0126 domain; Region: UPF0126; pfam03458 546269000204 Amino acid permease; Region: AA_permease_2; pfam13520 546269000205 Isochorismatase family; Region: Isochorismatase; pfam00857 546269000206 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 546269000207 catalytic triad [active] 546269000208 conserved cis-peptide bond; other site 546269000209 Integrase core domain; Region: rve; pfam00665 546269000210 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269000211 hypothetical protein; Reviewed; Region: PRK00024 546269000212 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 546269000213 MPN+ (JAMM) motif; other site 546269000214 Zinc-binding site [ion binding]; other site 546269000215 rod shape-determining protein MreC; Provisional; Region: PRK13922 546269000216 rod shape-determining protein MreC; Region: MreC; pfam04085 546269000217 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 546269000218 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 546269000219 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 546269000220 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 546269000221 Septum formation inhibitor [Cell division and chromosome partitioning]; Region: MinC; COG0850 546269000222 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 546269000223 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 546269000224 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 546269000225 Switch I; other site 546269000226 Switch II; other site 546269000227 Septum formation topological specificity factor MinE; Region: MinE; cl00538 546269000228 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 546269000229 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 546269000230 Protein of unknown function (DUF3793); Region: DUF3793; pfam12672 546269000231 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 546269000232 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 546269000233 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 546269000234 dimer interface [polypeptide binding]; other site 546269000235 motif 1; other site 546269000236 active site 546269000237 motif 2; other site 546269000238 motif 3; other site 546269000239 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 546269000240 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 546269000241 putative tRNA-binding site [nucleotide binding]; other site 546269000242 B3/4 domain; Region: B3_4; pfam03483 546269000243 tRNA synthetase B5 domain; Region: B5; smart00874 546269000244 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 546269000245 dimer interface [polypeptide binding]; other site 546269000246 motif 1; other site 546269000247 motif 3; other site 546269000248 motif 2; other site 546269000249 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 546269000250 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 546269000251 synthetase active site [active] 546269000252 NTP binding site [chemical binding]; other site 546269000253 metal binding site [ion binding]; metal-binding site 546269000254 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 546269000255 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 546269000256 active site 546269000257 metal binding site [ion binding]; metal-binding site 546269000258 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 546269000259 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 546269000260 CAAX protease self-immunity; Region: Abi; pfam02517 546269000261 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 546269000262 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases; Region: CE4_NodB_like_3; cd10959 546269000263 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 546269000264 NodB motif; other site 546269000265 putative active site [active] 546269000266 putative catalytic site [active] 546269000267 putative Zn binding site [ion binding]; other site 546269000268 diacylglycerol glucosyltransferase; Provisional; Region: PRK13609 546269000269 Monogalactosyldiacylglycerol (MGDG) synthase; Region: MGDG_synth; pfam06925 546269000270 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 546269000271 DNA-binding transcriptional regulator SoxS; Provisional; Region: PRK10219 546269000272 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 546269000273 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3708 546269000274 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 546269000275 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 546269000276 HIGH motif; other site 546269000277 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 546269000278 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 546269000279 active site 546269000280 KMSKS motif; other site 546269000281 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 546269000282 tRNA binding surface [nucleotide binding]; other site 546269000283 carbamate kinase; Reviewed; Region: PRK12686 546269000284 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 546269000285 putative substrate binding site [chemical binding]; other site 546269000286 nucleotide binding site [chemical binding]; other site 546269000287 nucleotide binding site [chemical binding]; other site 546269000288 homodimer interface [polypeptide binding]; other site 546269000289 Protein of unknown function (DUF1021); Region: DUF1021; pfam06257 546269000290 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14614 546269000291 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 546269000292 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 546269000293 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 546269000294 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 546269000295 ATP-grasp domain; Region: ATP-grasp_4; cl17255 546269000296 Domain of unknown function (DUF1934); Region: DUF1934; pfam09148 546269000297 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 546269000298 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 546269000299 Ligand Binding Site [chemical binding]; other site 546269000300 TilS substrate C-terminal domain; Region: TilS_C; smart00977 546269000301 FtsH Extracellular; Region: FtsH_ext; pfam06480 546269000302 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 546269000303 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 546269000304 Walker A motif; other site 546269000305 ATP binding site [chemical binding]; other site 546269000306 Walker B motif; other site 546269000307 arginine finger; other site 546269000308 Peptidase family M41; Region: Peptidase_M41; pfam01434 546269000309 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 546269000310 oligoendopeptidase F; Region: pepF; TIGR00181 546269000311 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_4; cd09609 546269000312 active site 546269000313 Zn binding site [ion binding]; other site 546269000314 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 546269000315 A new structural DNA glycosylase; Region: AlkD_like; cd06561 546269000316 active site 546269000317 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 546269000318 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 546269000319 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 546269000320 C-terminal peptidase (prc); Region: prc; TIGR00225 546269000321 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 546269000322 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 546269000323 Catalytic dyad [active] 546269000324 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 546269000325 Family of unknown function (DUF633); Region: DUF633; pfam04816 546269000326 Uncharacterized conserved protein [Function unknown]; Region: COG0327 546269000327 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 546269000328 RNAse HI family that includes Archaeal RNase HI; Region: RNase_HI_archaeal_like; cd09279 546269000329 RNA/DNA hybrid binding site [nucleotide binding]; other site 546269000330 active site 546269000331 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 546269000332 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 546269000333 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 546269000334 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 546269000335 TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low...; Region: TOPRIM_RNase_M5_like; cd01027 546269000336 putative active site [active] 546269000337 putative metal binding site [ion binding]; other site 546269000338 Domain of unknown function (DUF4093); Region: DUF4093; pfam13331 546269000339 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 546269000340 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 546269000341 S-adenosylmethionine binding site [chemical binding]; other site 546269000342 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 546269000343 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 546269000344 active site 546269000345 putative substrate binding pocket [chemical binding]; other site 546269000346 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 546269000347 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 546269000348 generic binding surface II; other site 546269000349 generic binding surface I; other site 546269000350 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 546269000351 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 546269000352 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 546269000353 substrate binding pocket [chemical binding]; other site 546269000354 chain length determination region; other site 546269000355 substrate-Mg2+ binding site; other site 546269000356 catalytic residues [active] 546269000357 aspartate-rich region 1; other site 546269000358 active site lid residues [active] 546269000359 aspartate-rich region 2; other site 546269000360 Divergent PAP2 family; Region: DUF212; pfam02681 546269000361 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 546269000362 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 546269000363 RNA binding surface [nucleotide binding]; other site 546269000364 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 546269000365 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 546269000366 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 546269000367 Walker A/P-loop; other site 546269000368 ATP binding site [chemical binding]; other site 546269000369 Q-loop/lid; other site 546269000370 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 546269000371 ABC transporter signature motif; other site 546269000372 Walker B; other site 546269000373 D-loop; other site 546269000374 H-loop/switch region; other site 546269000375 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 546269000376 dimer interface [polypeptide binding]; other site 546269000377 ADP-ribose binding site [chemical binding]; other site 546269000378 active site 546269000379 nudix motif; other site 546269000380 metal binding site [ion binding]; metal-binding site 546269000381 YceG-like family; Region: YceG; pfam02618 546269000382 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 546269000383 dimerization interface [polypeptide binding]; other site 546269000384 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 546269000385 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 546269000386 S-adenosylmethionine binding site [chemical binding]; other site 546269000387 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 546269000388 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 546269000389 Peptidase family U32; Region: Peptidase_U32; pfam01136 546269000390 phosphodiesterase; Provisional; Region: PRK12704 546269000391 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 546269000392 Zn2+ binding site [ion binding]; other site 546269000393 Mg2+ binding site [ion binding]; other site 546269000394 NAD-dependent deacetylase; Provisional; Region: PRK00481 546269000395 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 546269000396 NAD+ binding site [chemical binding]; other site 546269000397 substrate binding site [chemical binding]; other site 546269000398 Zn binding site [ion binding]; other site 546269000399 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269000400 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269000401 Integrase core domain; Region: rve; pfam00665 546269000402 AIR carboxylase; Region: AIRC; pfam00731 546269000403 Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]; Region: PurF; COG0034 546269000404 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 546269000405 active site 546269000406 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269000407 active site 546269000408 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 546269000409 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 546269000410 dimerization interface [polypeptide binding]; other site 546269000411 putative ATP binding site [chemical binding]; other site 546269000412 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 546269000413 active site 546269000414 cosubstrate binding site; other site 546269000415 substrate binding site [chemical binding]; other site 546269000416 catalytic site [active] 546269000417 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 546269000418 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 546269000419 purine monophosphate binding site [chemical binding]; other site 546269000420 dimer interface [polypeptide binding]; other site 546269000421 putative catalytic residues [active] 546269000422 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 546269000423 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 546269000424 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 546269000425 ATP-grasp domain; Region: ATP-grasp_4; cl17255 546269000426 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 546269000427 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 546269000428 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 546269000429 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 546269000430 dimerization interface [polypeptide binding]; other site 546269000431 ATP binding site [chemical binding]; other site 546269000432 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 546269000433 dimerization interface [polypeptide binding]; other site 546269000434 ATP binding site [chemical binding]; other site 546269000435 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 546269000436 conserved cys residue [active] 546269000437 aspartate aminotransferase; Provisional; Region: PRK07568 546269000438 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 546269000439 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269000440 homodimer interface [polypeptide binding]; other site 546269000441 catalytic residue [active] 546269000442 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 546269000443 Ligand Binding Site [chemical binding]; other site 546269000444 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269000445 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 546269000446 metal binding site 2 [ion binding]; metal-binding site 546269000447 putative DNA binding helix; other site 546269000448 metal binding site 1 [ion binding]; metal-binding site 546269000449 dimer interface [polypeptide binding]; other site 546269000450 structural Zn2+ binding site [ion binding]; other site 546269000451 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 546269000452 dimerization interface [polypeptide binding]; other site 546269000453 putative DNA binding site [nucleotide binding]; other site 546269000454 putative Zn2+ binding site [ion binding]; other site 546269000455 Heavy-metal-associated domain; Region: HMA; pfam00403 546269000456 metal-binding site [ion binding] 546269000457 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 546269000458 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 546269000459 Soluble P-type ATPase [General function prediction only]; Region: COG4087 546269000460 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 546269000461 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 546269000462 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 546269000463 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 546269000464 delta-lactam-biosynthetic de-N-acetylase; Region: spore_pdaA; TIGR02884 546269000465 Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins; Region: CE4_SmPgdA_like; cd10944 546269000466 NodB motif; other site 546269000467 active site 546269000468 catalytic site [active] 546269000469 Zn binding site [ion binding]; other site 546269000470 GTPase CgtA; Reviewed; Region: obgE; PRK12297 546269000471 GTP1/OBG; Region: GTP1_OBG; pfam01018 546269000472 Obg GTPase; Region: Obg; cd01898 546269000473 G1 box; other site 546269000474 GTP/Mg2+ binding site [chemical binding]; other site 546269000475 Switch I region; other site 546269000476 G2 box; other site 546269000477 G3 box; other site 546269000478 Switch II region; other site 546269000479 G4 box; other site 546269000480 G5 box; other site 546269000481 Domain of unknown function (DUF1967); Region: DUF1967; pfam09269 546269000482 Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly; Region: CRS1_YhbY; smart01103 546269000483 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 546269000484 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 546269000485 nucleotide binding pocket [chemical binding]; other site 546269000486 K-X-D-G motif; other site 546269000487 catalytic site [active] 546269000488 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 546269000489 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 546269000490 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 546269000491 Dimer interface [polypeptide binding]; other site 546269000492 BRCT sequence motif; other site 546269000493 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 546269000494 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 546269000495 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 546269000496 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 546269000497 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 546269000498 GatB domain; Region: GatB_Yqey; smart00845 546269000499 asparagine synthetase AsnA; Provisional; Region: PRK05425 546269000500 motif 1; other site 546269000501 dimer interface [polypeptide binding]; other site 546269000502 active site 546269000503 motif 2; other site 546269000504 motif 3; other site 546269000505 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]; Region: COG4100 546269000506 Aluminium resistance protein; Region: Alum_res; pfam06838 546269000507 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 546269000508 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 546269000509 pyruvate carboxylase; Reviewed; Region: PRK12999 546269000510 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 546269000511 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 546269000512 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 546269000513 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 546269000514 active site 546269000515 catalytic residues [active] 546269000516 metal binding site [ion binding]; metal-binding site 546269000517 homodimer binding site [polypeptide binding]; other site 546269000518 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 546269000519 carboxyltransferase (CT) interaction site; other site 546269000520 biotinylation site [posttranslational modification]; other site 546269000521 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; cl00644 546269000522 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; pfam01996 546269000523 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 546269000524 DHH family; Region: DHH; pfam01368 546269000525 DHHA1 domain; Region: DHHA1; pfam02272 546269000526 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269000527 active site 546269000528 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 546269000529 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 546269000530 Zn2+ binding site [ion binding]; other site 546269000531 Mg2+ binding site [ion binding]; other site 546269000532 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 546269000533 synthetase active site [active] 546269000534 NTP binding site [chemical binding]; other site 546269000535 metal binding site [ion binding]; metal-binding site 546269000536 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 546269000537 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 546269000538 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 546269000539 putative active site [active] 546269000540 dimerization interface [polypeptide binding]; other site 546269000541 putative tRNAtyr binding site [nucleotide binding]; other site 546269000542 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 546269000543 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 546269000544 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 546269000545 dimer interface [polypeptide binding]; other site 546269000546 anticodon binding site; other site 546269000547 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 546269000548 homodimer interface [polypeptide binding]; other site 546269000549 motif 1; other site 546269000550 active site 546269000551 motif 2; other site 546269000552 GAD domain; Region: GAD; pfam02938 546269000553 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 546269000554 active site 546269000555 motif 3; other site 546269000556 Predicted amino acid racemase [Amino acid transport and metabolism]; Region: COG3457 546269000557 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; Region: PLPDE_III_AR_like_1; cd06815 546269000558 dimer interface [polypeptide binding]; other site 546269000559 active site 546269000560 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 546269000561 substrate binding site [chemical binding]; other site 546269000562 catalytic residue [active] 546269000563 Uncharacterized conserved protein [Function unknown]; Region: COG5663 546269000564 gamma-glutamyl kinase; Provisional; Region: PRK05429 546269000565 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 546269000566 nucleotide binding site [chemical binding]; other site 546269000567 homotetrameric interface [polypeptide binding]; other site 546269000568 putative phosphate binding site [ion binding]; other site 546269000569 putative allosteric binding site; other site 546269000570 PUA domain; Region: PUA; pfam01472 546269000571 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 546269000572 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 546269000573 putative catalytic cysteine [active] 546269000574 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 546269000575 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 546269000576 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 546269000577 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK08664 546269000578 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 546269000579 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 546269000580 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269000581 NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase...; Region: NrdH; cd02976 546269000582 catalytic residues [active] 546269000583 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 546269000584 Hpr(Ser) kinase/phosphatase; Region: hpr-ser; TIGR00679 546269000585 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 546269000586 active site 546269000587 homohexamer subunit interaction site [polypeptide binding]; other site 546269000588 Hpr binding site; other site 546269000589 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 546269000590 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13299 546269000591 active site 546269000592 NTP binding site [chemical binding]; other site 546269000593 metal binding triad [ion binding]; metal-binding site 546269000594 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 546269000595 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 546269000596 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 546269000597 Part of AAA domain; Region: AAA_19; pfam13245 546269000598 Family description; Region: UvrD_C_2; pfam13538 546269000599 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 546269000600 trimer interface [polypeptide binding]; other site 546269000601 active site 546269000602 M20 Peptidase Arginine utilization protein, RocB; Region: M20_ArgE_RocB; cd05654 546269000603 putative metal binding site [ion binding]; other site 546269000604 putative dimer interface [polypeptide binding]; other site 546269000605 M18 Peptidase Aminopeptidase I; Region: M18_API; cd05659 546269000606 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 546269000607 oligomer interface [polypeptide binding]; other site 546269000608 putative active site [active] 546269000609 metal binding site [ion binding]; metal-binding site 546269000610 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 546269000611 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269000612 active site 546269000613 uracil-xanthine permease; Region: ncs2; TIGR00801 546269000614 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269000615 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269000616 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269000617 Integrase core domain; Region: rve; pfam00665 546269000618 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 546269000619 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 546269000620 16S rRNA methyltransferase B; Provisional; Region: PRK14902 546269000621 NusB family; Region: NusB; pfam01029 546269000622 putative RNA binding site [nucleotide binding]; other site 546269000623 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 546269000624 S-adenosylmethionine binding site [chemical binding]; other site 546269000625 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14454 546269000626 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 546269000627 FeS/SAM binding site; other site 546269000628 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 546269000629 Protein phosphatase 2C; Region: PP2C; pfam00481 546269000630 active site 546269000631 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 546269000632 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 546269000633 active site 546269000634 ATP binding site [chemical binding]; other site 546269000635 substrate binding site [chemical binding]; other site 546269000636 activation loop (A-loop); other site 546269000637 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 546269000638 PASTA domain; Region: PASTA; smart00740 546269000639 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 546269000640 GTPase RsgA; Reviewed; Region: PRK00098 546269000641 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 546269000642 RNA binding site [nucleotide binding]; other site 546269000643 homodimer interface [polypeptide binding]; other site 546269000644 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 546269000645 GTPase/Zn-binding domain interface [polypeptide binding]; other site 546269000646 GTP/Mg2+ binding site [chemical binding]; other site 546269000647 G4 box; other site 546269000648 G5 box; other site 546269000649 G1 box; other site 546269000650 Switch I region; other site 546269000651 G2 box; other site 546269000652 G3 box; other site 546269000653 Switch II region; other site 546269000654 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 546269000655 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 546269000656 substrate binding site [chemical binding]; other site 546269000657 hexamer interface [polypeptide binding]; other site 546269000658 metal binding site [ion binding]; metal-binding site 546269000659 Thiamine pyrophosphokinase; Region: TPK; cd07995 546269000660 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 546269000661 active site 546269000662 dimerization interface [polypeptide binding]; other site 546269000663 thiamine binding site [chemical binding]; other site 546269000664 Protein of unknown function (DUF1385); Region: DUF1385; pfam07136 546269000665 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 546269000666 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 546269000667 S-adenosylmethionine binding site [chemical binding]; other site 546269000668 peptide chain release factor 1; Validated; Region: prfA; PRK00591 546269000669 This domain is found in peptide chain release factors; Region: PCRF; smart00937 546269000670 RF-1 domain; Region: RF-1; pfam00472 546269000671 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 546269000672 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 546269000673 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 546269000674 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269000675 active site 546269000676 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 546269000677 Protein of unknown function (DUF464); Region: DUF464; pfam04327 546269000678 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 546269000679 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 546269000680 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 546269000681 dimer interface [polypeptide binding]; other site 546269000682 active site 546269000683 glycine-pyridoxal phosphate binding site [chemical binding]; other site 546269000684 folate binding site [chemical binding]; other site 546269000685 Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and...; Region: pyridoxal_pyridoxamine_kinase; cd01173 546269000686 dimer interface [polypeptide binding]; other site 546269000687 pyridoxal binding site [chemical binding]; other site 546269000688 ATP binding site [chemical binding]; other site 546269000689 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 546269000690 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 546269000691 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 546269000692 Walker A motif; other site 546269000693 ATP binding site [chemical binding]; other site 546269000694 Walker B motif; other site 546269000695 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 546269000696 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 546269000697 Walker A motif; other site 546269000698 ATP binding site [chemical binding]; other site 546269000699 Walker B motif; other site 546269000700 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 546269000701 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269000702 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269000703 Integrase core domain; Region: rve; pfam00665 546269000704 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 546269000705 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 546269000706 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 546269000707 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 546269000708 metal ion-dependent adhesion site (MIDAS); other site 546269000709 Cell division protein FtsA; Region: FtsA; cl17206 546269000710 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 546269000711 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 546269000712 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 546269000713 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 546269000714 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 546269000715 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 546269000716 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 546269000717 excinuclease ABC subunit B; Provisional; Region: PRK05298 546269000718 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 546269000719 ATP binding site [chemical binding]; other site 546269000720 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 546269000721 nucleotide binding region [chemical binding]; other site 546269000722 ATP-binding site [chemical binding]; other site 546269000723 Ultra-violet resistance protein B; Region: UvrB; pfam12344 546269000724 UvrB/uvrC motif; Region: UVR; pfam02151 546269000725 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 546269000726 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 546269000727 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 546269000728 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 546269000729 recombination regulator RecX; Reviewed; Region: recX; PRK00117 546269000730 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 546269000731 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 546269000732 G1 box; other site 546269000733 putative GEF interaction site [polypeptide binding]; other site 546269000734 GTP/Mg2+ binding site [chemical binding]; other site 546269000735 Switch I region; other site 546269000736 G2 box; other site 546269000737 G3 box; other site 546269000738 Switch II region; other site 546269000739 G4 box; other site 546269000740 G5 box; other site 546269000741 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 546269000742 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 546269000743 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269000744 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269000745 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 546269000746 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 546269000747 ATP binding site [chemical binding]; other site 546269000748 Mg2+ binding site [ion binding]; other site 546269000749 G-X-G motif; other site 546269000750 DNA gyrase B; Region: DNA_gyraseB; pfam00204 546269000751 ATP binding site [chemical binding]; other site 546269000752 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 546269000753 active site 546269000754 metal binding site [ion binding]; metal-binding site 546269000755 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 546269000756 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 546269000757 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; cl00148 546269000758 CAP-like domain; other site 546269000759 active site 546269000760 primary dimer interface [polypeptide binding]; other site 546269000761 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 546269000762 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt; cl00231 546269000763 ATP binding site [chemical binding]; other site 546269000764 active site 546269000765 substrate binding site [chemical binding]; other site 546269000766 ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; Region: ACT_1ZPV; cd04872 546269000767 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 546269000768 hypothetical protein; Validated; Region: PRK00110 546269000769 Domain of unknown function (DUF3783); Region: DUF3783; pfam12646 546269000770 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 546269000771 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 546269000772 RNA binding surface [nucleotide binding]; other site 546269000773 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 546269000774 active site 546269000775 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 546269000776 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 546269000777 active site 546269000778 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 546269000779 metal binding site 2 [ion binding]; metal-binding site 546269000780 putative DNA binding helix; other site 546269000781 metal binding site 1 [ion binding]; metal-binding site 546269000782 dimer interface [polypeptide binding]; other site 546269000783 structural Zn2+ binding site [ion binding]; other site 546269000784 arginyl-tRNA synthetase; Reviewed; Region: PRK12451 546269000785 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 546269000786 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 546269000787 active site 546269000788 HIGH motif; other site 546269000789 KMSK motif region; other site 546269000790 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 546269000791 tRNA binding surface [nucleotide binding]; other site 546269000792 anticodon binding site; other site 546269000793 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 546269000794 active site 546269000795 DNA binding site [nucleotide binding] 546269000796 Int/Topo IB signature motif; other site 546269000797 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 546269000798 pyruvate kinase; Provisional; Region: PRK06354 546269000799 domain interfaces; other site 546269000800 active site 546269000801 Phosphohistidine swiveling domain [Signal transduction mechanisms]; Region: COG3848 546269000802 6-phosphofructokinase; Provisional; Region: PRK03202 546269000803 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 546269000804 active site 546269000805 ADP/pyrophosphate binding site [chemical binding]; other site 546269000806 dimerization interface [polypeptide binding]; other site 546269000807 allosteric effector site; other site 546269000808 fructose-1,6-bisphosphate binding site; other site 546269000809 DNA polymerase III DnaE; Reviewed; Region: dnaE; PRK06826 546269000810 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 546269000811 active site 546269000812 PHP Thumb interface [polypeptide binding]; other site 546269000813 metal binding site [ion binding]; metal-binding site 546269000814 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 546269000815 generic binding surface I; other site 546269000816 generic binding surface II; other site 546269000817 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 546269000818 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 546269000819 dimerization interface [polypeptide binding]; other site 546269000820 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 546269000821 dimer interface [polypeptide binding]; other site 546269000822 phosphorylation site [posttranslational modification] 546269000823 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 546269000824 ATP binding site [chemical binding]; other site 546269000825 Mg2+ binding site [ion binding]; other site 546269000826 G-X-G motif; other site 546269000827 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 546269000828 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 546269000829 active site 546269000830 phosphorylation site [posttranslational modification] 546269000831 intermolecular recognition site; other site 546269000832 dimerization interface [polypeptide binding]; other site 546269000833 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 546269000834 DNA binding site [nucleotide binding] 546269000835 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 546269000836 DEAD-like helicases superfamily; Region: DEXDc; smart00487 546269000837 ATP binding site [chemical binding]; other site 546269000838 Mg++ binding site [ion binding]; other site 546269000839 motif III; other site 546269000840 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 546269000841 nucleotide binding region [chemical binding]; other site 546269000842 ATP-binding site [chemical binding]; other site 546269000843 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]; Region: COG2509 546269000844 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 546269000845 flavoprotein, HI0933 family; Region: TIGR00275 546269000846 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 546269000847 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 546269000848 Major Facilitator Superfamily; Region: MFS_1; pfam07690 546269000849 putative substrate translocation pore; other site 546269000850 Yqey-like protein; Region: YqeY; pfam09424 546269000851 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 546269000852 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269000853 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269000854 Integrase core domain; Region: rve; pfam00665 546269000855 hypothetical protein; Provisional; Region: PRK05590 546269000856 RNA polymerase sigma factor RpoD; Validated; Region: PRK09210 546269000857 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 546269000858 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 546269000859 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 546269000860 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 546269000861 DNA binding residues [nucleotide binding] 546269000862 DNA primase; Validated; Region: dnaG; PRK05667 546269000863 CHC2 zinc finger; Region: zf-CHC2; pfam01807 546269000864 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 546269000865 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 546269000866 active site 546269000867 metal binding site [ion binding]; metal-binding site 546269000868 interdomain interaction site; other site 546269000869 hypothetical protein; Provisional; Region: PRK04435 546269000870 C-terminal ACT domain of a small (; 147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains; Region: ACT_PheB-BS; cd04888 546269000871 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 546269000872 S-adenosylmethionine binding site [chemical binding]; other site 546269000873 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 546269000874 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 546269000875 RNA binding site [nucleotide binding]; other site 546269000876 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 546269000877 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 546269000878 active site 546269000879 substrate binding site [chemical binding]; other site 546269000880 metal binding site [ion binding]; metal-binding site 546269000881 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4856 546269000882 Uncharacterized conserved protein [Function unknown]; Region: COG1624 546269000883 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 546269000884 Chromate transporter; Region: Chromate_transp; pfam02417 546269000885 Chromate transporter; Region: Chromate_transp; pfam02417 546269000886 TPR repeat; Region: TPR_11; pfam13414 546269000887 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 546269000888 binding surface 546269000889 TPR motif; other site 546269000890 TPR repeat; Region: TPR_11; pfam13414 546269000891 Bacterial SH3 domain; Region: SH3_3; cl17532 546269000892 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269000893 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269000894 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 546269000895 RNA methyltransferase, RsmE family; Region: TIGR00046 546269000896 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 546269000897 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 546269000898 S-adenosylmethionine binding site [chemical binding]; other site 546269000899 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 546269000900 active site 546269000901 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 546269000902 IHF dimer interface [polypeptide binding]; other site 546269000903 IHF - DNA interface [nucleotide binding]; other site 546269000904 N-terminal S-AdoMet dependent methylase domain of Bacillus subtilis YabN and related proteins; Region: YabN_N; cd11723 546269000905 putative SAM binding site [chemical binding]; other site 546269000906 putative homodimer interface [polypeptide binding]; other site 546269000907 recombinase A; Provisional; Region: recA; PRK09354 546269000908 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 546269000909 hexamer interface [polypeptide binding]; other site 546269000910 Walker A motif; other site 546269000911 ATP binding site [chemical binding]; other site 546269000912 Walker B motif; other site 546269000913 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 546269000914 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 546269000915 putative dimer interface [polypeptide binding]; other site 546269000916 putative anticodon binding site; other site 546269000917 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 546269000918 homodimer interface [polypeptide binding]; other site 546269000919 motif 1; other site 546269000920 motif 2; other site 546269000921 active site 546269000922 motif 3; other site 546269000923 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 546269000924 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 546269000925 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 546269000926 active site 546269000927 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 546269000928 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 546269000929 active site 546269000930 HIGH motif; other site 546269000931 KMSKS motif; other site 546269000932 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 546269000933 tRNA binding surface [nucleotide binding]; other site 546269000934 anticodon binding site; other site 546269000935 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 546269000936 dimer interface [polypeptide binding]; other site 546269000937 putative tRNA-binding site [nucleotide binding]; other site 546269000938 Predicted membrane protein, putative toxin regulator [General function prediction only]; Region: PfoR; COG3641 546269000939 Phosphotransferase system, EIIC; Region: PTS_EIIC_2; pfam13303 546269000940 Uncharacterized protein conserved in bacteria containing a pentein-type domain [Function unknown]; Region: COG4874 546269000941 Amidinotransferase; Region: Amidinotransf; pfam02274 546269000942 PemK-like protein; Region: PemK; pfam02452 546269000943 alanine racemase; Reviewed; Region: alr; PRK00053 546269000944 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 546269000945 active site 546269000946 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 546269000947 dimer interface [polypeptide binding]; other site 546269000948 substrate binding site [chemical binding]; other site 546269000949 catalytic residues [active] 546269000950 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 546269000951 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 546269000952 GIY-YIG motif/motif A; other site 546269000953 putative active site [active] 546269000954 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 546269000955 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 546269000956 Walker A/P-loop; other site 546269000957 ATP binding site [chemical binding]; other site 546269000958 Q-loop/lid; other site 546269000959 ABC transporter signature motif; other site 546269000960 Walker B; other site 546269000961 D-loop; other site 546269000962 H-loop/switch region; other site 546269000963 NIL domain; Region: NIL; pfam09383 546269000964 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 546269000965 dimer interface [polypeptide binding]; other site 546269000966 conserved gate region; other site 546269000967 putative PBP binding loops; other site 546269000968 ABC-ATPase subunit interface; other site 546269000969 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 546269000970 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 546269000971 active site 546269000972 (T/H)XGH motif; other site 546269000973 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 546269000974 Zn2+ binding site [ion binding]; other site 546269000975 Mg2+ binding site [ion binding]; other site 546269000976 Transcriptional regulator [Transcription]; Region: LytR; COG1316 546269000977 LytR cell envelope-related transcriptional attenuator; Region: LytR_C; pfam13399 546269000978 Oligomerisation domain; Region: Oligomerisation; pfam02410 546269000979 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 546269000980 Rubredoxin; Region: Rubredoxin; pfam00301 546269000981 iron binding site [ion binding]; other site 546269000982 elongation factor Ts; Provisional; Region: tsf; PRK09377 546269000983 UBA/TS-N domain; Region: UBA; pfam00627 546269000984 Elongation factor TS; Region: EF_TS; pfam00889 546269000985 Elongation factor TS; Region: EF_TS; pfam00889 546269000986 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 546269000987 rRNA interaction site [nucleotide binding]; other site 546269000988 S8 interaction site; other site 546269000989 putative laminin-1 binding site; other site 546269000990 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 546269000991 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 546269000992 RNase E interface [polypeptide binding]; other site 546269000993 trimer interface [polypeptide binding]; other site 546269000994 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 546269000995 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 546269000996 RNase E interface [polypeptide binding]; other site 546269000997 trimer interface [polypeptide binding]; other site 546269000998 active site 546269000999 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 546269001000 putative nucleic acid binding region [nucleotide binding]; other site 546269001001 G-X-X-G motif; other site 546269001002 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 546269001003 RNA binding site [nucleotide binding]; other site 546269001004 domain interface; other site 546269001005 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 546269001006 16S/18S rRNA binding site [nucleotide binding]; other site 546269001007 S13e-L30e interaction site [polypeptide binding]; other site 546269001008 25S rRNA binding site [nucleotide binding]; other site 546269001009 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 546269001010 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 546269001011 active site 546269001012 Riboflavin kinase; Region: Flavokinase; pfam01687 546269001013 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 546269001014 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 546269001015 RNA binding site [nucleotide binding]; other site 546269001016 active site 546269001017 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 546269001018 DHH family; Region: DHH; pfam01368 546269001019 DHHA1 domain; Region: DHHA1; pfam02272 546269001020 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 546269001021 translation initiation factor IF-2; Validated; Region: infB; PRK05306 546269001022 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 546269001023 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 546269001024 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 546269001025 G1 box; other site 546269001026 putative GEF interaction site [polypeptide binding]; other site 546269001027 GTP/Mg2+ binding site [chemical binding]; other site 546269001028 Switch I region; other site 546269001029 G2 box; other site 546269001030 G3 box; other site 546269001031 Switch II region; other site 546269001032 G4 box; other site 546269001033 G5 box; other site 546269001034 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 546269001035 Translation-initiation factor 2; Region: IF-2; pfam11987 546269001036 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 546269001037 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 546269001038 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 546269001039 putative RNA binding cleft [nucleotide binding]; other site 546269001040 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 546269001041 NusA N-terminal domain; Region: NusA_N; pfam08529 546269001042 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 546269001043 RNA binding site [nucleotide binding]; other site 546269001044 homodimer interface [polypeptide binding]; other site 546269001045 NusA-like KH domain; Region: KH_5; pfam13184 546269001046 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 546269001047 G-X-X-G motif; other site 546269001048 ribosome maturation protein RimP; Reviewed; Region: PRK00092 546269001049 Sm and related proteins; Region: Sm_like; cl00259 546269001050 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 546269001051 putative oligomer interface [polypeptide binding]; other site 546269001052 putative RNA binding site [nucleotide binding]; other site 546269001053 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 546269001054 TRA-1 regulated protein R03H10.4; Region: TRA-1_regulated; pfam02343 546269001055 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 546269001056 Type II/IV secretion system protein; Region: T2SE; pfam00437 546269001057 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 546269001058 Walker A motif; other site 546269001059 ATP binding site [chemical binding]; other site 546269001060 Walker B motif; other site 546269001061 Superfamily I DNA and RNA helicases [General function prediction only]; Region: COG3972 546269001062 putative recombination protein RecB; Provisional; Region: PRK13909 546269001063 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 546269001064 ATP cone domain; Region: ATP-cone; pfam03477 546269001065 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 546269001066 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 546269001067 nucleotide binding site [chemical binding]; other site 546269001068 SulA interaction site; other site 546269001069 Protein of unknown function (DUF1290); Region: DUF1290; pfam06947 546269001070 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 546269001071 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3879 546269001072 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 546269001073 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 546269001074 Cell division protein FtsQ; Region: FtsQ; pfam03799 546269001075 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 546269001076 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 546269001077 active site 546269001078 homodimer interface [polypeptide binding]; other site 546269001079 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 546269001080 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK14106 546269001081 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 546269001082 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 546269001083 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 546269001084 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 546269001085 Mg++ binding site [ion binding]; other site 546269001086 putative catalytic motif [active] 546269001087 putative substrate binding site [chemical binding]; other site 546269001088 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 546269001089 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 546269001090 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 546269001091 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 546269001092 stage V sporulation protein D; Region: spoVD_pbp; TIGR02214 546269001093 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 546269001094 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 546269001095 PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis; Region: PASTA_pknB; cd06577 546269001096 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by...; Region: PASTA_Pbp2x-like_2; cd06575 546269001097 MraW methylase family; Region: Methyltransf_5; pfam01795 546269001098 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 546269001099 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK12437 546269001100 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 546269001101 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 546269001102 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 546269001103 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 546269001104 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 546269001105 Bacterial protein of unknown function (DUF896); Region: DUF896; pfam05979 546269001106 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 546269001107 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 546269001108 Ligand Binding Site [chemical binding]; other site 546269001109 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 546269001110 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 546269001111 ligand binding site [chemical binding]; other site 546269001112 dimerization interface [polypeptide binding]; other site 546269001113 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 546269001114 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 546269001115 TM-ABC transporter signature motif; other site 546269001116 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 546269001117 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 546269001118 Walker A/P-loop; other site 546269001119 ATP binding site [chemical binding]; other site 546269001120 Q-loop/lid; other site 546269001121 ABC transporter signature motif; other site 546269001122 Walker B; other site 546269001123 D-loop; other site 546269001124 H-loop/switch region; other site 546269001125 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 546269001126 D-ribose pyranase; Provisional; Region: PRK11797 546269001127 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 546269001128 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 546269001129 substrate binding site [chemical binding]; other site 546269001130 dimer interface [polypeptide binding]; other site 546269001131 ATP binding site [chemical binding]; other site 546269001132 Transcriptional regulators [Transcription]; Region: PurR; COG1609 546269001133 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 546269001134 DNA binding site [nucleotide binding] 546269001135 domain linker motif; other site 546269001136 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 546269001137 dimerization interface [polypeptide binding]; other site 546269001138 ligand binding site [chemical binding]; other site 546269001139 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 546269001140 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 546269001141 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 546269001142 Membrane protein of unknown function; Region: DUF360; pfam04020 546269001143 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 546269001144 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 546269001145 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 546269001146 Ligand Binding Site [chemical binding]; other site 546269001147 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 546269001148 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 546269001149 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 546269001150 catalytic residue [active] 546269001151 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 546269001152 Listerrria innocua Lin0431 is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (DII); Region: Lin0431_like; cd09911 546269001153 trimer interface [polypeptide binding]; other site 546269001154 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 546269001155 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 546269001156 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 546269001157 PhoU domain; Region: PhoU; pfam01895 546269001158 PhoU domain; Region: PhoU; pfam01895 546269001159 Bacterial protein of unknown function (DUF881); Region: DUF881; pfam05949 546269001160 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 546269001161 G1 box; other site 546269001162 GTP/Mg2+ binding site [chemical binding]; other site 546269001163 Switch I region; other site 546269001164 G2 box; other site 546269001165 G3 box; other site 546269001166 Switch II region; other site 546269001167 G4 box; other site 546269001168 G5 box; other site 546269001169 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 546269001170 Found in ATP-dependent protease La (LON); Region: LON; smart00464 546269001171 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 546269001172 Walker A motif; other site 546269001173 ATP binding site [chemical binding]; other site 546269001174 Walker B motif; other site 546269001175 arginine finger; other site 546269001176 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 546269001177 Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins; Region: MATE_SpoVB_like; cd13124 546269001178 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 546269001179 SurA N-terminal domain; Region: SurA_N_3; cl07813 546269001180 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 546269001181 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 546269001182 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 546269001183 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 546269001184 ATP binding site [chemical binding]; other site 546269001185 putative Mg++ binding site [ion binding]; other site 546269001186 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 546269001187 nucleotide binding region [chemical binding]; other site 546269001188 ATP-binding site [chemical binding]; other site 546269001189 TRCF domain; Region: TRCF; pfam03461 546269001190 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 546269001191 putative active site [active] 546269001192 catalytic residue [active] 546269001193 Ribonuclease III family protein [Replication, recombination, and repair]; Region: COG1939 546269001194 active site 546269001195 metal binding site [ion binding]; metal-binding site 546269001196 dimerization interface [polypeptide binding]; other site 546269001197 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 546269001198 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 546269001199 active site 546269001200 HIGH motif; other site 546269001201 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 546269001202 KMSKS motif; other site 546269001203 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 546269001204 tRNA binding surface [nucleotide binding]; other site 546269001205 anticodon binding site; other site 546269001206 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 546269001207 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 546269001208 Ligand Binding Site [chemical binding]; other site 546269001209 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 546269001210 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 546269001211 motif 1; other site 546269001212 active site 546269001213 motif 2; other site 546269001214 motif 3; other site 546269001215 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 546269001216 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 546269001217 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 546269001218 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 546269001219 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 546269001220 Int/Topo IB signature motif; other site 546269001221 Helix-turn-helix domain; Region: HTH_17; cl17695 546269001222 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269001223 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 546269001224 Hypothetical bacterial integral membrane protein (Trep_Strep); Region: Trep_Strep; cl09823 546269001225 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269001226 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 546269001227 Walker A/P-loop; other site 546269001228 ATP binding site [chemical binding]; other site 546269001229 Q-loop/lid; other site 546269001230 ABC transporter signature motif; other site 546269001231 Walker B; other site 546269001232 D-loop; other site 546269001233 H-loop/switch region; other site 546269001234 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001235 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269001236 Walker A/P-loop; other site 546269001237 ATP binding site [chemical binding]; other site 546269001238 Q-loop/lid; other site 546269001239 ABC transporter signature motif; other site 546269001240 Walker B; other site 546269001241 D-loop; other site 546269001242 H-loop/switch region; other site 546269001243 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 546269001244 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269001245 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269001246 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001247 Walker A/P-loop; other site 546269001248 ATP binding site [chemical binding]; other site 546269001249 Q-loop/lid; other site 546269001250 ABC transporter signature motif; other site 546269001251 Walker B; other site 546269001252 D-loop; other site 546269001253 H-loop/switch region; other site 546269001254 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269001255 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269001256 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001257 Walker A/P-loop; other site 546269001258 ATP binding site [chemical binding]; other site 546269001259 Q-loop/lid; other site 546269001260 ABC transporter signature motif; other site 546269001261 Walker B; other site 546269001262 D-loop; other site 546269001263 H-loop/switch region; other site 546269001264 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 546269001265 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 546269001266 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269001267 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269001268 Integrase core domain; Region: rve; pfam00665 546269001269 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 546269001270 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 546269001271 Antirestriction protein (ArdA); Region: ArdA; pfam07275 546269001272 Domain of unknown function (DUF3846); Region: DUF3846; pfam12957 546269001273 Domain of unknown function (DUF4316); Region: DUF4316; pfam14195 546269001274 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 546269001275 MPN+ (JAMM) motif; other site 546269001276 Zinc-binding site [ion binding]; other site 546269001277 RelB antitoxin; Region: RelB; cl01171 546269001278 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 546269001279 Domain of unknown function (DUF4366); Region: DUF4366; pfam14283 546269001280 Domain of unknown function (DUF4315); Region: DUF4315; pfam14193 546269001281 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269001282 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269001283 AAA-like domain; Region: AAA_10; pfam12846 546269001284 Domain of unknown function DUF87; Region: DUF87; pfam01935 546269001285 PrgI family protein; Region: PrgI; pfam12666 546269001286 MT-A70; Region: MT-A70; cl01947 546269001287 Maff2 family; Region: Maff2; pfam12750 546269001288 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 546269001289 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 546269001290 Protein of unknown function (DUF3801); Region: DUF3801; pfam12687 546269001291 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 546269001292 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 546269001293 cofactor binding site; other site 546269001294 DNA binding site [nucleotide binding] 546269001295 substrate interaction site [chemical binding]; other site 546269001296 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 546269001297 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 546269001298 active site 546269001299 metal binding site [ion binding]; metal-binding site 546269001300 interdomain interaction site; other site 546269001301 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269001302 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001303 Walker A/P-loop; other site 546269001304 ATP binding site [chemical binding]; other site 546269001305 Q-loop/lid; other site 546269001306 ABC transporter signature motif; other site 546269001307 Walker B; other site 546269001308 D-loop; other site 546269001309 H-loop/switch region; other site 546269001310 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269001311 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269001312 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001313 Walker A/P-loop; other site 546269001314 ATP binding site [chemical binding]; other site 546269001315 Q-loop/lid; other site 546269001316 ABC transporter signature motif; other site 546269001317 Walker B; other site 546269001318 D-loop; other site 546269001319 H-loop/switch region; other site 546269001320 acetyl coenzyme A synthetase (ADP forming), alpha domain; Region: AcCoA-syn-alpha; TIGR02717 546269001321 CoA binding domain; Region: CoA_binding_2; pfam13380 546269001322 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 546269001323 helix_turn_helix ASNC type; Region: HTH_ASNC; smart00344 546269001324 S-layer homology domain; Region: SLH; pfam00395 546269001325 S-layer homology domain; Region: SLH; pfam00395 546269001326 Family of unknown function (DUF695); Region: DUF695; pfam05117 546269001327 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 546269001328 Uncharacterized protein conserved in bacteria (DUF2262); Region: DUF2262; pfam10020 546269001329 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 546269001330 CRISPR/Cas system-associated protein Csn2; Region: Csn2; cd09644 546269001331 CRISPR type II-A/NMEMI-associated protein Csn2; Region: cas_Csn2; TIGR01866 546269001332 tetramer interface [polypeptide binding]; other site 546269001333 putative DNA binding site [nucleotide binding]; other site 546269001334 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 546269001335 CRISPR/Cas system-associated protein Cas1; Region: Cas1_II; cd09720 546269001336 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; cl00083 546269001337 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; cl00083 546269001338 DNA binding domain of tn916 integrase; Region: Integrase_DNA; pfam02920 546269001339 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 546269001340 Int/Topo IB signature motif; other site 546269001341 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269001342 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269001343 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269001344 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 546269001345 FtsX-like permease family; Region: FtsX; pfam02687 546269001346 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269001347 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 546269001348 Walker A/P-loop; other site 546269001349 ATP binding site [chemical binding]; other site 546269001350 Q-loop/lid; other site 546269001351 ABC transporter signature motif; other site 546269001352 Walker B; other site 546269001353 D-loop; other site 546269001354 H-loop/switch region; other site 546269001355 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 546269001356 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 546269001357 dimer interface [polypeptide binding]; other site 546269001358 phosphorylation site [posttranslational modification] 546269001359 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 546269001360 ATP binding site [chemical binding]; other site 546269001361 Mg2+ binding site [ion binding]; other site 546269001362 G-X-G motif; other site 546269001363 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 546269001364 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 546269001365 active site 546269001366 phosphorylation site [posttranslational modification] 546269001367 intermolecular recognition site; other site 546269001368 dimerization interface [polypeptide binding]; other site 546269001369 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 546269001370 DNA binding site [nucleotide binding] 546269001371 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 546269001372 non-specific DNA binding site [nucleotide binding]; other site 546269001373 salt bridge; other site 546269001374 sequence-specific DNA binding site [nucleotide binding]; other site 546269001375 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 546269001376 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 546269001377 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 546269001378 active site 546269001379 DNA binding site [nucleotide binding] 546269001380 Int/Topo IB signature motif; other site 546269001381 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 546269001382 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 546269001383 generic binding surface II; other site 546269001384 generic binding surface I; other site 546269001385 Uncharacterized conserved protein [Function unknown]; Region: COG4983 546269001386 Methyltransferase domain; Region: Methyltransf_26; pfam13659 546269001387 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 546269001388 DEAD-like helicases superfamily; Region: DEXDc; smart00487 546269001389 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 546269001390 helicase superfamily c-terminal domain; Region: HELICc; smart00490 546269001391 nucleotide binding region [chemical binding]; other site 546269001392 ATP-binding site [chemical binding]; other site 546269001393 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 546269001394 DNA topoisomerase III; Provisional; Region: PRK07726 546269001395 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 546269001396 active site 546269001397 putative interdomain interaction site [polypeptide binding]; other site 546269001398 putative metal-binding site [ion binding]; other site 546269001399 putative nucleotide binding site [chemical binding]; other site 546269001400 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 546269001401 domain I; other site 546269001402 DNA binding groove [nucleotide binding] 546269001403 phosphate binding site [ion binding]; other site 546269001404 domain II; other site 546269001405 domain III; other site 546269001406 nucleotide binding site [chemical binding]; other site 546269001407 catalytic site [active] 546269001408 domain IV; other site 546269001409 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 546269001410 Divergent AAA domain; Region: AAA_4; pfam04326 546269001411 ATP-dependent DNA helicase recG C-terminal; Region: HATPase_c_4; pfam13749 546269001412 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; cl17531 546269001413 Domain of unknown function (DUF4366); Region: DUF4366; pfam14283 546269001414 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269001415 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269001416 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 546269001417 DNA methylase; Region: N6_N4_Mtase; pfam01555 546269001418 AAA-like domain; Region: AAA_10; pfam12846 546269001419 PrgI family protein; Region: PrgI; pfam12666 546269001420 Maff2 family; Region: Maff2; pfam12750 546269001421 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 546269001422 generic binding surface II; other site 546269001423 generic binding surface I; other site 546269001424 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 546269001425 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 546269001426 Transposon-encoded protein TnpW; Region: TnpW; pfam14202 546269001427 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 546269001428 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 546269001429 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 546269001430 MobA/MobL family; Region: MobA_MobL; pfam03389 546269001431 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269001432 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; cl17257 546269001433 DNA binding residues [nucleotide binding] 546269001434 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 546269001435 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 546269001436 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269001437 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 546269001438 Walker A/P-loop; other site 546269001439 ATP binding site [chemical binding]; other site 546269001440 Q-loop/lid; other site 546269001441 ABC transporter signature motif; other site 546269001442 Walker B; other site 546269001443 D-loop; other site 546269001444 H-loop/switch region; other site 546269001445 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001446 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 546269001447 Walker A/P-loop; other site 546269001448 ATP binding site [chemical binding]; other site 546269001449 Q-loop/lid; other site 546269001450 ABC transporter signature motif; other site 546269001451 Walker B; other site 546269001452 D-loop; other site 546269001453 H-loop/switch region; other site 546269001454 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 546269001455 Hypothetical bacterial integral membrane protein (Trep_Strep); Region: Trep_Strep; pfam09605 546269001456 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 546269001457 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 546269001458 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 546269001459 Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a...; Region: SR_TndX_transposase; cd03770 546269001460 putative catalytic residues [active] 546269001461 catalytic nucleophile [active] 546269001462 Recombinase; Region: Recombinase; pfam07508 546269001463 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 546269001464 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 546269001465 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 546269001466 Transposon-encoded protein TnpW; Region: TnpW; pfam14202 546269001467 MobA/MobL family; Region: MobA_MobL; pfam03389 546269001468 DNA adenine methylase (dam); Region: dam; TIGR00571 546269001469 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 546269001470 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 546269001471 Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a...; Region: SR_TndX_transposase; cd03770 546269001472 putative catalytic residues [active] 546269001473 catalytic nucleophile [active] 546269001474 Recombinase; Region: Recombinase; pfam07508 546269001475 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 546269001476 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 546269001477 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 546269001478 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 546269001479 Walker A motif; other site 546269001480 ATP binding site [chemical binding]; other site 546269001481 Protein of unknown function (DUF3801); Region: DUF3801; pfam12687 546269001482 hypothetical protein; Validated; Region: PRK08116 546269001483 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 546269001484 Walker A motif; other site 546269001485 ATP binding site [chemical binding]; other site 546269001486 Walker B motif; other site 546269001487 arginine finger; other site 546269001488 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 546269001489 BRO family, N-terminal domain; Region: Bro-N; smart01040 546269001490 ParB-like nuclease domain; Region: ParBc; pfam02195 546269001491 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 546269001492 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 546269001493 P-loop; other site 546269001494 Magnesium ion binding site [ion binding]; other site 546269001495 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 546269001496 Magnesium ion binding site [ion binding]; other site 546269001497 hypothetical protein; Validated; Region: PRK08116 546269001498 Replication initiator protein A (RepA) N-terminus; Region: RepA_N; pfam06970 546269001499 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 546269001500 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 546269001501 dimer interface [polypeptide binding]; other site 546269001502 putative anticodon binding site; other site 546269001503 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 546269001504 motif 1; other site 546269001505 active site 546269001506 motif 2; other site 546269001507 motif 3; other site 546269001508 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 546269001509 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 546269001510 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 546269001511 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 546269001512 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 546269001513 FMN binding site [chemical binding]; other site 546269001514 active site 546269001515 catalytic residues [active] 546269001516 substrate binding site [chemical binding]; other site 546269001517 pantothenate kinase; Reviewed; Region: PRK13318 546269001518 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 546269001519 Biotin operon repressor [Transcription]; Region: BirA; COG1654 546269001520 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 546269001521 Protein of unknown function (DUF1049); Region: DUF1049; pfam06305 546269001522 Predicted membrane protein [Function unknown]; Region: COG2119 546269001523 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 546269001524 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 546269001525 UPF0489 domain; Region: UPF0489; pfam12640 546269001526 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 546269001527 pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric; Region: pyruv_ox_red; TIGR02176 546269001528 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 546269001529 dimer interface [polypeptide binding]; other site 546269001530 PYR/PP interface [polypeptide binding]; other site 546269001531 TPP binding site [chemical binding]; other site 546269001532 substrate binding site [chemical binding]; other site 546269001533 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 546269001534 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 546269001535 Domain of unknown function; Region: EKR; pfam10371 546269001536 4Fe-4S binding domain; Region: Fer4_6; pfam12837 546269001537 4Fe-4S binding domain; Region: Fer4; pfam00037 546269001538 Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This...; Region: TPP_PFOR_PNO; cd03377 546269001539 TPP-binding site [chemical binding]; other site 546269001540 dimer interface [polypeptide binding]; other site 546269001541 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 546269001542 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 546269001543 trimerization site [polypeptide binding]; other site 546269001544 active site 546269001545 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 546269001546 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 546269001547 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 546269001548 catalytic residue [active] 546269001549 Rrf2 family protein; Region: rrf2_super; TIGR00738 546269001550 Transcriptional regulator; Region: Rrf2; pfam02082 546269001551 hypothetical protein; Reviewed; Region: PRK12497 546269001552 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 546269001553 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 546269001554 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 546269001555 Walker A motif; other site 546269001556 ATP binding site [chemical binding]; other site 546269001557 Walker B motif; other site 546269001558 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 546269001559 DNA protecting protein DprA; Region: dprA; TIGR00732 546269001560 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 546269001561 DNA topoisomerase I; Validated; Region: PRK05582 546269001562 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 546269001563 active site 546269001564 interdomain interaction site; other site 546269001565 putative metal-binding site [ion binding]; other site 546269001566 nucleotide binding site [chemical binding]; other site 546269001567 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 546269001568 domain I; other site 546269001569 DNA binding groove [nucleotide binding] 546269001570 phosphate binding site [ion binding]; other site 546269001571 domain II; other site 546269001572 domain III; other site 546269001573 nucleotide binding site [chemical binding]; other site 546269001574 catalytic site [active] 546269001575 domain IV; other site 546269001576 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 546269001577 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 546269001578 transcriptional repressor CodY; Validated; Region: PRK04158 546269001579 CodY GAF-like domain; Region: CodY; pfam06018 546269001580 CodY helix-turn-helix domain; Region: HTH_CodY; pfam08222 546269001581 recombination factor protein RarA; Reviewed; Region: PRK13342 546269001582 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 546269001583 Walker A motif; other site 546269001584 ATP binding site [chemical binding]; other site 546269001585 Walker B motif; other site 546269001586 arginine finger; other site 546269001587 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 546269001588 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 546269001589 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 546269001590 metal binding site [ion binding]; metal-binding site 546269001591 dimer interface [polypeptide binding]; other site 546269001592 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 546269001593 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 546269001594 dimerization interface 3.5A [polypeptide binding]; other site 546269001595 active site 546269001596 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 546269001597 ApbE family; Region: ApbE; pfam02424 546269001598 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 546269001599 MutS domain III; Region: MutS_III; pfam05192 546269001600 ATP-binding cassette domain of MutS2; Region: ABC_MutS2; cd03280 546269001601 Walker A/P-loop; other site 546269001602 ATP binding site [chemical binding]; other site 546269001603 Q-loop/lid; other site 546269001604 ABC transporter signature motif; other site 546269001605 Walker B; other site 546269001606 D-loop; other site 546269001607 H-loop/switch region; other site 546269001608 Smr domain; Region: Smr; pfam01713 546269001609 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 546269001610 Peptidase family U32; Region: Peptidase_U32; pfam01136 546269001611 Collagenase; Region: DUF3656; pfam12392 546269001612 Cell division protein ZapA; Region: ZapA; cl01146 546269001613 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cd02062 546269001614 FMN binding site [chemical binding]; other site 546269001615 dimer interface [polypeptide binding]; other site 546269001616 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 546269001617 pyrroline-5-carboxylate reductase; Region: PLN02688 546269001618 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]; Region: COG4545 546269001619 threonine-phosphate decarboxylase; Provisional; Region: PRK06358 546269001620 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 546269001621 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269001622 homodimer interface [polypeptide binding]; other site 546269001623 catalytic residue [active] 546269001624 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 546269001625 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 546269001626 active site 546269001627 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 546269001628 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 546269001629 Catalytic site [active] 546269001630 DNA polymerase III PolC; Validated; Region: polC; PRK00448 546269001631 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 546269001632 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 546269001633 generic binding surface II; other site 546269001634 generic binding surface I; other site 546269001635 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 546269001636 active site 546269001637 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 546269001638 active site 546269001639 catalytic site [active] 546269001640 substrate binding site [chemical binding]; other site 546269001641 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; Region: PHP_PolIIIA_POLC; cd07435 546269001642 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 546269001643 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 546269001644 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 546269001645 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 546269001646 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 546269001647 active site 546269001648 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 546269001649 protein binding site [polypeptide binding]; other site 546269001650 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 546269001651 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 546269001652 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 546269001653 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 546269001654 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 546269001655 catalytic residue [active] 546269001656 putative FPP diphosphate binding site; other site 546269001657 putative FPP binding hydrophobic cleft; other site 546269001658 dimer interface [polypeptide binding]; other site 546269001659 putative IPP diphosphate binding site; other site 546269001660 ribosome recycling factor; Reviewed; Region: frr; PRK00083 546269001661 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 546269001662 hinge region; other site 546269001663 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 546269001664 putative nucleotide binding site [chemical binding]; other site 546269001665 uridine monophosphate binding site [chemical binding]; other site 546269001666 homohexameric interface [polypeptide binding]; other site 546269001667 Predicted amidohydrolase [General function prediction only]; Region: COG0388 546269001668 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases); Region: nitrilase_5; cd07583 546269001669 putative active site [active] 546269001670 catalytic triad [active] 546269001671 putative dimer interface [polypeptide binding]; other site 546269001672 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 546269001673 trimer interface [polypeptide binding]; other site 546269001674 active site 546269001675 SCIFF radical SAM maturase; Region: rSAM_six_Cys; TIGR03974 546269001676 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 546269001677 FeS/SAM binding site; other site 546269001678 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 546269001679 six-cysteine peptide SCIFF; Region: six_Cys_in_45; TIGR03973 546269001680 six-cysteine peptide SCIFF; Region: six_Cys_in_45; TIGR03973 546269001681 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 546269001682 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 546269001683 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 546269001684 catalytic residue [active] 546269001685 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 546269001686 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 546269001687 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 546269001688 active site 546269001689 glutamate racemase; Provisional; Region: PRK00865 546269001690 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 546269001691 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 546269001692 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 546269001693 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 546269001694 ligand binding site [chemical binding]; other site 546269001695 active site 546269001696 UGI interface [polypeptide binding]; other site 546269001697 catalytic site [active] 546269001698 helicase 45; Provisional; Region: PTZ00424 546269001699 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 546269001700 ATP binding site [chemical binding]; other site 546269001701 Mg++ binding site [ion binding]; other site 546269001702 motif III; other site 546269001703 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 546269001704 nucleotide binding region [chemical binding]; other site 546269001705 ATP-binding site [chemical binding]; other site 546269001706 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 546269001707 RNA binding site [nucleotide binding]; other site 546269001708 LysM domain; Region: LysM; pfam01476 546269001709 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 546269001710 LexA repressor; Validated; Region: PRK00215 546269001711 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 546269001712 Catalytic site [active] 546269001713 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 546269001714 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 546269001715 chaperone protein DnaJ; Provisional; Region: PRK10767 546269001716 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 546269001717 HSP70 interaction site [polypeptide binding]; other site 546269001718 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 546269001719 substrate binding site [polypeptide binding]; other site 546269001720 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 546269001721 Zn binding sites [ion binding]; other site 546269001722 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 546269001723 dimer interface [polypeptide binding]; other site 546269001724 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 546269001725 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 546269001726 nucleotide binding site [chemical binding]; other site 546269001727 NEF interaction site [polypeptide binding]; other site 546269001728 SBD interface [polypeptide binding]; other site 546269001729 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 546269001730 GrpE; Region: GrpE; pfam01025 546269001731 dimer interface [polypeptide binding]; other site 546269001732 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 546269001733 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 546269001734 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 546269001735 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 546269001736 putative homodimer interface [polypeptide binding]; other site 546269001737 putative homotetramer interface [polypeptide binding]; other site 546269001738 putative allosteric switch controlling residues; other site 546269001739 putative metal binding site [ion binding]; other site 546269001740 putative homodimer-homodimer interface [polypeptide binding]; other site 546269001741 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 546269001742 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 546269001743 metal-binding site [ion binding] 546269001744 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 546269001745 Soluble P-type ATPase [General function prediction only]; Region: COG4087 546269001746 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 546269001747 metal-binding site [ion binding] 546269001748 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 546269001749 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269001750 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 546269001751 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 546269001752 23S rRNA interface [nucleotide binding]; other site 546269001753 L3 interface [polypeptide binding]; other site 546269001754 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 546269001755 nucleotide binding site/active site [active] 546269001756 HIT family signature motif; other site 546269001757 catalytic residue [active] 546269001758 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 546269001759 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 546269001760 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 546269001761 FeS/SAM binding site; other site 546269001762 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 546269001763 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 546269001764 BioY family; Region: BioY; pfam02632 546269001765 Predicted permeases [General function prediction only]; Region: COG0679 546269001766 rod shape-determining protein Mbl; Provisional; Region: PRK13928 546269001767 MreB and similar proteins; Region: MreB_like; cd10225 546269001768 nucleotide binding site [chemical binding]; other site 546269001769 Mg binding site [ion binding]; other site 546269001770 putative protofilament interaction site [polypeptide binding]; other site 546269001771 RodZ interaction site [polypeptide binding]; other site 546269001772 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 546269001773 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 546269001774 hinge; other site 546269001775 active site 546269001776 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 546269001777 Domain of unknown function DUF20; Region: UPF0118; pfam01594 546269001778 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 546269001779 Putative peptidoglycan binding domain; Region: PG_binding_4; pfam12229 546269001780 VanW like protein; Region: VanW; pfam04294 546269001781 G5 domain; Region: G5; pfam07501 546269001782 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 546269001783 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 546269001784 minor groove reading motif; other site 546269001785 helix-hairpin-helix signature motif; other site 546269001786 substrate binding pocket [chemical binding]; other site 546269001787 active site 546269001788 Protein of unknown function (DUF503); Region: DUF503; pfam04456 546269001789 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 546269001790 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269001791 Walker A/P-loop; other site 546269001792 ATP binding site [chemical binding]; other site 546269001793 Q-loop/lid; other site 546269001794 ABC transporter signature motif; other site 546269001795 Walker B; other site 546269001796 D-loop; other site 546269001797 H-loop/switch region; other site 546269001798 ABC transporter; Region: ABC_tran_2; pfam12848 546269001799 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 546269001800 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 546269001801 Domain of unknown function DUF20; Region: UPF0118; pfam01594 546269001802 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 546269001803 Isochorismatase family; Region: Isochorismatase; pfam00857 546269001804 catalytic triad [active] 546269001805 dimer interface [polypeptide binding]; other site 546269001806 conserved cis-peptide bond; other site 546269001807 Integral membrane protein (PIN domain superfamily) [General function prediction only]; Region: COG4956 546269001808 PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs; Region: PIN_YacL; cd09877 546269001809 putative active site [active] 546269001810 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269001811 active site 546269001812 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 546269001813 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 546269001814 Flavoprotein; Region: Flavoprotein; pfam02441 546269001815 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 546269001816 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 546269001817 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 546269001818 catalytic site [active] 546269001819 G-X2-G-X-G-K; other site 546269001820 hypothetical protein; Provisional; Region: PRK11820 546269001821 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 546269001822 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 546269001823 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 546269001824 Acetyltransferase (GNAT) domain; Region: Acetyltransf_7; pfam13508 546269001825 Coenzyme A binding pocket [chemical binding]; other site 546269001826 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 546269001827 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 546269001828 ABC-ATPase subunit interface; other site 546269001829 dimer interface [polypeptide binding]; other site 546269001830 putative PBP binding regions; other site 546269001831 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269001832 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 546269001833 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 546269001834 Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor...; Region: AdcA; cd01017 546269001835 metal binding site [ion binding]; metal-binding site 546269001836 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 546269001837 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 546269001838 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 546269001839 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 546269001840 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 546269001841 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 546269001842 M18 Peptidase Aspartyl aminopeptidase; Region: M18_DAP; cd05658 546269001843 Aminopeptidase I zinc metalloprotease (M18); Region: Peptidase_M18; pfam02127 546269001844 active site 546269001845 metal binding site [ion binding]; metal-binding site 546269001846 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 546269001847 putative active site [active] 546269001848 putative CoA binding site [chemical binding]; other site 546269001849 nudix motif; other site 546269001850 metal binding site [ion binding]; metal-binding site 546269001851 GTP-binding protein YchF; Reviewed; Region: PRK09601 546269001852 YchF GTPase; Region: YchF; cd01900 546269001853 G1 box; other site 546269001854 GTP/Mg2+ binding site [chemical binding]; other site 546269001855 Switch I region; other site 546269001856 G2 box; other site 546269001857 Switch II region; other site 546269001858 G3 box; other site 546269001859 G4 box; other site 546269001860 G5 box; other site 546269001861 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 546269001862 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 546269001863 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 546269001864 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 546269001865 putative oxidoreductase; Provisional; Region: PRK12831 546269001866 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 546269001867 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 546269001868 ferredoxin-NADP(+) reductase subunit alpha; Reviewed; Region: PRK06222 546269001869 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)...; Region: DHOD_e_trans_like1; cd06219 546269001870 FAD binding pocket [chemical binding]; other site 546269001871 FAD binding motif [chemical binding]; other site 546269001872 phosphate binding motif [ion binding]; other site 546269001873 beta-alpha-beta structure motif; other site 546269001874 NAD binding pocket [chemical binding]; other site 546269001875 Iron coordination center [ion binding]; other site 546269001876 fructose-1,6-bisphosphate aldolase; Reviewed; Region: PRK05377 546269001877 catalytic residue [active] 546269001878 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 546269001879 Zinc peptidases M18, M20, M28, and M42; Region: Zinc_peptidase_like; cl14876 546269001880 metal binding site [ion binding]; metal-binding site 546269001881 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 546269001882 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 546269001883 dimerization interface [polypeptide binding]; other site 546269001884 domain crossover interface; other site 546269001885 redox-dependent activation switch; other site 546269001886 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 546269001887 S-adenosylmethionine binding site [chemical binding]; other site 546269001888 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269001889 active site 546269001890 Transcriptional regulators [Transcription]; Region: PurR; COG1609 546269001891 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 546269001892 DNA binding site [nucleotide binding] 546269001893 domain linker motif; other site 546269001894 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 546269001895 ligand binding site [chemical binding]; other site 546269001896 dimerization interface [polypeptide binding]; other site 546269001897 Putative methyltransferase; Region: Methyltransf_4; cl17290 546269001898 acyl carrier protein; Provisional; Region: acpP; PRK00982 546269001899 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 546269001900 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 546269001901 active site 546269001902 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 546269001903 ATP-NAD kinase; Region: NAD_kinase; pfam01513 546269001904 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 546269001905 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 546269001906 active site 546269001907 HIGH motif; other site 546269001908 nucleotide binding site [chemical binding]; other site 546269001909 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 546269001910 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 546269001911 active site 546269001912 KMSKS motif; other site 546269001913 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 546269001914 tRNA binding surface [nucleotide binding]; other site 546269001915 anticodon binding site; other site 546269001916 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 546269001917 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 546269001918 non-specific DNA binding site [nucleotide binding]; other site 546269001919 salt bridge; other site 546269001920 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 546269001921 sequence-specific DNA binding site [nucleotide binding]; other site 546269001922 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 546269001923 Catalytic site [active] 546269001924 GTP-binding protein LepA; Provisional; Region: PRK05433 546269001925 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 546269001926 G1 box; other site 546269001927 putative GEF interaction site [polypeptide binding]; other site 546269001928 GTP/Mg2+ binding site [chemical binding]; other site 546269001929 Switch I region; other site 546269001930 G2 box; other site 546269001931 G3 box; other site 546269001932 Switch II region; other site 546269001933 G4 box; other site 546269001934 G5 box; other site 546269001935 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 546269001936 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 546269001937 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 546269001938 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 546269001939 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 546269001940 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 546269001941 Competence protein; Region: Competence; pfam03772 546269001942 Predicted acetyltransferase involved in intracellular survival and related acetyltransferases [General function prediction only]; Region: Eis; COG4552 546269001943 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269001944 Coenzyme A binding pocket [chemical binding]; other site 546269001945 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 546269001946 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 546269001947 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 546269001948 YARHG domain; Region: YARHG; pfam13308 546269001949 elongation factor Tu; Reviewed; Region: PRK00049 546269001950 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 546269001951 G1 box; other site 546269001952 GEF interaction site [polypeptide binding]; other site 546269001953 GTP/Mg2+ binding site [chemical binding]; other site 546269001954 Switch I region; other site 546269001955 G2 box; other site 546269001956 G3 box; other site 546269001957 Switch II region; other site 546269001958 G4 box; other site 546269001959 G5 box; other site 546269001960 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 546269001961 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 546269001962 Antibiotic Binding Site [chemical binding]; other site 546269001963 elongation factor G; Reviewed; Region: PRK00007 546269001964 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 546269001965 G1 box; other site 546269001966 putative GEF interaction site [polypeptide binding]; other site 546269001967 GTP/Mg2+ binding site [chemical binding]; other site 546269001968 Switch I region; other site 546269001969 G2 box; other site 546269001970 G3 box; other site 546269001971 Switch II region; other site 546269001972 G4 box; other site 546269001973 G5 box; other site 546269001974 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 546269001975 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 546269001976 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 546269001977 30S ribosomal protein S7; Validated; Region: PRK05302 546269001978 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 546269001979 S17 interaction site [polypeptide binding]; other site 546269001980 S8 interaction site; other site 546269001981 16S rRNA interaction site [nucleotide binding]; other site 546269001982 streptomycin interaction site [chemical binding]; other site 546269001983 23S rRNA interaction site [nucleotide binding]; other site 546269001984 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 546269001985 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_1; cd13140 546269001986 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 546269001987 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 546269001988 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 546269001989 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 546269001990 Zn2+ binding site [ion binding]; other site 546269001991 Mg2+ binding site [ion binding]; other site 546269001992 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 546269001993 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 546269001994 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 546269001995 GIY-YIG motif/motif A; other site 546269001996 active site 546269001997 catalytic site [active] 546269001998 putative DNA binding site [nucleotide binding]; other site 546269001999 metal binding site [ion binding]; metal-binding site 546269002000 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 546269002001 phosphoenolpyruvate synthase; Validated; Region: PRK06241 546269002002 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 546269002003 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 546269002004 prenyltransferase; Provisional; Region: ubiA; PRK13592 546269002005 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 546269002006 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 546269002007 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 546269002008 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 546269002009 phosphoenolpyruvate synthase; Validated; Region: PRK06241 546269002010 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 546269002011 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 546269002012 Putative integral membrane protein DUF46; Region: DUF46; cl17511 546269002013 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 546269002014 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 546269002015 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 546269002016 propionate/acetate kinase; Provisional; Region: PRK12379 546269002017 Predicted membrane protein [Function unknown]; Region: COG2855 546269002018 Domain of unknown function (DUF4364); Region: DUF4364; pfam14277 546269002019 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 546269002020 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 546269002021 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 546269002022 dimerization interface [polypeptide binding]; other site 546269002023 DPS ferroxidase diiron center [ion binding]; other site 546269002024 ion pore; other site 546269002025 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 546269002026 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 546269002027 motif II; other site 546269002028 competence damage-inducible protein A; Provisional; Region: PRK00549 546269002029 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 546269002030 putative MPT binding site; other site 546269002031 Competence-damaged protein; Region: CinA; pfam02464 546269002032 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269002033 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269002034 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 546269002035 Walker A/P-loop; other site 546269002036 ATP binding site [chemical binding]; other site 546269002037 Q-loop/lid; other site 546269002038 ABC transporter signature motif; other site 546269002039 Walker B; other site 546269002040 D-loop; other site 546269002041 H-loop/switch region; other site 546269002042 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 546269002043 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 546269002044 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 546269002045 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 546269002046 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 546269002047 NAD(P) binding site [chemical binding]; other site 546269002048 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 546269002049 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 546269002050 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 546269002051 Walker A motif; other site 546269002052 ATP binding site [chemical binding]; other site 546269002053 Walker B motif; other site 546269002054 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 546269002055 Clp protease; Region: CLP_protease; pfam00574 546269002056 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 546269002057 oligomer interface [polypeptide binding]; other site 546269002058 active site residues [active] 546269002059 trigger factor; Provisional; Region: tig; PRK01490 546269002060 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 546269002061 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 546269002062 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269002063 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269002064 Integrase core domain; Region: rve; pfam00665 546269002065 MAC/Perforin domain; Region: MACPF; cl02616 546269002066 DNA repair protein RadA; Provisional; Region: PRK11823 546269002067 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 546269002068 Walker A motif/ATP binding site; other site 546269002069 ATP binding site [chemical binding]; other site 546269002070 Walker B motif; other site 546269002071 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 546269002072 Na+-transporting oxaloacetate decarboxylase beta subunit; Region: OAD_beta; cl00816 546269002073 Uncharacterized BCR, COG1636; Region: DUF208; pfam02677 546269002074 Protein of unknown function (DUF1307); Region: DUF1307; cl01981 546269002075 integral membrane protein MviN; Region: mviN; TIGR01695 546269002076 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 546269002077 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 546269002078 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269002079 Coenzyme A binding pocket [chemical binding]; other site 546269002080 replicative DNA helicase; Region: DnaB; TIGR00665 546269002081 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 546269002082 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 546269002083 Walker A motif; other site 546269002084 ATP binding site [chemical binding]; other site 546269002085 Walker B motif; other site 546269002086 DNA binding loops [nucleotide binding] 546269002087 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 546269002088 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 546269002089 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 546269002090 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 546269002091 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 546269002092 DHH family; Region: DHH; pfam01368 546269002093 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 546269002094 nucleoside/Zn binding site; other site 546269002095 dimer interface [polypeptide binding]; other site 546269002096 catalytic motif [active] 546269002097 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 546269002098 AAA domain; Region: AAA_30; pfam13604 546269002099 Family description; Region: UvrD_C_2; pfam13538 546269002100 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 546269002101 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 546269002102 active site 546269002103 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 546269002104 S-adenosylmethionine synthetase; Validated; Region: PRK05250 546269002105 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 546269002106 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 546269002107 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 546269002108 EDD domain protein, DegV family; Region: DegV; TIGR00762 546269002109 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 546269002110 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 546269002111 dimer interface [polypeptide binding]; other site 546269002112 putative radical transfer pathway; other site 546269002113 diiron center [ion binding]; other site 546269002114 tyrosyl radical; other site 546269002115 ribonucleotide-diphosphate reductase subunit alpha; Provisional; Region: PRK12364 546269002116 ATP cone domain; Region: ATP-cone; pfam03477 546269002117 Class I ribonucleotide reductase; Region: RNR_I; cd01679 546269002118 active site 546269002119 dimer interface [polypeptide binding]; other site 546269002120 catalytic residues [active] 546269002121 effector binding site; other site 546269002122 R2 peptide binding site; other site 546269002123 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 546269002124 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 546269002125 ligand binding site [chemical binding]; other site 546269002126 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; cl17320 546269002127 Ferredoxin [Energy production and conversion]; Region: COG1146 546269002128 4Fe-4S binding domain; Region: Fer4_6; pfam12837 546269002129 Uncharacterized conserved protein (DUF2249); Region: DUF2249; pfam10006 546269002130 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 546269002131 TIGR04076 family protein; Region: TIGR04076 546269002132 hybrid cluster protein; Provisional; Region: PRK05290 546269002133 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 546269002134 ACS interaction site; other site 546269002135 Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a...; Region: HCP; cd01914 546269002136 hybrid metal cluster; other site 546269002137 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 546269002138 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 546269002139 inhibitor-cofactor binding pocket; inhibition site 546269002140 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269002141 catalytic residue [active] 546269002142 AAA domain; Region: AAA_26; pfam13500 546269002143 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 546269002144 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 546269002145 Serine dehydratase alpha chain; Region: SDH_alpha; cl12120 546269002146 L-serine deaminase [Amino acid transport and metabolism]; Region: SdaA; COG1760 546269002147 L-serine dehydratase, iron-sulfur-dependent, beta subunit; Region: sda_beta; TIGR00719 546269002148 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 546269002149 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 546269002150 Formiminotransferase-cyclodeaminase; Region: FTCD_C; pfam04961 546269002151 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 546269002152 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 546269002153 Potassium binding sites [ion binding]; other site 546269002154 Cesium cation binding sites [ion binding]; other site 546269002155 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 546269002156 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 546269002157 active site 546269002158 HIGH motif; other site 546269002159 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 546269002160 active site 546269002161 KMSKS motif; other site 546269002162 poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; Region: PHA_synth_III_C; TIGR01836 546269002163 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 546269002164 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 546269002165 Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E); Region: PHA_synth_III_E; cl09914 546269002166 (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 546269002167 dimer interaction site [polypeptide binding]; other site 546269002168 substrate-binding tunnel; other site 546269002169 active site 546269002170 catalytic site [active] 546269002171 substrate binding site [chemical binding]; other site 546269002172 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 546269002173 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 546269002174 Ligand binding site [chemical binding]; other site 546269002175 Electron transfer flavoprotein domain; Region: ETF; pfam01012 546269002176 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 546269002177 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 546269002178 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 546269002179 VanW like protein; Region: VanW; pfam04294 546269002180 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 546269002181 synthetase active site [active] 546269002182 NTP binding site [chemical binding]; other site 546269002183 metal binding site [ion binding]; metal-binding site 546269002184 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 546269002185 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 546269002186 dimer interface [polypeptide binding]; other site 546269002187 active site 546269002188 metal binding site [ion binding]; metal-binding site 546269002189 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269002190 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269002191 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269002192 Walker A/P-loop; other site 546269002193 ATP binding site [chemical binding]; other site 546269002194 Q-loop/lid; other site 546269002195 ABC transporter signature motif; other site 546269002196 Walker B; other site 546269002197 D-loop; other site 546269002198 H-loop/switch region; other site 546269002199 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269002200 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269002201 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269002202 Walker A/P-loop; other site 546269002203 ATP binding site [chemical binding]; other site 546269002204 Q-loop/lid; other site 546269002205 ABC transporter signature motif; other site 546269002206 Walker B; other site 546269002207 D-loop; other site 546269002208 H-loop/switch region; other site 546269002209 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 546269002210 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 546269002211 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 546269002212 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 546269002213 aspartate racemase; Region: asp_race; TIGR00035 546269002214 DNA replication protein DnaC; Validated; Region: PRK06835 546269002215 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 546269002216 Replication initiation and membrane attachment; Region: DnaB_2; pfam07261 546269002217 Replication initiation and membrane attachment; Region: DnaB_2; pfam07261 546269002218 arginine deiminase; Provisional; Region: PRK01388 546269002219 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 546269002220 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 546269002221 putative active site [active] 546269002222 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 546269002223 catalytic core [active] 546269002224 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 546269002225 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 546269002226 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 546269002227 HlyD family secretion protein; Region: HlyD_3; pfam13437 546269002228 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 546269002229 putative active site [active] 546269002230 type I secretion system ABC transporter, HlyB family; Region: type_I_sec_HlyB; TIGR01846 546269002231 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269002232 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269002233 Walker A/P-loop; other site 546269002234 ATP binding site [chemical binding]; other site 546269002235 Q-loop/lid; other site 546269002236 ABC transporter signature motif; other site 546269002237 Walker B; other site 546269002238 D-loop; other site 546269002239 H-loop/switch region; other site 546269002240 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 546269002241 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 546269002242 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 546269002243 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 546269002244 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 546269002245 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 546269002246 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 546269002247 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 546269002248 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 546269002249 S-layer homology domain; Region: SLH; pfam00395 546269002250 S-layer homology domain; Region: SLH; pfam00395 546269002251 acetylornithine aminotransferase; Provisional; Region: PRK02627 546269002252 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 546269002253 inhibitor-cofactor binding pocket; inhibition site 546269002254 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269002255 catalytic residue [active] 546269002256 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 546269002257 feedback inhibition sensing region; other site 546269002258 homohexameric interface [polypeptide binding]; other site 546269002259 nucleotide binding site [chemical binding]; other site 546269002260 N-acetyl-L-glutamate binding site [chemical binding]; other site 546269002261 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 546269002262 heterotetramer interface [polypeptide binding]; other site 546269002263 active site pocket [active] 546269002264 cleavage site 546269002265 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 546269002266 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 546269002267 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269002268 Cytochrome P450; Region: p450; cl12078 546269002269 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269002270 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 546269002271 FtsX-like permease family; Region: FtsX; pfam02687 546269002272 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269002273 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 546269002274 Walker A/P-loop; other site 546269002275 ATP binding site [chemical binding]; other site 546269002276 Q-loop/lid; other site 546269002277 ABC transporter signature motif; other site 546269002278 Walker B; other site 546269002279 D-loop; other site 546269002280 H-loop/switch region; other site 546269002281 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 546269002282 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 546269002283 HlyD family secretion protein; Region: HlyD_3; pfam13437 546269002284 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 546269002285 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 546269002286 Cl- selectivity filter; other site 546269002287 Cl- binding residues [ion binding]; other site 546269002288 pore gating glutamate residue; other site 546269002289 dimer interface [polypeptide binding]; other site 546269002290 H+/Cl- coupling transport residue; other site 546269002291 TrkA-C domain; Region: TrkA_C; pfam02080 546269002292 Uncharacterized protein family (UPF0167); Region: UPF0167; cl01252 546269002293 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 546269002294 Low molecular weight phosphatase family; Region: LMWPc; cd00115 546269002295 active site 546269002296 Tellurite resistance protein TerB; Region: TerB; cl17311 546269002297 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 546269002298 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 546269002299 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 546269002300 O-Antigen ligase; Region: Wzy_C; pfam04932 546269002301 Outer membrane efflux protein; Region: OEP; pfam02321 546269002302 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269002303 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269002304 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 546269002305 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 546269002306 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 546269002307 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 546269002308 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 546269002309 Walker A/P-loop; other site 546269002310 ATP binding site [chemical binding]; other site 546269002311 Q-loop/lid; other site 546269002312 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 546269002313 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 546269002314 Q-loop/lid; other site 546269002315 ABC transporter signature motif; other site 546269002316 Walker B; other site 546269002317 D-loop; other site 546269002318 H-loop/switch region; other site 546269002319 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 546269002320 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 546269002321 FeS/SAM binding site; other site 546269002322 ribonuclease III; Reviewed; Region: rnc; PRK00102 546269002323 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 546269002324 dimerization interface [polypeptide binding]; other site 546269002325 active site 546269002326 metal binding site [ion binding]; metal-binding site 546269002327 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 546269002328 dsRNA binding site [nucleotide binding]; other site 546269002329 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 546269002330 elongation factor P; Validated; Region: PRK00529 546269002331 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 546269002332 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 546269002333 RNA binding site [nucleotide binding]; other site 546269002334 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 546269002335 RNA binding site [nucleotide binding]; other site 546269002336 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 546269002337 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 546269002338 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 546269002339 active site 546269002340 S-layer homology domain; Region: SLH; pfam00395 546269002341 S-layer homology domain; Region: SLH; pfam00395 546269002342 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 546269002343 Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation," the...; Region: Lipase_3; cd00519 546269002344 active site flap/lid [active] 546269002345 nucleophilic elbow; other site 546269002346 catalytic triad [active] 546269002347 transcription termination factor Rho; Provisional; Region: PRK12608 546269002348 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 546269002349 RNA binding site [nucleotide binding]; other site 546269002350 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 546269002351 multimer interface [polypeptide binding]; other site 546269002352 Walker A motif; other site 546269002353 ATP binding site [chemical binding]; other site 546269002354 Walker B motif; other site 546269002355 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 546269002356 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 546269002357 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 546269002358 putative active site [active] 546269002359 catalytic site [active] 546269002360 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 546269002361 putative active site [active] 546269002362 catalytic site [active] 546269002363 8-oxoguanine DNA glycosylase, N-terminal domain; Region: OGG_N; pfam07934 546269002364 8-oxoguanine DNA-glycosylase (ogg); Region: ogg; TIGR00588 546269002365 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 546269002366 minor groove reading motif; other site 546269002367 helix-hairpin-helix signature motif; other site 546269002368 substrate binding pocket [chemical binding]; other site 546269002369 active site 546269002370 Predicted permeases [General function prediction only]; Region: COG0679 546269002371 thymidine kinase; Provisional; Region: PRK04296 546269002372 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 546269002373 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 546269002374 active site 546269002375 HIGH motif; other site 546269002376 dimer interface [polypeptide binding]; other site 546269002377 KMSKS motif; other site 546269002378 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 546269002379 RNA binding surface [nucleotide binding]; other site 546269002380 Protein of unknown function (DUF1706); Region: DUF1706; pfam08020 546269002381 GyrI-like small molecule binding domain; Region: GyrI-like; cl01368 546269002382 Predicted transcriptional regulator [Transcription]; Region: COG2378 546269002383 HTH domain; Region: HTH_11; pfam08279 546269002384 WYL domain; Region: WYL; pfam13280 546269002385 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 546269002386 Transporter associated domain; Region: CorC_HlyC; pfam03471 546269002387 Protein of unknown function (DUF2004); Region: DUF2004; pfam09406 546269002388 Protein of unknown function (DUF970); Region: DUF970; cl17525 546269002389 RNA polymerase sigma factor RpoE; Provisional; Region: PRK09652 546269002390 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 546269002391 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 546269002392 DNA binding residues [nucleotide binding] 546269002393 Transglycosylase; Region: Transgly; pfam00912 546269002394 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 546269002395 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 546269002396 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 546269002397 N-acetyl-D-glucosamine binding site [chemical binding]; other site 546269002398 catalytic residue [active] 546269002399 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 546269002400 Predicted transcriptional regulators [Transcription]; Region: COG1725 546269002401 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 546269002402 DNA-binding site [nucleotide binding]; DNA binding site 546269002403 ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system; Region: PQQ_ABC_ATP; TIGR03864 546269002404 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269002405 Walker A/P-loop; other site 546269002406 ATP binding site [chemical binding]; other site 546269002407 Q-loop/lid; other site 546269002408 ABC transporter signature motif; other site 546269002409 Walker B; other site 546269002410 D-loop; other site 546269002411 H-loop/switch region; other site 546269002412 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 546269002413 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 546269002414 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 546269002415 active site 546269002416 homodimer interface [polypeptide binding]; other site 546269002417 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 546269002418 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 546269002419 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 546269002420 gamma subunit interface [polypeptide binding]; other site 546269002421 epsilon subunit interface [polypeptide binding]; other site 546269002422 LBP interface [polypeptide binding]; other site 546269002423 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 546269002424 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 546269002425 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 546269002426 alpha subunit interaction interface [polypeptide binding]; other site 546269002427 Walker A motif; other site 546269002428 ATP binding site [chemical binding]; other site 546269002429 Walker B motif; other site 546269002430 inhibitor binding site; inhibition site 546269002431 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 546269002432 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 546269002433 core domain interface [polypeptide binding]; other site 546269002434 delta subunit interface [polypeptide binding]; other site 546269002435 epsilon subunit interface [polypeptide binding]; other site 546269002436 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 546269002437 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 546269002438 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 546269002439 beta subunit interaction interface [polypeptide binding]; other site 546269002440 Walker A motif; other site 546269002441 ATP binding site [chemical binding]; other site 546269002442 Walker B motif; other site 546269002443 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 546269002444 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 546269002445 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 546269002446 F0F1 ATP synthase subunit B; Provisional; Region: PRK13461 546269002447 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 546269002448 F0F1 ATP synthase subunit C; Provisional; Region: PRK13469 546269002449 F0F1 ATP synthase subunit C; Provisional; Region: PRK13469 546269002450 ATP synthase subunit C; Region: ATP-synt_C; cl00466 546269002451 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 546269002452 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 546269002453 ATP synthase I chain; Region: ATP_synt_I; pfam03899 546269002454 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 546269002455 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269002456 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 546269002457 active site 546269002458 putative DNA-binding cleft [nucleotide binding]; other site 546269002459 dimer interface [polypeptide binding]; other site 546269002460 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 546269002461 RuvA N terminal domain; Region: RuvA_N; pfam01330 546269002462 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 546269002463 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 546269002464 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 546269002465 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 546269002466 Walker A motif; other site 546269002467 ATP binding site [chemical binding]; other site 546269002468 Walker B motif; other site 546269002469 arginine finger; other site 546269002470 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 546269002471 SpoIID/LytB domain; Region: SpoIID_LytB; TIGR02669 546269002472 Stage II sporulation protein; Region: SpoIID; pfam08486 546269002473 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 546269002474 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 546269002475 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 546269002476 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 546269002477 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 546269002478 DNA methylase; Region: N6_N4_Mtase; pfam01555 546269002479 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 546269002480 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 546269002481 active site 546269002482 motif I; other site 546269002483 motif II; other site 546269002484 Preprotein translocase subunit; Region: YajC; pfam02699 546269002485 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 546269002486 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 546269002487 trimer interface [polypeptide binding]; other site 546269002488 putative metal binding site [ion binding]; other site 546269002489 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 546269002490 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 546269002491 Protein export membrane protein; Region: SecD_SecF; cl14618 546269002492 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 546269002493 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 546269002494 Domain of unknown function (DUF1836); Region: DUF1836; pfam08876 546269002495 Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]; Region: HgdB; COG1775 546269002496 benzoyl-CoA reductase, subunit C; Region: benz_CoA_red_C; TIGR02263 546269002497 Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]; Region: HgdB; COG1775 546269002498 benzoyl-CoA reductase, bcr type, subunit B; Region: benz_CoA_red_B; TIGR02260 546269002499 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; Region: COG1924 546269002500 BadF/BadG/BcrA/BcrD ATPase family; Region: BcrAD_BadFG; cl17271 546269002501 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 546269002502 Coenzyme A transferase; Region: CoA_trans; cl17247 546269002503 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 546269002504 Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit [Energy production and conversion]; Region: OadB; COG1883 546269002505 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 546269002506 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 546269002507 carboxyltransferase (CT) interaction site; other site 546269002508 biotinylation site [posttranslational modification]; other site 546269002509 Protein of unknown function (DUF2974); Region: DUF2974; pfam11187 546269002510 Domain of unknown function (DUF4153); Region: DUF4153; pfam13687 546269002511 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 546269002512 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 546269002513 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 546269002514 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 546269002515 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 546269002516 FAD binding site [chemical binding]; other site 546269002517 homotetramer interface [polypeptide binding]; other site 546269002518 substrate binding pocket [chemical binding]; other site 546269002519 catalytic base [active] 546269002520 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 546269002521 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 546269002522 Rubredoxin [Energy production and conversion]; Region: COG1773 546269002523 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 546269002524 iron binding site [ion binding]; other site 546269002525 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 546269002526 MgtE intracellular N domain; Region: MgtE_N; pfam03448 546269002527 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 546269002528 Divalent cation transporter; Region: MgtE; pfam01769 546269002529 periplasmic serine pepetdase DegS; Region: protease_degS; TIGR02038 546269002530 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 546269002531 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 546269002532 protein binding site [polypeptide binding]; other site 546269002533 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 546269002534 seryl-tRNA synthetase; Provisional; Region: PRK05431 546269002535 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 546269002536 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 546269002537 dimer interface [polypeptide binding]; other site 546269002538 active site 546269002539 motif 1; other site 546269002540 motif 2; other site 546269002541 motif 3; other site 546269002542 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 546269002543 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 546269002544 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 546269002545 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_subfamily5; cd08019 546269002546 metal binding site [ion binding]; metal-binding site 546269002547 putative dimer interface [polypeptide binding]; other site 546269002548 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 546269002549 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 546269002550 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 546269002551 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 546269002552 catalytic residues [active] 546269002553 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269002554 FtsX-like permease family; Region: FtsX; pfam02687 546269002555 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 546269002556 S-layer domain [Cell envelope biogenesis, outer membrane]; Region: COG1361 546269002557 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 546269002558 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269002559 Walker A/P-loop; other site 546269002560 ATP binding site [chemical binding]; other site 546269002561 Q-loop/lid; other site 546269002562 ABC transporter signature motif; other site 546269002563 Walker B; other site 546269002564 D-loop; other site 546269002565 H-loop/switch region; other site 546269002566 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 546269002567 putative substrate binding site 2 [chemical binding]; other site 546269002568 putative substrate binding site 1 [chemical binding]; other site 546269002569 Na binding site 1 [ion binding]; other site 546269002570 Na2 binding site [ion binding]; other site 546269002571 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 546269002572 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_4; cd13144 546269002573 S-layer homology domain; Region: SLH; pfam00395 546269002574 comF family protein; Region: comF; TIGR00201 546269002575 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269002576 active site 546269002577 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 546269002578 UGMP family protein; Validated; Region: PRK09604 546269002579 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 546269002580 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 546269002581 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269002582 Coenzyme A binding pocket [chemical binding]; other site 546269002583 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 546269002584 Glycoprotease family; Region: Peptidase_M22; pfam00814 546269002585 aspartate aminotransferase; Provisional; Region: PRK05764 546269002586 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 546269002587 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269002588 homodimer interface [polypeptide binding]; other site 546269002589 catalytic residue [active] 546269002590 Glucitol operon activator protein (GutM); Region: GutM; cl01890 546269002591 Uncharacterized conserved protein [Function unknown]; Region: COG4938 546269002592 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 546269002593 recombination protein RecR; Reviewed; Region: recR; PRK00076 546269002594 RecR protein; Region: RecR; pfam02132 546269002595 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 546269002596 putative active site [active] 546269002597 putative metal-binding site [ion binding]; other site 546269002598 tetramer interface [polypeptide binding]; other site 546269002599 hypothetical protein; Validated; Region: PRK00153 546269002600 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 546269002601 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 546269002602 Walker A motif; other site 546269002603 ATP binding site [chemical binding]; other site 546269002604 DNA polymerase III subunit delta'; Validated; Region: PRK08485 546269002605 Walker B motif; other site 546269002606 arginine finger; other site 546269002607 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 546269002608 putative deacylase active site [active] 546269002609 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 546269002610 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 546269002611 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 546269002612 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 546269002613 Domain of unknown function (DUF4261); Region: DUF4261; pfam14080 546269002614 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 546269002615 Predicted membrane protein [Function unknown]; Region: COG3212 546269002616 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 546269002617 Predicted membrane protein [Function unknown]; Region: COG3212 546269002618 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 546269002619 TraX protein; Region: TraX; pfam05857 546269002620 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 546269002621 A new structural DNA glycosylase; Region: AlkD_like; cl11434 546269002622 HEAT repeats; Region: HEAT_2; pfam13646 546269002623 active site 546269002624 AAA ATPase domain; Region: AAA_16; pfam13191 546269002625 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]; Region: COG1205 546269002626 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 546269002627 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 546269002628 ATP binding site [chemical binding]; other site 546269002629 putative Mg++ binding site [ion binding]; other site 546269002630 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 546269002631 ATP-binding site [chemical binding]; other site 546269002632 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 546269002633 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 546269002634 non-specific DNA binding site [nucleotide binding]; other site 546269002635 salt bridge; other site 546269002636 sequence-specific DNA binding site [nucleotide binding]; other site 546269002637 Integrase core domain; Region: rve; pfam00665 546269002638 Integrase core domain; Region: rve_3; pfam13683 546269002639 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 546269002640 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 546269002641 S-adenosylmethionine binding site [chemical binding]; other site 546269002642 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 546269002643 catalytic residues [active] 546269002644 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 546269002645 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 546269002646 active site 546269002647 metal-binding site [ion binding] 546269002648 nucleotide-binding site [chemical binding]; other site 546269002649 YARHG domain; Region: YARHG; pfam13308 546269002650 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 546269002651 SmpB-tmRNA interface; other site 546269002652 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 546269002653 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 546269002654 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 546269002655 ribonuclease R; Region: RNase_R; TIGR02063 546269002656 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 546269002657 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 546269002658 RNB domain; Region: RNB; pfam00773 546269002659 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 546269002660 RNA binding site [nucleotide binding]; other site 546269002661 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 546269002662 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 546269002663 hypothetical protein; Provisional; Region: PRK13665 546269002664 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 546269002665 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 546269002666 active site residue [active] 546269002667 coproporphyrinogen III oxidase; Provisional; Region: PRK05799 546269002668 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 546269002669 FeS/SAM binding site; other site 546269002670 HemN C-terminal domain; Region: HemN_C; pfam06969 546269002671 Protein of unknown function (DUF1451); Region: DUF1451; pfam07295 546269002672 S-layer homology domain; Region: SLH; pfam00395 546269002673 S-layer homology domain; Region: SLH; pfam00395 546269002674 S-layer homology domain; Region: SLH; pfam00395 546269002675 S-layer homology domain; Region: SLH; pfam00395 546269002676 S-layer homology domain; Region: SLH; pfam00395 546269002677 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 546269002678 active site 546269002679 8-oxo-dGMP binding site [chemical binding]; other site 546269002680 nudix motif; other site 546269002681 metal binding site [ion binding]; metal-binding site 546269002682 Ferrous iron transport protein B; Region: FeoB_N; pfam02421 546269002683 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 546269002684 G1 box; other site 546269002685 GTP/Mg2+ binding site [chemical binding]; other site 546269002686 Switch I region; other site 546269002687 G2 box; other site 546269002688 G3 box; other site 546269002689 Switch II region; other site 546269002690 G4 box; other site 546269002691 G5 box; other site 546269002692 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 546269002693 Nucleoside recognition; Region: Gate; pfam07670 546269002694 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 546269002695 Nucleoside recognition; Region: Gate; pfam07670 546269002696 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 546269002697 FeoA domain; Region: FeoA; pfam04023 546269002698 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 546269002699 MgtE intracellular N domain; Region: MgtE_N; pfam03448 546269002700 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 546269002701 Divalent cation transporter; Region: MgtE; pfam01769 546269002702 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 546269002703 Macro domain, Appr-1"-pase_like family. The macro domain is 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...; Region: Macro_Appr_pase_like; cd02908 546269002704 putative ADP-ribose binding site [chemical binding]; other site 546269002705 putative active site [active] 546269002706 DKNYY family; Region: DKNYY; pfam13644 546269002707 DKNYY family; Region: DKNYY; pfam13644 546269002708 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 546269002709 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 546269002710 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 546269002711 alanine racemase; Reviewed; Region: alr; PRK00053 546269002712 active site 546269002713 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 546269002714 dimer interface [polypeptide binding]; other site 546269002715 substrate binding site [chemical binding]; other site 546269002716 catalytic residues [active] 546269002717 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 546269002718 Short C-terminal domain; Region: SHOCT; pfam09851 546269002719 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 546269002720 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 546269002721 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 546269002722 active site 546269002723 HIGH motif; other site 546269002724 nucleotide binding site [chemical binding]; other site 546269002725 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 546269002726 active site 546269002727 KMSKS motif; other site 546269002728 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 546269002729 tRNA binding surface [nucleotide binding]; other site 546269002730 anticodon binding site; other site 546269002731 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269002732 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269002733 heat shock protein 90; Provisional; Region: PRK05218 546269002734 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 546269002735 ATP binding site [chemical binding]; other site 546269002736 Mg2+ binding site [ion binding]; other site 546269002737 G-X-G motif; other site 546269002738 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 546269002739 WXG100 protein secretion system (Wss), protein YukC; Region: YukC; cl01868 546269002740 Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is...; Region: Sortase; cl09098 546269002741 active site 546269002742 catalytic site [active] 546269002743 EDD domain protein, DegV family; Region: DegV; TIGR00762 546269002744 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 546269002745 helicase-exonuclease AddAB, AddA subunit, Firmicutes type; Region: addA_Gpos; TIGR02785 546269002746 Family description; Region: UvrD_C_2; pfam13538 546269002747 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 546269002748 helicase-exonuclease AddAB, AddB subunit; Region: addB_Gpos; TIGR02773 546269002749 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 546269002750 Isochorismatase family; Region: Isochorismatase; pfam00857 546269002751 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 546269002752 catalytic triad [active] 546269002753 conserved cis-peptide bond; other site 546269002754 multifunctional aminopeptidase A; Provisional; Region: PRK00913 546269002755 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 546269002756 interface (dimer of trimers) [polypeptide binding]; other site 546269002757 Substrate-binding/catalytic site; other site 546269002758 Zn-binding sites [ion binding]; other site 546269002759 Transcriptional regulators [Transcription]; Region: GntR; COG1802 546269002760 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 546269002761 DNA-binding site [nucleotide binding]; DNA binding site 546269002762 FCD domain; Region: FCD; pfam07729 546269002763 M20 Peptidase Arginine utilization protein, RocB; Region: M20_ArgE_RocB; cd05654 546269002764 putative metal binding site [ion binding]; other site 546269002765 Peptidase family M20/M25/M40; Region: Peptidase_M20; pfam01546 546269002766 putative dimer interface [polypeptide binding]; other site 546269002767 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 546269002768 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 546269002769 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 546269002770 Amidinotransferase; Region: Amidinotransf; pfam02274 546269002771 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 546269002772 Amidinotransferase; Region: Amidinotransf; pfam02274 546269002773 Virulence factor BrkB; Region: Virul_fac_BrkB; pfam03631 546269002774 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3314 546269002775 Nucleoside recognition; Region: Gate; pfam07670 546269002776 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269002777 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269002778 Integrase core domain; Region: rve; pfam00665 546269002779 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 546269002780 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 546269002781 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 546269002782 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 546269002783 RNA binding site [nucleotide binding]; other site 546269002784 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 546269002785 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 546269002786 FeS/SAM binding site; other site 546269002787 G5 domain; Region: G5; pfam07501 546269002788 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269002789 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269002790 Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and similar proteins; Region: CE4_yadE_5s; cd10966 546269002791 putative active site [active] 546269002792 putative metal binding site [ion binding]; other site 546269002793 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 546269002794 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 546269002795 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 546269002796 propionate/acetate kinase; Provisional; Region: PRK12379 546269002797 Predicted membrane protein [Function unknown]; Region: COG2855 546269002798 Domain of unknown function (DUF4364); Region: DUF4364; pfam14277 546269002799 Predicted membrane protein (DUF2157); Region: DUF2157; cl10480 546269002800 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 546269002801 dimerization interface [polypeptide binding]; other site 546269002802 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 546269002803 DPS ferroxidase diiron center [ion binding]; other site 546269002804 ion pore; other site 546269002805 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 546269002806 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 546269002807 motif II; other site 546269002808 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269002809 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269002810 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 546269002811 Walker A/P-loop; other site 546269002812 ATP binding site [chemical binding]; other site 546269002813 Q-loop/lid; other site 546269002814 ABC transporter signature motif; other site 546269002815 Walker B; other site 546269002816 D-loop; other site 546269002817 H-loop/switch region; other site 546269002818 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 546269002819 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 546269002820 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 546269002821 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 546269002822 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 546269002823 NAD(P) binding site [chemical binding]; other site 546269002824 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 546269002825 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 546269002826 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 546269002827 Walker A motif; other site 546269002828 ATP binding site [chemical binding]; other site 546269002829 Walker B motif; other site 546269002830 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 546269002831 Clp protease; Region: CLP_protease; pfam00574 546269002832 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 546269002833 oligomer interface [polypeptide binding]; other site 546269002834 active site residues [active] 546269002835 trigger factor; Provisional; Region: tig; PRK01490 546269002836 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 546269002837 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 546269002838 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269002839 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269002840 Integrase core domain; Region: rve; pfam00665 546269002841 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard...; Region: Maf_Ham1; cl00276 546269002842 putative active site [active] 546269002843 general stress protein 13; Validated; Region: PRK08059 546269002844 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_hs4; cd05692 546269002845 RNA binding site [nucleotide binding]; other site 546269002846 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 546269002847 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 546269002848 enolase; Provisional; Region: eno; PRK00077 546269002849 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 546269002850 dimer interface [polypeptide binding]; other site 546269002851 metal binding site [ion binding]; metal-binding site 546269002852 substrate binding pocket [chemical binding]; other site 546269002853 triosephosphate isomerase; Provisional; Region: PRK14567 546269002854 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 546269002855 substrate binding site [chemical binding]; other site 546269002856 dimer interface [polypeptide binding]; other site 546269002857 catalytic triad [active] 546269002858 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 546269002859 Phosphoglycerate kinase; Region: PGK; pfam00162 546269002860 substrate binding site [chemical binding]; other site 546269002861 hinge regions; other site 546269002862 ADP binding site [chemical binding]; other site 546269002863 catalytic site [active] 546269002864 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 546269002865 glyceraldehyde-3-phosphate dehydrogenase; Validated; Region: PRK07729 546269002866 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 546269002867 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 546269002868 Glutaminase; Region: Glutaminase; cl00907 546269002869 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 546269002870 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 546269002871 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 546269002872 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 546269002873 ATP binding site [chemical binding]; other site 546269002874 Mg2+ binding site [ion binding]; other site 546269002875 G-X-G motif; other site 546269002876 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 546269002877 ATP binding site [chemical binding]; other site 546269002878 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 546269002879 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 546269002880 MutS domain I; Region: MutS_I; pfam01624 546269002881 MutS domain II; Region: MutS_II; pfam05188 546269002882 MutS domain III; Region: MutS_III; pfam05192 546269002883 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 546269002884 Walker A/P-loop; other site 546269002885 ATP binding site [chemical binding]; other site 546269002886 Q-loop/lid; other site 546269002887 ABC transporter signature motif; other site 546269002888 Walker B; other site 546269002889 D-loop; other site 546269002890 H-loop/switch region; other site 546269002891 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14328 546269002892 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 546269002893 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 546269002894 FeS/SAM binding site; other site 546269002895 TRAM domain; Region: TRAM; cl01282 546269002896 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 546269002897 putative dimer interface [polypeptide binding]; other site 546269002898 catalytic triad [active] 546269002899 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269002900 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 546269002901 DNA binding residues [nucleotide binding] 546269002902 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of...; Region: MTH1175; cd00851 546269002903 Fibronectin-binding protein A N-terminus (FbpA); Region: FbpA; pfam05833 546269002904 Domain of unknown function (DUF814); Region: DUF814; pfam05670 546269002905 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 546269002906 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 546269002907 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269002908 active site 546269002909 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 546269002910 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 546269002911 Substrate binding site; other site 546269002912 Mg++ binding site; other site 546269002913 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 546269002914 active site 546269002915 substrate binding site [chemical binding]; other site 546269002916 CoA binding site [chemical binding]; other site 546269002917 FOG: CBS domain [General function prediction only]; Region: COG0517 546269002918 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; cd02205 546269002919 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cd02116 546269002920 Domain of unknown function DUF21; Region: DUF21; pfam01595 546269002921 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 546269002922 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 546269002923 Transporter associated domain; Region: CorC_HlyC; smart01091 546269002924 exopolyphosphatase; Region: exo_poly_only; TIGR03706 546269002925 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 546269002926 Septum formation initiator; Region: DivIC; cl17659 546269002927 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 546269002928 RNA binding surface [nucleotide binding]; other site 546269002929 Predicted methyltransferases [General function prediction only]; Region: COG0313 546269002930 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 546269002931 putative SAM binding site [chemical binding]; other site 546269002932 putative homodimer interface [polypeptide binding]; other site 546269002933 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 546269002934 Methyltransferase domain; Region: Methyltransf_26; pfam13659 546269002935 Uncharacterized homolog of PSP1 [Function unknown]; Region: COG1774 546269002936 DNA polymerase III, delta subunit; Region: DNA_pol3_delta2; pfam13177 546269002937 DNA polymerase III subunit delta'; Validated; Region: PRK08485 546269002938 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 546269002939 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 546269002940 TMP-binding site; other site 546269002941 ATP-binding site [chemical binding]; other site 546269002942 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 546269002943 homotrimer interaction site [polypeptide binding]; other site 546269002944 putative active site [active] 546269002945 SpoVG; Region: SpoVG; cl00915 546269002946 CAAX protease self-immunity; Region: Abi; pfam02517 546269002947 pur operon repressor; Provisional; Region: PRK09213 546269002948 Bacterial purine repressor, N-terminal; Region: PuR_N; pfam09182 546269002949 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269002950 active site 546269002951 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 546269002952 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 546269002953 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 546269002954 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 546269002955 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 546269002956 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 546269002957 glycosyltransferase; Provisional; Region: PRK13481 546269002958 Transglycosylase; Region: Transgly; pfam00912 546269002959 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 546269002960 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 546269002961 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 546269002962 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 546269002963 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 546269002964 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 546269002965 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 546269002966 Predicted membrane protein [Function unknown]; Region: COG4129 546269002967 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 546269002968 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269002969 Coenzyme A binding pocket [chemical binding]; other site 546269002970 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 546269002971 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 546269002972 NAD(P) binding site [chemical binding]; other site 546269002973 active site 546269002974 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 546269002975 DNA-binding site [nucleotide binding]; DNA binding site 546269002976 RNA-binding motif; other site 546269002977 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 546269002978 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 546269002979 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 546269002980 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 546269002981 N-acetyl-D-glucosamine binding site [chemical binding]; other site 546269002982 catalytic residue [active] 546269002983 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 546269002984 dephospho-CoA kinase; Region: TIGR00152 546269002985 CoA-binding site [chemical binding]; other site 546269002986 DNA polymerase I; Provisional; Region: PRK05755 546269002987 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 546269002988 active site 546269002989 metal binding site 1 [ion binding]; metal-binding site 546269002990 putative 5' ssDNA interaction site; other site 546269002991 metal binding site 3; metal-binding site 546269002992 metal binding site 2 [ion binding]; metal-binding site 546269002993 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 546269002994 putative DNA binding site [nucleotide binding]; other site 546269002995 putative metal binding site [ion binding]; other site 546269002996 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 546269002997 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 546269002998 active site 546269002999 DNA binding site [nucleotide binding] 546269003000 catalytic site [active] 546269003001 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269003002 Uncharacterized protein with SCP/PR1 domains [Function unknown]; Region: COG2340 546269003003 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 546269003004 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 546269003005 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 546269003006 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 546269003007 TRAM domain; Region: TRAM; cl01282 546269003008 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 546269003009 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 546269003010 S-adenosylmethionine binding site [chemical binding]; other site 546269003011 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 546269003012 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 546269003013 catalytic residues [active] 546269003014 catalytic nucleophile [active] 546269003015 Recombinase; Region: Recombinase; pfam07508 546269003016 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 546269003017 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 546269003018 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269003019 catalytic residue [active] 546269003020 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 546269003021 ORF6N domain; Region: ORF6N; pfam10543 546269003022 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 546269003023 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; cl02788 546269003024 catalytic residues [active] 546269003025 Recombinase; Region: Recombinase; pfam07508 546269003026 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 546269003027 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 546269003028 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; cl02788 546269003029 catalytic residues [active] 546269003030 catalytic nucleophile [active] 546269003031 Recombinase; Region: Recombinase; pfam07508 546269003032 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 546269003033 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 546269003034 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; cl02788 546269003035 catalytic residues [active] 546269003036 catalytic nucleophile [active] 546269003037 Recombinase; Region: Recombinase; pfam07508 546269003038 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 546269003039 Domain of unknown function (DUF4368); Region: DUF4368; pfam14287 546269003040 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269003041 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269003042 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269003043 Q-loop/lid; other site 546269003044 ABC transporter signature motif; other site 546269003045 Walker B; other site 546269003046 D-loop; other site 546269003047 H-loop/switch region; other site 546269003048 DNA binding domain of tn916 integrase; Region: Integrase_DNA; pfam02920 546269003049 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 546269003050 Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and...; Region: INT_Tn1545_C; cd01199 546269003051 Int/Topo IB signature motif; other site 546269003052 Excisionase from transposon Tn916; Region: Tn916-Xis; pfam09035 546269003053 Helix-turn-helix domain; Region: HTH_16; pfam12645 546269003054 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269003055 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 546269003056 DNA binding residues [nucleotide binding] 546269003057 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 546269003058 non-specific DNA binding site [nucleotide binding]; other site 546269003059 salt bridge; other site 546269003060 sequence-specific DNA binding site [nucleotide binding]; other site 546269003061 Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]; Region: FusA; COG0480 546269003062 Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline resistant proteins; Region: TetM_like; cd04168 546269003063 G1 box; other site 546269003064 putative GEF interaction site [polypeptide binding]; other site 546269003065 GTP/Mg2+ binding site [chemical binding]; other site 546269003066 Switch I region; other site 546269003067 G2 box; other site 546269003068 G3 box; other site 546269003069 Switch II region; other site 546269003070 G4 box; other site 546269003071 G5 box; other site 546269003072 Tet_II: This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome...; Region: Tet_II; cd03690 546269003073 EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit...; Region: Tet_like_IV; cd01684 546269003074 Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a...; Region: Tet_C; cd03711 546269003075 Conjugative transposon protein TcpC; Region: TpcC; pfam12642 546269003076 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 546269003077 N-acetyl-D-glucosamine binding site [chemical binding]; other site 546269003078 catalytic residue [active] 546269003079 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269003080 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269003081 ABC-2 family transporter protein; Region: ABC2_membrane_5; pfam13346 546269003082 Haemolysin-III related; Region: HlyIII; cl03831 546269003083 MAP7 (E-MAP-115) family; Region: MAP7; pfam05672 546269003084 AAA-like domain; Region: AAA_10; pfam12846 546269003085 TcpE family; Region: TcpE; pfam12648 546269003086 Antirestriction protein (ArdA); Region: ArdA; pfam07275 546269003087 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 546269003088 non-specific DNA binding site [nucleotide binding]; other site 546269003089 salt bridge; other site 546269003090 sequence-specific DNA binding site [nucleotide binding]; other site 546269003091 Replication initiation factor; Region: Rep_trans; pfam02486 546269003092 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 546269003093 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 546269003094 Walker A motif; other site 546269003095 ATP binding site [chemical binding]; other site 546269003096 Walker B motif; other site 546269003097 arginine finger; other site 546269003098 Bacterial protein of unknown function (DUF961); Region: DUF961; pfam06125 546269003099 Bacterial protein of unknown function (DUF961); Region: DUF961; pfam06125 546269003100 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269003101 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 546269003102 Walker A/P-loop; other site 546269003103 ATP binding site [chemical binding]; other site 546269003104 Q-loop/lid; other site 546269003105 ABC transporter signature motif; other site 546269003106 Walker B; other site 546269003107 D-loop; other site 546269003108 H-loop/switch region; other site 546269003109 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269003110 Walker A/P-loop; other site 546269003111 ATP binding site [chemical binding]; other site 546269003112 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 546269003113 Hypothetical bacterial integral membrane protein (Trep_Strep); Region: Trep_Strep; cl09823 546269003114 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 546269003115 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269003116 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269003117 Walker A/P-loop; other site 546269003118 ATP binding site [chemical binding]; other site 546269003119 Q-loop/lid; other site 546269003120 ABC transporter signature motif; other site 546269003121 Walker B; other site 546269003122 D-loop; other site 546269003123 H-loop/switch region; other site 546269003124 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 546269003125 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269003126 Walker A/P-loop; other site 546269003127 ATP binding site [chemical binding]; other site 546269003128 Q-loop/lid; other site 546269003129 ABC transporter signature motif; other site 546269003130 Walker B; other site 546269003131 D-loop; other site 546269003132 H-loop/switch region; other site 546269003133 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 546269003134 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 546269003135 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 546269003136 Methyltransferase domain; Region: Methyltransf_26; pfam13659 546269003137 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 546269003138 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 546269003139 DEAD-like helicases superfamily; Region: DEXDc; smart00487 546269003140 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 546269003141 helicase superfamily c-terminal domain; Region: HELICc; smart00490 546269003142 nucleotide binding region [chemical binding]; other site 546269003143 ATP-binding site [chemical binding]; other site 546269003144 TATA element modulatory factor 1 TATA binding; Region: TMF_TATA_bd; pfam12325 546269003145 DNA topoisomerase III; Provisional; Region: PRK07726 546269003146 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 546269003147 active site 546269003148 putative interdomain interaction site [polypeptide binding]; other site 546269003149 putative metal-binding site [ion binding]; other site 546269003150 putative nucleotide binding site [chemical binding]; other site 546269003151 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 546269003152 domain I; other site 546269003153 DNA binding groove [nucleotide binding] 546269003154 phosphate binding site [ion binding]; other site 546269003155 domain II; other site 546269003156 domain III; other site 546269003157 nucleotide binding site [chemical binding]; other site 546269003158 catalytic site [active] 546269003159 domain IV; other site 546269003160 Domain of unknown function (DUF4366); Region: DUF4366; pfam14283 546269003161 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 546269003162 NlpC/P60 family; Region: NLPC_P60; pfam00877 546269003163 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 546269003164 AAA-like domain; Region: AAA_10; pfam12846 546269003165 Domain of unknown function DUF87; Region: DUF87; pfam01935 546269003166 PrgI family protein; Region: PrgI; pfam12666 546269003167 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11864 546269003168 Maff2 family; Region: Maff2; pfam12750 546269003169 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 546269003170 generic binding surface II; other site 546269003171 generic binding surface I; other site 546269003172 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 546269003173 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 546269003174 potential frameshift: common BLAST hit: gi|256821181|ref|YP_003142380.1| prophage antirepressor 546269003175 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 546269003176 Prophage antirepressor [Transcription]; Region: COG3617 546269003177 BRO family, N-terminal domain; Region: Bro-N; smart01040 546269003178 Protein of unknown function (DUF3801); Region: DUF3801; pfam12687 546269003179 DJ-1 family protein; Region: not_thiJ; TIGR01383 546269003180 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 546269003181 conserved cys residue [active] 546269003182 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 546269003183 Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation; Region: GlyDH; cd08170 546269003184 dimer interface [polypeptide binding]; other site 546269003185 active site 546269003186 metal binding site [ion binding]; metal-binding site 546269003187 CAAX protease self-immunity; Region: Abi; pfam02517 546269003188 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 546269003189 Zn2+ binding site [ion binding]; other site 546269003190 Mg2+ binding site [ion binding]; other site 546269003191 Isochorismatase family; Region: Isochorismatase; pfam00857 546269003192 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 546269003193 catalytic triad [active] 546269003194 conserved cis-peptide bond; other site 546269003195 pyruvate phosphate dikinase; Provisional; Region: PRK09279 546269003196 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 546269003197 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 546269003198 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 546269003199 PEP synthetase regulatory protein; Provisional; Region: PRK05339 546269003200 HTH domain; Region: HTH_11; pfam08279 546269003201 FOG: CBS domain [General function prediction only]; Region: COG0517 546269003202 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 546269003203 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 546269003204 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 546269003205 catalytic residue [active] 546269003206 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 546269003207 Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Region: PGDH_2; cd05303 546269003208 putative ligand binding site [chemical binding]; other site 546269003209 NAD binding site [chemical binding]; other site 546269003210 dimerization interface [polypeptide binding]; other site 546269003211 catalytic site [active] 546269003212 Protein of unknown function (DUF1015); Region: DUF1015; pfam06245 546269003213 Uncharacterized conserved protein [Function unknown]; Region: COG4198 546269003214 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269003215 Domain of unknown function (DUF4342); Region: DUF4342; pfam14242 546269003216 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 546269003217 Recombination protein O N terminal; Region: RecO_N; pfam11967 546269003218 Recombination protein O C terminal; Region: RecO_C; pfam02565 546269003219 GTPase Era; Reviewed; Region: era; PRK00089 546269003220 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 546269003221 G1 box; other site 546269003222 GTP/Mg2+ binding site [chemical binding]; other site 546269003223 Switch I region; other site 546269003224 G2 box; other site 546269003225 Switch II region; other site 546269003226 G3 box; other site 546269003227 G4 box; other site 546269003228 G5 box; other site 546269003229 metal-binding heat shock protein; Provisional; Region: PRK00016 546269003230 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 546269003231 PhoH-like protein; Region: PhoH; pfam02562 546269003232 ribonuclease PH; Reviewed; Region: rph; PRK00173 546269003233 Ribonuclease PH; Region: RNase_PH_bact; cd11362 546269003234 hexamer interface [polypeptide binding]; other site 546269003235 active site 546269003236 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 546269003237 active site 546269003238 dimerization interface [polypeptide binding]; other site 546269003239 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269003240 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 546269003241 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 546269003242 active site 546269003243 metal binding site [ion binding]; metal-binding site 546269003244 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 546269003245 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 546269003246 homodimer interface [polypeptide binding]; other site 546269003247 substrate-cofactor binding pocket; other site 546269003248 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269003249 catalytic residue [active] 546269003250 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 546269003251 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 546269003252 dimer interface [polypeptide binding]; other site 546269003253 phosphorylation site [posttranslational modification] 546269003254 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 546269003255 ATP binding site [chemical binding]; other site 546269003256 Mg2+ binding site [ion binding]; other site 546269003257 G-X-G motif; other site 546269003258 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 546269003259 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 546269003260 active site 546269003261 phosphorylation site [posttranslational modification] 546269003262 intermolecular recognition site; other site 546269003263 dimerization interface [polypeptide binding]; other site 546269003264 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 546269003265 DNA binding site [nucleotide binding] 546269003266 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 546269003267 RNA/DNA hybrid binding site [nucleotide binding]; other site 546269003268 active site 546269003269 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 546269003270 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 546269003271 GTP/Mg2+ binding site [chemical binding]; other site 546269003272 G4 box; other site 546269003273 G5 box; other site 546269003274 G1 box; other site 546269003275 Switch I region; other site 546269003276 G2 box; other site 546269003277 G3 box; other site 546269003278 Switch II region; other site 546269003279 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 546269003280 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 546269003281 TRAP transporter, 4TM/12TM fusion protein; Region: TRAP_fused; TIGR02123 546269003282 DctM-like transporters; Region: DctM; pfam06808 546269003283 Domain of unknown function (DUF1850); Region: DUF1850; cl01950 546269003284 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 546269003285 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 546269003286 membrane-bound complex binding site; other site 546269003287 Domain of unknown function (DUF4300); Region: DUF4300; pfam14133 546269003288 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 546269003289 putative RNA binding site [nucleotide binding]; other site 546269003290 Asp23 family; Region: Asp23; pfam03780 546269003291 putative phosphate acyltransferase; Provisional; Region: PRK05331 546269003292 Predicted membrane protein [Function unknown]; Region: COG3326 546269003293 RmuC family; Region: RmuC; pfam02646 546269003294 L-aspartate dehydrogenase; Provisional; Region: PRK13303 546269003295 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 546269003296 Domain of unknown function DUF108; Region: DUF108; pfam01958 546269003297 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 546269003298 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 546269003299 dimerization interface [polypeptide binding]; other site 546269003300 active site 546269003301 Quinolinate synthetase A protein; Region: NadA; pfam02445 546269003302 Nuclease-related domain; Region: NERD; pfam08378 546269003303 HRDC domain; Region: HRDC; pfam00570 546269003304 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 546269003305 Bacterial extracellular solute-binding protein; Region: SBP_bac_6; pfam13343 546269003306 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 546269003307 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 546269003308 dimer interface [polypeptide binding]; other site 546269003309 conserved gate region; other site 546269003310 putative PBP binding loops; other site 546269003311 ABC-ATPase subunit interface; other site 546269003312 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 546269003313 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 546269003314 dimer interface [polypeptide binding]; other site 546269003315 conserved gate region; other site 546269003316 putative PBP binding loops; other site 546269003317 ABC-ATPase subunit interface; other site 546269003318 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 546269003319 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269003320 Walker A/P-loop; other site 546269003321 ATP binding site [chemical binding]; other site 546269003322 Q-loop/lid; other site 546269003323 ABC transporter signature motif; other site 546269003324 Walker B; other site 546269003325 D-loop; other site 546269003326 H-loop/switch region; other site 546269003327 TOBE domain; Region: TOBE_2; pfam08402 546269003328 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269003329 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 546269003330 Clp amino terminal domain; Region: Clp_N; pfam02861 546269003331 Clp amino terminal domain; Region: Clp_N; pfam02861 546269003332 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 546269003333 Walker A motif; other site 546269003334 ATP binding site [chemical binding]; other site 546269003335 Walker B motif; other site 546269003336 arginine finger; other site 546269003337 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 546269003338 Walker A motif; other site 546269003339 ATP binding site [chemical binding]; other site 546269003340 Walker B motif; other site 546269003341 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 546269003342 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 546269003343 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 546269003344 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 546269003345 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 546269003346 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 546269003347 active site 1 [active] 546269003348 active site 2 [active] 546269003349 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 546269003350 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 546269003351 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 546269003352 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 546269003353 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 546269003354 FMN-binding domain; Region: FMN_bind; pfam04205 546269003355 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269003356 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 546269003357 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 546269003358 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 546269003359 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 546269003360 GTP-binding protein Der; Reviewed; Region: PRK00093 546269003361 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 546269003362 G1 box; other site 546269003363 GTP/Mg2+ binding site [chemical binding]; other site 546269003364 Switch I region; other site 546269003365 G2 box; other site 546269003366 Switch II region; other site 546269003367 G3 box; other site 546269003368 G4 box; other site 546269003369 G5 box; other site 546269003370 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 546269003371 G1 box; other site 546269003372 GTP/Mg2+ binding site [chemical binding]; other site 546269003373 Switch I region; other site 546269003374 G2 box; other site 546269003375 G3 box; other site 546269003376 Switch II region; other site 546269003377 G4 box; other site 546269003378 G5 box; other site 546269003379 serine O-acetyltransferase; Region: cysE; TIGR01172 546269003380 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 546269003381 trimer interface [polypeptide binding]; other site 546269003382 active site 546269003383 substrate binding site [chemical binding]; other site 546269003384 CoA binding site [chemical binding]; other site 546269003385 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 546269003386 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 546269003387 dimer interface [polypeptide binding]; other site 546269003388 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269003389 catalytic residue [active] 546269003390 TIGR03943 family protein; Region: TIGR03943 546269003391 Predicted permeases [General function prediction only]; Region: COG0701 546269003392 Integral membrane protein (intg_mem_TP0381); Region: Intg_mem_TP0381; pfam09529 546269003393 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269003394 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 546269003395 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 546269003396 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 546269003397 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 546269003398 Ligand binding site [chemical binding]; other site 546269003399 Electron transfer flavoprotein domain; Region: ETF; pfam01012 546269003400 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 546269003401 Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases; Region: SCAD_SBCAD; cd01158 546269003402 FAD binding site [chemical binding]; other site 546269003403 homotetramer interface [polypeptide binding]; other site 546269003404 substrate binding pocket [chemical binding]; other site 546269003405 catalytic base [active] 546269003406 putative acyltransferase; Provisional; Region: PRK05790 546269003407 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 546269003408 dimer interface [polypeptide binding]; other site 546269003409 active site 546269003410 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 546269003411 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 546269003412 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 546269003413 3-hydroxybutyryl-CoA dehydratase; Validated; Region: PRK05809 546269003414 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 546269003415 substrate binding site [chemical binding]; other site 546269003416 oxyanion hole (OAH) forming residues; other site 546269003417 trimer interface [polypeptide binding]; other site 546269003418 Protein of unknown function (DUF523); Region: DUF523; pfam04463 546269003419 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 546269003420 23S rRNA binding site [nucleotide binding]; other site 546269003421 L21 binding site [polypeptide binding]; other site 546269003422 L13 binding site [polypeptide binding]; other site 546269003423 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 546269003424 Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]; Region: InfC; COG0290 546269003425 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 546269003426 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 546269003427 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 546269003428 Coenzyme A binding pocket [chemical binding]; other site 546269003429 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 546269003430 RNA binding site [nucleotide binding]; other site 546269003431 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 546269003432 RNA binding site [nucleotide binding]; other site 546269003433 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 546269003434 RNA binding site [nucleotide binding]; other site 546269003435 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 546269003436 RNA binding site [nucleotide binding]; other site 546269003437 LytB protein; Region: LYTB; cl00507 546269003438 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 546269003439 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 546269003440 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 546269003441 putative acyl-acceptor binding pocket; other site 546269003442 cytidylate kinase; Provisional; Region: cmk; PRK00023 546269003443 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 546269003444 CMP-binding site; other site 546269003445 The sites determining sugar specificity; other site 546269003446 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 546269003447 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 546269003448 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 546269003449 putative active site [active] 546269003450 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 546269003451 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 546269003452 RNA binding surface [nucleotide binding]; other site 546269003453 Pseudouridine synthases, RsuA subfamily; Region: PseudoU_synth_RsuA_like; cd02870 546269003454 active site 546269003455 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 546269003456 non-specific DNA binding site [nucleotide binding]; other site 546269003457 salt bridge; other site 546269003458 sequence-specific DNA binding site [nucleotide binding]; other site 546269003459 Cupin domain; Region: Cupin_2; pfam07883 546269003460 aspartate kinase; Reviewed; Region: PRK06635 546269003461 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 546269003462 putative nucleotide binding site [chemical binding]; other site 546269003463 putative catalytic residues [active] 546269003464 putative Mg ion binding site [ion binding]; other site 546269003465 putative aspartate binding site [chemical binding]; other site 546269003466 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 546269003467 putative allosteric regulatory site; other site 546269003468 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 546269003469 putative allosteric regulatory residue; other site 546269003470 homoserine kinase; Provisional; Region: PRK01212 546269003471 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 546269003472 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 546269003473 threonine synthase; Reviewed; Region: PRK06721 546269003474 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 546269003475 homodimer interface [polypeptide binding]; other site 546269003476 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269003477 catalytic residue [active] 546269003478 homoserine dehydrogenase; Provisional; Region: PRK06349 546269003479 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 546269003480 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 546269003481 elongation factor Tu; Reviewed; Region: PRK00049 546269003482 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 546269003483 G1 box; other site 546269003484 GEF interaction site [polypeptide binding]; other site 546269003485 GTP/Mg2+ binding site [chemical binding]; other site 546269003486 Switch I region; other site 546269003487 G2 box; other site 546269003488 G3 box; other site 546269003489 Switch II region; other site 546269003490 G4 box; other site 546269003491 G5 box; other site 546269003492 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 546269003493 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 546269003494 Antibiotic Binding Site [chemical binding]; other site 546269003495 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 546269003496 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 546269003497 dimer interface [polypeptide binding]; other site 546269003498 decamer (pentamer of dimers) interface [polypeptide binding]; other site 546269003499 catalytic triad [active] 546269003500 peroxidatic and resolving cysteines [active] 546269003501 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 546269003502 amidase catalytic site [active] 546269003503 Zn binding residues [ion binding]; other site 546269003504 substrate binding site [chemical binding]; other site 546269003505 Protein of unknown function (DUF2922); Region: DUF2922; pfam11148 546269003506 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 546269003507 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 546269003508 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 546269003509 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 546269003510 metal binding site [ion binding]; metal-binding site 546269003511 dimer interface [polypeptide binding]; other site 546269003512 Domain of unknown function (DUF3784); Region: DUF3784; pfam12650 546269003513 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 546269003514 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 546269003515 S-adenosylmethionine binding site [chemical binding]; other site 546269003516 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 546269003517 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 546269003518 Nitroreductase family; Region: Nitroreductase; pfam00881 546269003519 dimer interface [polypeptide binding]; other site 546269003520 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 546269003521 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 546269003522 redox-sensing transcriptional repressor Rex; Provisional; Region: PRK05472 546269003523 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 546269003524 CoA binding domain; Region: CoA_binding; pfam02629 546269003525 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 546269003526 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269003527 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269003528 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269003529 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 546269003530 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 546269003531 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 546269003532 ABC transporter; Region: ABC_tran_2; pfam12848 546269003533 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 546269003534 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 546269003535 active site 546269003536 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 546269003537 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine...; Region: DHOD_1B_like; cd04740 546269003538 heterodimer interface [polypeptide binding]; other site 546269003539 active site 546269003540 FMN binding site [chemical binding]; other site 546269003541 homodimer interface [polypeptide binding]; other site 546269003542 substrate binding site [chemical binding]; other site 546269003543 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 546269003544 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 546269003545 FAD binding pocket [chemical binding]; other site 546269003546 FAD binding motif [chemical binding]; other site 546269003547 phosphate binding motif [ion binding]; other site 546269003548 beta-alpha-beta structure motif; other site 546269003549 NAD binding pocket [chemical binding]; other site 546269003550 Iron coordination center [ion binding]; other site 546269003551 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 546269003552 active site 546269003553 dimer interface [polypeptide binding]; other site 546269003554 dihydroorotase; Validated; Region: pyrC; PRK09357 546269003555 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 546269003556 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 546269003557 active site 546269003558 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 546269003559 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 546269003560 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 546269003561 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 546269003562 Superoxide reductase-like (SORL) domain, class II; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals...; Region: SORL_classII; cd03172 546269003563 non-heme iron binding site [ion binding]; other site 546269003564 tetramer interface [polypeptide binding]; other site 546269003565 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 546269003566 Catalytic site [active] 546269003567 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 546269003568 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 546269003569 active site 546269003570 phosphorylation site [posttranslational modification] 546269003571 intermolecular recognition site; other site 546269003572 dimerization interface [polypeptide binding]; other site 546269003573 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 546269003574 dimerization interface [polypeptide binding]; other site 546269003575 DNA binding residues [nucleotide binding] 546269003576 Histidine kinase; Region: HisKA_3; pfam07730 546269003577 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 546269003578 ATP binding site [chemical binding]; other site 546269003579 Mg2+ binding site [ion binding]; other site 546269003580 G-X-G motif; other site 546269003581 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 546269003582 The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold; Region: PBP2_OppA; cd08504 546269003583 peptide binding site [polypeptide binding]; other site 546269003584 oligopeptide ABC transporter ATP-binding protein OppF; Provisional; Region: PRK15079 546269003585 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 546269003586 Walker A/P-loop; other site 546269003587 ATP binding site [chemical binding]; other site 546269003588 Q-loop/lid; other site 546269003589 ABC transporter signature motif; other site 546269003590 Walker B; other site 546269003591 D-loop; other site 546269003592 H-loop/switch region; other site 546269003593 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 546269003594 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 546269003595 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 546269003596 Walker A/P-loop; other site 546269003597 ATP binding site [chemical binding]; other site 546269003598 Q-loop/lid; other site 546269003599 ABC transporter signature motif; other site 546269003600 Walker B; other site 546269003601 D-loop; other site 546269003602 H-loop/switch region; other site 546269003603 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 546269003604 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 546269003605 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 546269003606 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 546269003607 dimer interface [polypeptide binding]; other site 546269003608 conserved gate region; other site 546269003609 putative PBP binding loops; other site 546269003610 ABC-ATPase subunit interface; other site 546269003611 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 546269003612 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 546269003613 dimer interface [polypeptide binding]; other site 546269003614 conserved gate region; other site 546269003615 putative PBP binding loops; other site 546269003616 ABC-ATPase subunit interface; other site 546269003617 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 546269003618 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 546269003619 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 546269003620 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 546269003621 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 546269003622 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 546269003623 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 546269003624 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 546269003625 G-loop; other site 546269003626 DNA binding site [nucleotide binding] 546269003627 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 546269003628 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 546269003629 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 546269003630 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 546269003631 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 546269003632 RPB10 interaction site [polypeptide binding]; other site 546269003633 RPB1 interaction site [polypeptide binding]; other site 546269003634 RPB11 interaction site [polypeptide binding]; other site 546269003635 RPB3 interaction site [polypeptide binding]; other site 546269003636 RPB12 interaction site [polypeptide binding]; other site 546269003637 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 546269003638 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 546269003639 RimM N-terminal domain; Region: RimM; pfam01782 546269003640 PRC-barrel domain; Region: PRC; pfam05239 546269003641 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 546269003642 hypothetical protein; Provisional; Region: PRK00468 546269003643 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 546269003644 signal recognition particle protein; Provisional; Region: PRK10867 546269003645 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 546269003646 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 546269003647 P loop; other site 546269003648 GTP binding site [chemical binding]; other site 546269003649 Signal peptide binding domain; Region: SRP_SPB; pfam02978 546269003650 Putative helix-turn-helix protein, YlxM / p13 like; Region: UPF0122; pfam04297 546269003651 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 546269003652 DNA binding residues [nucleotide binding] 546269003653 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 546269003654 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 546269003655 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 546269003656 alphaNTD homodimer interface [polypeptide binding]; other site 546269003657 alphaNTD - beta interaction site [polypeptide binding]; other site 546269003658 alphaNTD - beta' interaction site [polypeptide binding]; other site 546269003659 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 546269003660 30S ribosomal protein S11; Validated; Region: PRK05309 546269003661 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 546269003662 30S ribosomal protein S13; Region: bact_S13; TIGR03631 546269003663 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 546269003664 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 546269003665 rRNA binding site [nucleotide binding]; other site 546269003666 predicted 30S ribosome binding site; other site 546269003667 KOW motif of Ribosomal Protein L14; Region: KOW_RPL14; cd06088 546269003668 RNA binding site [nucleotide binding]; other site 546269003669 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 546269003670 active site 546269003671 adenylate kinase; Reviewed; Region: adk; PRK00279 546269003672 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 546269003673 AMP-binding site [chemical binding]; other site 546269003674 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 546269003675 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 546269003676 SecY translocase; Region: SecY; pfam00344 546269003677 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 546269003678 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 546269003679 23S rRNA binding site [nucleotide binding]; other site 546269003680 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 546269003681 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 546269003682 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 546269003683 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 546269003684 5S rRNA interface [nucleotide binding]; other site 546269003685 L27 interface [polypeptide binding]; other site 546269003686 23S rRNA interface [nucleotide binding]; other site 546269003687 L5 interface [polypeptide binding]; other site 546269003688 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 546269003689 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 546269003690 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 546269003691 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 546269003692 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 546269003693 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 546269003694 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 546269003695 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 546269003696 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 546269003697 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 546269003698 RNA binding site [nucleotide binding]; other site 546269003699 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 546269003700 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 546269003701 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 546269003702 putative translocon interaction site; other site 546269003703 23S rRNA interface [nucleotide binding]; other site 546269003704 signal recognition particle (SRP54) interaction site; other site 546269003705 L23 interface [polypeptide binding]; other site 546269003706 trigger factor interaction site; other site 546269003707 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 546269003708 23S rRNA interface [nucleotide binding]; other site 546269003709 5S rRNA interface [nucleotide binding]; other site 546269003710 putative antibiotic binding site [chemical binding]; other site 546269003711 L25 interface [polypeptide binding]; other site 546269003712 L27 interface [polypeptide binding]; other site 546269003713 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 546269003714 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 546269003715 G-X-X-G motif; other site 546269003716 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 546269003717 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 546269003718 putative translocon binding site; other site 546269003719 protein-rRNA interface [nucleotide binding]; other site 546269003720 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 546269003721 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 546269003722 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 546269003723 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 546269003724 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 546269003725 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 546269003726 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 546269003727 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 546269003728 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 546269003729 catalytic core [active] 546269003730 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 546269003731 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 546269003732 N-acetyl-D-glucosamine binding site [chemical binding]; other site 546269003733 catalytic residue [active] 546269003734 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 546269003735 core dimer interface [polypeptide binding]; other site 546269003736 peripheral dimer interface [polypeptide binding]; other site 546269003737 L10 interface [polypeptide binding]; other site 546269003738 L11 interface [polypeptide binding]; other site 546269003739 putative EF-Tu interaction site [polypeptide binding]; other site 546269003740 putative EF-G interaction site [polypeptide binding]; other site 546269003741 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 546269003742 23S rRNA interface [nucleotide binding]; other site 546269003743 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 546269003744 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 546269003745 mRNA/rRNA interface [nucleotide binding]; other site 546269003746 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 546269003747 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 546269003748 23S rRNA interface [nucleotide binding]; other site 546269003749 L7/L12 interface [polypeptide binding]; other site 546269003750 putative thiostrepton binding site; other site 546269003751 L25 interface [polypeptide binding]; other site 546269003752 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 546269003753 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 546269003754 putative homodimer interface [polypeptide binding]; other site 546269003755 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 546269003756 heterodimer interface [polypeptide binding]; other site 546269003757 homodimer interface [polypeptide binding]; other site 546269003758 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 546269003759 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 546269003760 PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some...; Region: pdxS; cd04727 546269003761 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1; Region: TIGR00343 546269003762 active site 546269003763 multimer interface [polypeptide binding]; other site 546269003764 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 546269003765 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 546269003766 DNA-binding site [nucleotide binding]; DNA binding site 546269003767 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 546269003768 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269003769 homodimer interface [polypeptide binding]; other site 546269003770 catalytic residue [active] 546269003771 biotin synthase; Region: bioB; TIGR00433 546269003772 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 546269003773 FeS/SAM binding site; other site 546269003774 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 546269003775 Staphylococcal nuclease homologues; Region: SNc; smart00318 546269003776 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 546269003777 Catalytic site; other site 546269003778 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 546269003779 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 546269003780 putative ATP binding site [chemical binding]; other site 546269003781 putative substrate interface [chemical binding]; other site 546269003782 HIGH Nucleotidyl Transferase; Region: HIGH_NTase1; cl17673 546269003783 hypothetical protein; Provisional; Region: PRK13670 546269003784 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 546269003785 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 546269003786 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 546269003787 active site 546269003788 (T/H)XGH motif; other site 546269003789 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 546269003790 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 546269003791 S-adenosylmethionine binding site [chemical binding]; other site 546269003792 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 546269003793 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 546269003794 generic binding surface I; other site 546269003795 generic binding surface II; other site 546269003796 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 546269003797 ATP binding site [chemical binding]; other site 546269003798 putative Mg++ binding site [ion binding]; other site 546269003799 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 546269003800 nucleotide binding region [chemical binding]; other site 546269003801 ATP-binding site [chemical binding]; other site 546269003802 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 546269003803 DAK2 domain; Region: Dak2; pfam02734 546269003804 Asp23 family; Region: Asp23; pfam03780 546269003805 Homoserine O-succinyltransferase; Region: HTS; pfam04204 546269003806 Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS); Region: GATase1_HTS; cd03131 546269003807 proposed active site lysine [active] 546269003808 conserved cys residue [active] 546269003809 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 546269003810 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 546269003811 homodimer interface [polypeptide binding]; other site 546269003812 substrate-cofactor binding pocket; other site 546269003813 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269003814 catalytic residue [active] 546269003815 Uncharacterized protein family (UPF0157); Region: UPF0157; pfam04229 546269003816 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 546269003817 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 546269003818 Predicted membrane protein [Function unknown]; Region: XynA; COG2314 546269003819 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 546269003820 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 546269003821 FeS/SAM binding site; other site 546269003822 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269003823 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269003824 Integrase core domain; Region: rve; pfam00665 546269003825 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 546269003826 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 546269003827 catalytic motif [active] 546269003828 Zn binding site [ion binding]; other site 546269003829 RibD C-terminal domain; Region: RibD_C; cl17279 546269003830 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 546269003831 Lumazine binding domain; Region: Lum_binding; pfam00677 546269003832 Lumazine binding domain; Region: Lum_binding; pfam00677 546269003833 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 546269003834 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 546269003835 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 546269003836 dimerization interface [polypeptide binding]; other site 546269003837 active site 546269003838 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 546269003839 homopentamer interface [polypeptide binding]; other site 546269003840 active site 546269003841 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 546269003842 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 546269003843 motif II; other site 546269003844 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 546269003845 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 546269003846 substrate binding pocket [chemical binding]; other site 546269003847 membrane-bound complex binding site; other site 546269003848 hinge residues; other site 546269003849 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 546269003850 dimer interface [polypeptide binding]; other site 546269003851 conserved gate region; other site 546269003852 putative PBP binding loops; other site 546269003853 ABC-ATPase subunit interface; other site 546269003854 arginine transporter ATP-binding subunit; Provisional; Region: artP; PRK11124 546269003855 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269003856 Walker A/P-loop; other site 546269003857 ATP binding site [chemical binding]; other site 546269003858 Q-loop/lid; other site 546269003859 ABC transporter signature motif; other site 546269003860 Walker B; other site 546269003861 D-loop; other site 546269003862 H-loop/switch region; other site 546269003863 phosphoglucomutase-2-like protein; Provisional; Region: PTZ00150 546269003864 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 546269003865 active site 546269003866 substrate binding site [chemical binding]; other site 546269003867 metal binding site [ion binding]; metal-binding site 546269003868 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 546269003869 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 546269003870 intersubunit interface [polypeptide binding]; other site 546269003871 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 546269003872 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 546269003873 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 546269003874 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 546269003875 ABC-ATPase subunit interface; other site 546269003876 dimer interface [polypeptide binding]; other site 546269003877 putative PBP binding regions; other site 546269003878 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 546269003879 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 546269003880 ABC-ATPase subunit interface; other site 546269003881 dimer interface [polypeptide binding]; other site 546269003882 putative PBP binding regions; other site 546269003883 Acetyltransferase (GNAT) domain; Region: Acetyltransf_8; pfam13523 546269003884 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269003885 Coenzyme A binding pocket [chemical binding]; other site 546269003886 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 546269003887 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13637 546269003888 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 546269003889 Walker A/P-loop; other site 546269003890 ATP binding site [chemical binding]; other site 546269003891 Q-loop/lid; other site 546269003892 ABC transporter signature motif; other site 546269003893 Walker B; other site 546269003894 D-loop; other site 546269003895 H-loop/switch region; other site 546269003896 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13633 546269003897 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 546269003898 Walker A/P-loop; other site 546269003899 ATP binding site [chemical binding]; other site 546269003900 Q-loop/lid; other site 546269003901 ABC transporter signature motif; other site 546269003902 Walker B; other site 546269003903 D-loop; other site 546269003904 H-loop/switch region; other site 546269003905 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 546269003906 active site 546269003907 homodimer interface [polypeptide binding]; other site 546269003908 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 546269003909 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 546269003910 NAD(P) binding site [chemical binding]; other site 546269003911 active site 546269003912 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 546269003913 Na2 binding site [ion binding]; other site 546269003914 putative substrate binding site 1 [chemical binding]; other site 546269003915 Na binding site 1 [ion binding]; other site 546269003916 putative substrate binding site 2 [chemical binding]; other site 546269003917 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 546269003918 Helix-turn-helix domain; Region: HTH_38; pfam13936 546269003919 Integrase core domain; Region: rve; pfam00665 546269003920 Uncharacterized conserved protein [Function unknown]; Region: COG1434 546269003921 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 546269003922 putative active site [active] 546269003923 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 546269003924 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 546269003925 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 546269003926 Leucine carboxyl methyltransferase; Region: LCM; pfam04072 546269003927 Acetyl-CoA hydrolase [Energy production and conversion]; Region: ACH1; COG0427 546269003928 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 546269003929 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 546269003930 Solo B3/4 domain (OB-fold DNA/RNA-binding) of Phe-aaRS-beta [General function prediction only]; Region: COG3382 546269003931 B3/4 domain; Region: B3_4; pfam03483 546269003932 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 546269003933 ATP cone domain; Region: ATP-cone; pfam03477 546269003934 Class III ribonucleotide reductase; Region: RNR_III; cd01675 546269003935 effector binding site; other site 546269003936 active site 546269003937 Zn binding site [ion binding]; other site 546269003938 glycine loop; other site 546269003939 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; cl15804 546269003940 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 546269003941 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 546269003942 Cache domain; Region: Cache_1; pfam02743 546269003943 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 546269003944 Histidine kinase; Region: His_kinase; pfam06580 546269003945 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 546269003946 ATP binding site [chemical binding]; other site 546269003947 Mg2+ binding site [ion binding]; other site 546269003948 G-X-G motif; other site 546269003949 Response regulator receiver domain; Region: Response_reg; pfam00072 546269003950 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 546269003951 active site 546269003952 phosphorylation site [posttranslational modification] 546269003953 intermolecular recognition site; other site 546269003954 dimerization interface [polypeptide binding]; other site 546269003955 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 546269003956 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 546269003957 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 546269003958 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 546269003959 SelR domain; Region: SelR; pfam01641 546269003960 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 546269003961 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 546269003962 catalytic residues [active] 546269003963 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 546269003964 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 546269003965 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 546269003966 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 546269003967 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 546269003968 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 546269003969 TM1410 hypothetical-related protein; Region: DUF297; pfam03537 546269003970 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 546269003971 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 546269003972 TPP-binding site; other site 546269003973 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 546269003974 PYR/PP interface [polypeptide binding]; other site 546269003975 dimer interface [polypeptide binding]; other site 546269003976 TPP binding site [chemical binding]; other site 546269003977 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 546269003978 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_1; cd09606 546269003979 oligoendopeptidase, M3 family; Region: M3_not_pepF; TIGR02289 546269003980 active site 546269003981 Zn binding site [ion binding]; other site 546269003982 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 546269003983 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 546269003984 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 546269003985 dimer interface [polypeptide binding]; other site 546269003986 active site 546269003987 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 546269003988 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 546269003989 NAD(P) binding site [chemical binding]; other site 546269003990 homotetramer interface [polypeptide binding]; other site 546269003991 homodimer interface [polypeptide binding]; other site 546269003992 active site 546269003993 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 546269003994 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 546269003995 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 546269003996 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 546269003997 FMN binding site [chemical binding]; other site 546269003998 substrate binding site [chemical binding]; other site 546269003999 putative catalytic residue [active] 546269004000 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 546269004001 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 546269004002 FMN binding site [chemical binding]; other site 546269004003 substrate binding site [chemical binding]; other site 546269004004 putative catalytic residue [active] 546269004005 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 546269004006 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 546269004007 dimer interface [polypeptide binding]; other site 546269004008 active site 546269004009 CoA binding pocket [chemical binding]; other site 546269004010 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 546269004011 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 546269004012 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 546269004013 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 546269004014 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 546269004015 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 546269004016 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 546269004017 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 546269004018 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 546269004019 BPG-independent PGAM N-terminus (iPGM_N); Region: iPGM_N; cl17463 546269004020 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 546269004021 carboxyltransferase (CT) interaction site; other site 546269004022 biotinylation site [posttranslational modification]; other site 546269004023 acyl carrier protein; Provisional; Region: acpP; PRK00982 546269004024 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 546269004025 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 546269004026 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 546269004027 homodimer interface [polypeptide binding]; other site 546269004028 NAD binding pocket [chemical binding]; other site 546269004029 ATP binding pocket [chemical binding]; other site 546269004030 Mg binding site [ion binding]; other site 546269004031 active-site loop [active] 546269004032 Uncharacterized conserved protein [Function unknown]; Region: COG1739 546269004033 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 546269004034 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 546269004035 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 546269004036 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 546269004037 HflX GTPase family; Region: HflX; cd01878 546269004038 G1 box; other site 546269004039 GTP/Mg2+ binding site [chemical binding]; other site 546269004040 Switch I region; other site 546269004041 G2 box; other site 546269004042 G3 box; other site 546269004043 Switch II region; other site 546269004044 G4 box; other site 546269004045 G5 box; other site 546269004046 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269004047 Coenzyme A binding pocket [chemical binding]; other site 546269004048 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 546269004049 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 546269004050 C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related repressor; Region: CtBP_dh; cd05299 546269004051 ligand binding site [chemical binding]; other site 546269004052 NAD binding site [chemical binding]; other site 546269004053 catalytic site [active] 546269004054 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 546269004055 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 546269004056 DctM-like transporters; Region: DctM; pfam06808 546269004057 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 546269004058 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 546269004059 aspartate aminotransferase; Provisional; Region: PRK07568 546269004060 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 546269004061 pyridoxal 5'-phosphate binding site [chemical binding]; other site 546269004062 homodimer interface [polypeptide binding]; other site 546269004063 catalytic residue [active] 546269004064 Transcriptional regulators [Transcription]; Region: FadR; COG2186 546269004065 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 546269004066 DNA-binding site [nucleotide binding]; DNA binding site 546269004067 FCD domain; Region: FCD; pfam07729 546269004068 Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]; Region: COG1237 546269004069 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 546269004070 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 546269004071 minor groove reading motif; other site 546269004072 helix-hairpin-helix signature motif; other site 546269004073 substrate binding pocket [chemical binding]; other site 546269004074 active site 546269004075 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 546269004076 DNA binding and oxoG recognition site [nucleotide binding] 546269004077 LemA family; Region: LemA; cl00742 546269004078 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 546269004079 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 546269004080 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 546269004081 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 546269004082 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 546269004083 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 546269004084 ScpA/B protein; Region: ScpA_ScpB; cl00598 546269004085 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 546269004086 Peptidase family M50; Region: Peptidase_M50; pfam02163 546269004087 active site 546269004088 putative substrate binding region [chemical binding]; other site 546269004089 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 546269004090 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 546269004091 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 546269004092 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 546269004093 metal binding site 2 [ion binding]; metal-binding site 546269004094 putative DNA binding helix; other site 546269004095 metal binding site 1 [ion binding]; metal-binding site 546269004096 dimer interface [polypeptide binding]; other site 546269004097 structural Zn2+ binding site [ion binding]; other site 546269004098 Protein of unknown function (DUF1292); Region: DUF1292; cl01608 546269004099 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 546269004100 hypothetical protein; Provisional; Region: PRK05473 546269004101 Formate/nitrite transporter; Region: Form_Nir_trans; pfam01226 546269004102 flavodoxin; Provisional; Region: PRK06242 546269004103 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 546269004104 putative deacylase active site [active] 546269004105 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 546269004106 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 546269004107 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 546269004108 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 546269004109 non-specific DNA binding site [nucleotide binding]; other site 546269004110 salt bridge; other site 546269004111 sequence-specific DNA binding site [nucleotide binding]; other site 546269004112 Acetyltransferase (GNAT) domain; Region: Acetyltransf_4; pfam13420 546269004113 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 546269004114 Coenzyme A binding pocket [chemical binding]; other site 546269004115 Predicted ATPase [General function prediction only]; Region: COG3910 546269004116 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269004117 Walker A/P-loop; other site 546269004118 ATP binding site [chemical binding]; other site 546269004119 Q-loop/lid; other site 546269004120 ABC transporter signature motif; other site 546269004121 Walker B; other site 546269004122 D-loop; other site 546269004123 H-loop/switch region; other site 546269004124 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 546269004125 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 546269004126 Mg++ binding site [ion binding]; other site 546269004127 putative catalytic motif [active] 546269004128 substrate binding site [chemical binding]; other site 546269004129 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 546269004130 ATP-binding cassette domain of sbcCD; Region: ABC_sbcCD; cd03279 546269004131 Walker A/P-loop; other site 546269004132 ATP binding site [chemical binding]; other site 546269004133 Q-loop/lid; other site 546269004134 Violaxanthin de-epoxidase (VDE); Region: VDE; cl06253 546269004135 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269004136 Walker B; other site 546269004137 D-loop; other site 546269004138 H-loop/switch region; other site 546269004139 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 546269004140 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 546269004141 active site 546269004142 metal binding site [ion binding]; metal-binding site 546269004143 DNA binding site [nucleotide binding] 546269004144 Type 5 capsule protein repressor C-terminal domain; Region: SbcD_C; pfam12320 546269004145 histidyl-tRNA synthetase; Region: hisS; TIGR00442 546269004146 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 546269004147 dimer interface [polypeptide binding]; other site 546269004148 motif 1; other site 546269004149 active site 546269004150 motif 2; other site 546269004151 motif 3; other site 546269004152 Uncharacterized conserved protein [Function unknown]; Region: COG1284 546269004153 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 546269004154 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 546269004155 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 546269004156 Transcriptional regulator [Transcription]; Region: LytR; COG1316 546269004157 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 546269004158 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 546269004159 peptide chain release factor 2; Validated; Region: prfB; PRK00578 546269004160 PCRF domain; Region: PCRF; pfam03462 546269004161 RF-1 domain; Region: RF-1; pfam00472 546269004162 L-cysteine desulfidase [Amino acid transport and metabolism]; Region: COG3681 546269004163 Uncharacterized conserved protein [Function unknown]; Region: COG1284 546269004164 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 546269004165 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 546269004166 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 546269004167 glycyl-tRNA synthetase; Provisional; Region: PRK04173 546269004168 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 546269004169 motif 1; other site 546269004170 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 546269004171 active site 546269004172 motif 2; other site 546269004173 motif 3; other site 546269004174 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 546269004175 anticodon binding site; other site 546269004176 Peptidase family C69; Region: Peptidase_C69; pfam03577 546269004177 Predicted membrane protein [Function unknown]; Region: COG3601 546269004178 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 546269004179 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 546269004180 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 546269004181 dimer interface [polypeptide binding]; other site 546269004182 phosphorylation site [posttranslational modification] 546269004183 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 546269004184 ATP binding site [chemical binding]; other site 546269004185 Mg2+ binding site [ion binding]; other site 546269004186 G-X-G motif; other site 546269004187 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 546269004188 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 546269004189 active site 546269004190 phosphorylation site [posttranslational modification] 546269004191 intermolecular recognition site; other site 546269004192 dimerization interface [polypeptide binding]; other site 546269004193 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 546269004194 DNA binding site [nucleotide binding] 546269004195 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 546269004196 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cd00838 546269004197 active site 546269004198 metal binding site [ion binding]; metal-binding site 546269004199 Putative neutral zinc metallopeptidase; Region: Zn_peptidase_2; pfam04298 546269004200 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 546269004201 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 546269004202 putative active site [active] 546269004203 substrate binding site [chemical binding]; other site 546269004204 putative cosubstrate binding site; other site 546269004205 catalytic site [active] 546269004206 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 546269004207 substrate binding site [chemical binding]; other site 546269004208 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 546269004209 active site 546269004210 catalytic residues [active] 546269004211 metal binding site [ion binding]; metal-binding site 546269004212 primosome assembly protein PriA; Validated; Region: PRK05580 546269004213 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 546269004214 ATP binding site [chemical binding]; other site 546269004215 putative Mg++ binding site [ion binding]; other site 546269004216 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 546269004217 nucleotide binding region [chemical binding]; other site 546269004218 ATP-binding site [chemical binding]; other site 546269004219 Protein involved in polysaccharide intercellular adhesin (PIA) synthesis/biofilm formation [Carbohydrate transport and metabolism]; Region: COG3936 546269004220 Acyltransferase family; Region: Acyl_transf_3; pfam01757 546269004221 Collagen binding domain; Region: Collagen_bind; pfam05737 546269004222 Cna protein B-type domain; Region: Cna_B; pfam05738 546269004223 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004224 domain interaction interfaces [polypeptide binding]; other site 546269004225 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004226 domain interaction interfaces [polypeptide binding]; other site 546269004227 purine nucleoside phosphorylase; Provisional; Region: PRK08202 546269004228 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 546269004229 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 546269004230 ligand binding site [chemical binding]; other site 546269004231 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 546269004232 intersubunit interface [polypeptide binding]; other site 546269004233 active site 546269004234 catalytic residue [active] 546269004235 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 546269004236 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 546269004237 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 546269004238 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 546269004239 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 546269004240 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 546269004241 TM-ABC transporter signature motif; other site 546269004242 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 546269004243 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 546269004244 TM-ABC transporter signature motif; other site 546269004245 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 546269004246 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 546269004247 Walker A/P-loop; other site 546269004248 ATP binding site [chemical binding]; other site 546269004249 Q-loop/lid; other site 546269004250 ABC transporter signature motif; other site 546269004251 Walker B; other site 546269004252 D-loop; other site 546269004253 H-loop/switch region; other site 546269004254 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 546269004255 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 546269004256 active site 546269004257 catalytic motif [active] 546269004258 Zn binding site [ion binding]; other site 546269004259 Kynurenine formamidase [Amino acid transport and metabolism]; Region: COG1878 546269004260 Bacillus subtilis aldehyde dehydrogenase ywdH-like; Region: ALDH_YwdH-P39616; cd07136 546269004261 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 546269004262 NAD(P) binding site [chemical binding]; other site 546269004263 catalytic residues [active] 546269004264 dUTPase; Provisional; Region: PHA03129 546269004265 Protein of unknown function (DUF1113); Region: DUF1113; pfam06541 546269004266 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 546269004267 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 546269004268 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 546269004269 ATP binding site [chemical binding]; other site 546269004270 putative Mg++ binding site [ion binding]; other site 546269004271 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 546269004272 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 546269004273 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 546269004274 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 546269004275 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 546269004276 HsdM N-terminal domain; Region: HsdM_N; pfam12161 546269004277 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 546269004278 Methyltransferase domain; Region: Methyltransf_26; pfam13659 546269004279 Domain of unknown function (DUF1877); Region: DUF1877; pfam08974 546269004280 gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit; Region: galliderm_ABC; TIGR03740 546269004281 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269004282 Walker A/P-loop; other site 546269004283 ATP binding site [chemical binding]; other site 546269004284 Q-loop/lid; other site 546269004285 ABC transporter signature motif; other site 546269004286 Walker B; other site 546269004287 D-loop; other site 546269004288 H-loop/switch region; other site 546269004289 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 546269004290 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 546269004291 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 546269004292 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 546269004293 non-specific DNA binding site [nucleotide binding]; other site 546269004294 salt bridge; other site 546269004295 sequence-specific DNA binding site [nucleotide binding]; other site 546269004296 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 546269004297 HD domain; Region: HD_4; pfam13328 546269004298 EcoKI restriction-modification system protein HsdS; Provisional; Region: PRK09737 546269004299 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 546269004300 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 546269004301 HsdM N-terminal domain; Region: HsdM_N; pfam12161 546269004302 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 546269004303 Methyltransferase domain; Region: Methyltransf_26; pfam13659 546269004304 type I restriction enzyme EcoKI subunit R; Provisional; Region: hsdR; PRK11448 546269004305 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 546269004306 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 546269004307 ATP binding site [chemical binding]; other site 546269004308 putative Mg++ binding site [ion binding]; other site 546269004309 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 546269004310 nucleotide binding region [chemical binding]; other site 546269004311 ATP-binding site [chemical binding]; other site 546269004312 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 546269004313 Cation efflux family; Region: Cation_efflux; pfam01545 546269004314 Helix-turn-helix domain; Region: HTH_17; cl17695 546269004315 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 546269004316 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 546269004317 non-specific DNA binding site [nucleotide binding]; other site 546269004318 salt bridge; other site 546269004319 sequence-specific DNA binding site [nucleotide binding]; other site 546269004320 GMP synthase; Reviewed; Region: guaA; PRK00074 546269004321 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 546269004322 AMP/PPi binding site [chemical binding]; other site 546269004323 candidate oxyanion hole; other site 546269004324 catalytic triad [active] 546269004325 potential glutamine specificity residues [chemical binding]; other site 546269004326 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 546269004327 ATP Binding subdomain [chemical binding]; other site 546269004328 Ligand Binding sites [chemical binding]; other site 546269004329 Dimerization subdomain; other site 546269004330 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 546269004331 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 546269004332 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 546269004333 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 546269004334 active site 546269004335 Thiamine transporter protein (Thia_YuaJ); Region: Thia_YuaJ; pfam09515 546269004336 Glutaminase [Amino acid transport and metabolism]; Region: GlsA; COG2066 546269004337 Glutaminase; Region: Glutaminase; cl00907 546269004338 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 546269004339 amino acid carrier protein; Region: agcS; TIGR00835 546269004340 Uncharacterized conserved protein, contains S4-like domain [Function unknown]; Region: COG2302 546269004341 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 546269004342 RNA binding surface [nucleotide binding]; other site 546269004343 YGGT family; Region: YGGT; pfam02325 546269004344 Protein of unknown function (DUF552); Region: DUF552; pfam04472 546269004345 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 546269004346 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 546269004347 catalytic residue [active] 546269004348 HlyD family secretion protein; Region: HlyD_2; pfam12700 546269004349 putative membrane fusion protein; Region: TIGR02828 546269004350 RNA polymerase factor sigma-70; Validated; Region: PRK08295 546269004351 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 546269004352 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 546269004353 YacP-like NYN domain; Region: NYN_YacP; pfam05991 546269004354 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 546269004355 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 546269004356 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 546269004357 Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]; Region: WecG; COG1922 546269004358 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 546269004359 Polysaccharide pyruvyl transferase family protein [Cell wall/membrane/envelope biogenesis]; Region: WcaK; COG2327 546269004360 polysaccharide pyruvyl transferase CsaB; Region: S_layer_CsaB; TIGR03609 546269004361 Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX)...; Region: ArsC_like; cd03036 546269004362 ArsC family; Region: ArsC; pfam03960 546269004363 putative ArsC-like catalytic residues; other site 546269004364 putative TRX-like catalytic residues [active] 546269004365 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 546269004366 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269004367 4Fe-4S binding domain; Region: Fer4_5; pfam12801 546269004368 4Fe-4S dicluster domain; Region: Fer4_9; pfam13187 546269004369 4Fe-4S binding domain; Region: Fer4; pfam00037 546269004370 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 546269004371 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 546269004372 catalytic residues [active] 546269004373 CAAX protease self-immunity; Region: Abi; pfam02517 546269004374 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 546269004375 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 546269004376 active site 546269004377 phosphorylation site [posttranslational modification] 546269004378 intermolecular recognition site; other site 546269004379 dimerization interface [polypeptide binding]; other site 546269004380 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 546269004381 DNA binding site [nucleotide binding] 546269004382 HAMP domain; Region: HAMP; pfam00672 546269004383 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 546269004384 dimer interface [polypeptide binding]; other site 546269004385 phosphorylation site [posttranslational modification] 546269004386 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 546269004387 ATP binding site [chemical binding]; other site 546269004388 Mg2+ binding site [ion binding]; other site 546269004389 G-X-G motif; other site 546269004390 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 546269004391 elongation factor G; Reviewed; Region: PRK12740 546269004392 G1 box; other site 546269004393 putative GEF interaction site [polypeptide binding]; other site 546269004394 GTP/Mg2+ binding site [chemical binding]; other site 546269004395 G3 box; other site 546269004396 Switch II region; other site 546269004397 G4 box; other site 546269004398 G5 box; other site 546269004399 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 546269004400 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 546269004401 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 546269004402 hypothetical protein; Provisional; Region: PRK07329 546269004403 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 546269004404 active site 546269004405 Transposase IS200 like; Region: Y1_Tnp; pfam01797 546269004406 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 546269004407 S-layer homology domain; Region: SLH; pfam00395 546269004408 S-layer homology domain; Region: SLH; pfam00395 546269004409 S-layer homology domain; Region: SLH; pfam00395 546269004410 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 546269004411 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 546269004412 active site 546269004413 phosphorylation site [posttranslational modification] 546269004414 intermolecular recognition site; other site 546269004415 dimerization interface [polypeptide binding]; other site 546269004416 LytTr DNA-binding domain; Region: LytTR; pfam04397 546269004417 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 546269004418 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 546269004419 ATP binding site [chemical binding]; other site 546269004420 Mg2+ binding site [ion binding]; other site 546269004421 G-X-G motif; other site 546269004422 HIRAN domain; Region: HIRAN; pfam08797 546269004423 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 546269004424 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 546269004425 L-2-amino-thiazoline-4-carboxylic acid hydrolase; Region: ATC_hydrolase; pfam14196 546269004426 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269004427 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 546269004428 Walker A/P-loop; other site 546269004429 ATP binding site [chemical binding]; other site 546269004430 Q-loop/lid; other site 546269004431 ABC transporter signature motif; other site 546269004432 Walker B; other site 546269004433 D-loop; other site 546269004434 H-loop/switch region; other site 546269004435 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 546269004436 Second domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain2; cd03226 546269004437 Walker A/P-loop; other site 546269004438 ATP binding site [chemical binding]; other site 546269004439 Q-loop/lid; other site 546269004440 ABC transporter signature motif; other site 546269004441 Walker B; other site 546269004442 D-loop; other site 546269004443 H-loop/switch region; other site 546269004444 ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]; Region: CbiQ; COG0619 546269004445 Hypothetical bacterial integral membrane protein (Trep_Strep); Region: Trep_Strep; pfam09605 546269004446 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 546269004447 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 546269004448 Predicted transcriptional regulator [Transcription]; Region: COG2378 546269004449 WYL domain; Region: WYL; pfam13280 546269004450 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 546269004451 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 546269004452 trimerization site [polypeptide binding]; other site 546269004453 active site 546269004454 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 546269004455 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 546269004456 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 546269004457 catalytic residue [active] 546269004458 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 546269004459 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 546269004460 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 546269004461 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 546269004462 Walker A/P-loop; other site 546269004463 ATP binding site [chemical binding]; other site 546269004464 Q-loop/lid; other site 546269004465 ABC transporter signature motif; other site 546269004466 Walker B; other site 546269004467 D-loop; other site 546269004468 H-loop/switch region; other site 546269004469 Peptidase S8 family domain in Streptococcal C5a peptidases; Region: Peptidases_S8_C5a_Peptidase; cd07475 546269004470 putative active site [active] 546269004471 catalytic triad [active] 546269004472 PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain; Region: PA; cl08238 546269004473 PA/protease or protease-like domain interface [polypeptide binding]; other site 546269004474 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 546269004475 catalytic residues [active] 546269004476 Fn3-like domain (DUF1034); Region: DUF1034; pfam06280 546269004477 S-layer homology domain; Region: SLH; pfam00395 546269004478 S-layer homology domain; Region: SLH; pfam00395 546269004479 S-layer homology domain; Region: SLH; pfam00395 546269004480 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 546269004481 classical (c) SDRs; Region: SDR_c; cd05233 546269004482 NAD(P) binding site [chemical binding]; other site 546269004483 active site 546269004484 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 546269004485 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 546269004486 folate binding site [chemical binding]; other site 546269004487 NADP+ binding site [chemical binding]; other site 546269004488 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 546269004489 thymidylate synthase; Reviewed; Region: thyA; PRK01827 546269004490 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 546269004491 dimerization interface [polypeptide binding]; other site 546269004492 active site 546269004493 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 546269004494 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 546269004495 motif II; other site 546269004496 Predicted flavin-nucleotide-binding protein [General function prediction only]; Region: COG3467 546269004497 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 546269004498 Mechanosensitive ion channel; Region: MS_channel; pfam00924 546269004499 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 546269004500 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 546269004501 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 546269004502 RNA binding surface [nucleotide binding]; other site 546269004503 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 546269004504 transketolase; Reviewed; Region: PRK05899 546269004505 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 546269004506 TPP-binding site [chemical binding]; other site 546269004507 dimer interface [polypeptide binding]; other site 546269004508 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]; Region: COG3958 546269004509 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 546269004510 PYR/PP interface [polypeptide binding]; other site 546269004511 dimer interface [polypeptide binding]; other site 546269004512 TPP binding site [chemical binding]; other site 546269004513 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 546269004514 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 546269004515 Na+/H+ antiporter NhaC; Region: antiport_nhaC; TIGR00931 546269004516 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 546269004517 active site 546269004518 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 546269004519 substrate binding site [chemical binding]; other site 546269004520 metal binding site [ion binding]; metal-binding site 546269004521 HEAT repeats; Region: HEAT_2; pfam13646 546269004522 Cna protein B-type domain; Region: Cna_B; pfam05738 546269004523 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004524 domain interaction interfaces [polypeptide binding]; other site 546269004525 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004526 domain interaction interfaces [polypeptide binding]; other site 546269004527 Collagen binding domain; Region: Collagen_bind; pfam05737 546269004528 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004529 domain interaction interfaces [polypeptide binding]; other site 546269004530 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004531 domain interaction interfaces [polypeptide binding]; other site 546269004532 Repeat unit of collagen-binding protein domain B; Region: CollagenBindB; cd00222 546269004533 domain interaction interfaces [polypeptide binding]; other site 546269004534 Leucine-rich repeat (LRR) protein [Function unknown]; Region: COG4886 546269004535 TfoX N-terminal domain; Region: TfoX_N; pfam04993 546269004536 Protein of unknown function (DUF2185); Region: DUF2185; cl02019 546269004537 Uncharacterized protein conserved in bacteria (DUF2262); Region: DUF2262; pfam10020 546269004538 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 546269004539 30S subunit binding site; other site 546269004540 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 546269004541 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 546269004542 Membrane protein of unknown function (DUF340); Region: DUF340; pfam03956 546269004543 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 546269004544 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 546269004545 ring oligomerisation interface [polypeptide binding]; other site 546269004546 ATP/Mg binding site [chemical binding]; other site 546269004547 stacking interactions; other site 546269004548 hinge regions; other site 546269004549 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 546269004550 oligomerisation interface [polypeptide binding]; other site 546269004551 mobile loop; other site 546269004552 roof hairpin; other site 546269004553 ATP synthase subunit D; Region: ATP-synt_D; pfam01813 546269004554 V-type ATP synthase subunit B; Provisional; Region: PRK04196 546269004555 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 546269004556 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 546269004557 Walker A motif homologous position; other site 546269004558 Walker B motif; other site 546269004559 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 546269004560 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 546269004561 V-type ATP synthase subunit A; Provisional; Region: PRK04192 546269004562 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 546269004563 Walker A motif/ATP binding site; other site 546269004564 Walker B motif; other site 546269004565 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 546269004566 Protein of unknown function (DUF737); Region: DUF737; pfam05300 546269004567 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; pfam01990 546269004568 V-type ATP synthase subunit I; Validated; Region: PRK05771 546269004569 Archaeal/vacuolar-type H+-ATPase subunit C [Energy production and conversion]; Region: NtpC; COG1527 546269004570 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 546269004571 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 546269004572 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 546269004573 SelR domain; Region: SelR; pfam01641 546269004574 DHHW protein; Region: DHHW; pfam14286 546269004575 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 546269004576 HI0933-like protein; Region: HI0933_like; pfam03486 546269004577 FMN-binding domain; Region: FMN_bind; cl01081 546269004578 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269004579 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 546269004580 Walker A/P-loop; other site 546269004581 ATP binding site [chemical binding]; other site 546269004582 Q-loop/lid; other site 546269004583 ABC transporter signature motif; other site 546269004584 Walker B; other site 546269004585 D-loop; other site 546269004586 H-loop/switch region; other site 546269004587 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269004588 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 546269004589 FtsX-like permease family; Region: FtsX; pfam02687 546269004590 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269004591 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 546269004592 FtsX-like permease family; Region: FtsX; pfam02687 546269004593 Predicted membrane protein [Function unknown]; Region: COG4393 546269004594 Predicted membrane protein (DUF2318); Region: DUF2318; pfam10080 546269004595 Fe2+ transport protein; Region: Iron_transport; pfam10634 546269004596 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 546269004597 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 546269004598 FtsX-like permease family; Region: FtsX; pfam02687 546269004599 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 546269004600 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 546269004601 Walker A/P-loop; other site 546269004602 ATP binding site [chemical binding]; other site 546269004603 Q-loop/lid; other site 546269004604 ABC transporter signature motif; other site 546269004605 Walker B; other site 546269004606 D-loop; other site 546269004607 H-loop/switch region; other site 546269004608 Domain of unknown function (DUF4418); Region: DUF4418; pfam14387 546269004609 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 546269004610 Substrate binding domain of ABC-type glycine betaine transport system; Region: OpuAC; pfam04069 546269004611 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 546269004612 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 546269004613 dimer interface [polypeptide binding]; other site 546269004614 conserved gate region; other site 546269004615 putative PBP binding loops; other site 546269004616 ABC-ATPase subunit interface; other site 546269004617 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269004618 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 546269004619 Walker A/P-loop; other site 546269004620 ATP binding site [chemical binding]; other site 546269004621 Q-loop/lid; other site 546269004622 ABC transporter signature motif; other site 546269004623 Walker B; other site 546269004624 D-loop; other site 546269004625 H-loop/switch region; other site 546269004626 HTH domain; Region: HTH_11; pfam08279 546269004627 Predicted small molecule binding protein (contains 3H domain) [General function prediction only]; Region: COG1827 546269004628 3H domain; Region: 3H; pfam02829 546269004629 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 546269004630 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 546269004631 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 546269004632 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 546269004633 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 546269004634 Soluble P-type ATPase [General function prediction only]; Region: COG4087 546269004635 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 546269004636 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 546269004637 dimerization domain swap beta strand [polypeptide binding]; other site 546269004638 regulatory protein interface [polypeptide binding]; other site 546269004639 active site 546269004640 regulatory phosphorylation site [posttranslational modification]; other site 546269004641 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 546269004642 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 546269004643 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 546269004644 active site 546269004645 Ap6A binding site [chemical binding]; other site 546269004646 nudix motif; other site 546269004647 metal binding site [ion binding]; metal-binding site 546269004648 conserved hypothetical protein, cofD-related; Region: CofD_related; TIGR01826 546269004649 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 546269004650 putative substrate binding pocket [chemical binding]; other site 546269004651 dimer interface [polypeptide binding]; other site 546269004652 phosphate binding site [ion binding]; other site 546269004653 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 546269004654 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 546269004655 active site 546269004656 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 546269004657 FAD binding domain; Region: FAD_binding_4; pfam01565 546269004658 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 546269004659 Uncharacterized conserved protein [Function unknown]; Region: COG1615 546269004660 Uncharacterized protein family (UPF0182); Region: UPF0182; pfam03699 546269004661 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 546269004662 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 546269004663 SLBB domain; Region: SLBB; pfam10531 546269004664 comEA protein; Region: comE; TIGR01259 546269004665 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 546269004666 binding surface 546269004667 TPR motif; other site 546269004668 Tetratricopeptide repeat; Region: TPR_12; pfam13424 546269004669 Protein of unknown function (DUF4026); Region: DUF4026; pfam13218 546269004670 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 546269004671 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 546269004672 ribonuclease P; Reviewed; Region: rnpA; PRK00499 546269004673 Haemolytic domain; Region: Haemolytic; pfam01809 546269004674 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 546269004675 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 546269004676 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 546269004677 G-X-X-G motif; other site 546269004678 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 546269004679 RxxxH motif; other site 546269004680 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 546269004681 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 546269004682 DNA binding site [nucleotide binding] 546269004683 active site 546269004684 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 546269004685 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 546269004686 trmE is a tRNA modification GTPase; Region: trmE; cd04164 546269004687 G1 box; other site 546269004688 GTP/Mg2+ binding site [chemical binding]; other site 546269004689 Switch I region; other site 546269004690 G2 box; other site 546269004691 Switch II region; other site 546269004692 G3 box; other site 546269004693 G4 box; other site 546269004694 G5 box; other site 546269004695 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 546269004696 EDD domain protein, DegV family; Region: DegV; TIGR00762 546269004697 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 546269004698 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 546269004699 putative efflux protein, MATE family; Region: matE; TIGR00797 546269004700 Predicted membrane protein [Function unknown]; Region: COG4684 546269004701 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 546269004702 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 546269004703 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 546269004704 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 546269004705 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 546269004706 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 546269004707 dimer interface [polypeptide binding]; other site 546269004708 ssDNA binding site [nucleotide binding]; other site 546269004709 tetramer (dimer of dimers) interface [polypeptide binding]; other site 546269004710 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 546269004711 PspC domain; Region: PspC; pfam04024 546269004712 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 546269004713 catalytic residues [active] 546269004714 dimer interface [polypeptide binding]; other site 546269004715 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 546269004716 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 546269004717 Transcriptional regulator [Transcription]; Region: IclR; COG1414 546269004718 Bacterial transcriptional regulator; Region: IclR; pfam01614 546269004719 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 546269004720 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 546269004721 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 546269004722 glutaminase active site [active] 546269004723 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 546269004724 dimer interface [polypeptide binding]; other site 546269004725 active site 546269004726 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 546269004727 dimer interface [polypeptide binding]; other site 546269004728 active site 546269004729 RloB-like protein; Region: RloB; pfam13707 546269004730 RloB-like protein; Region: RloB; pfam13707 546269004731 Predicted ATPases [General function prediction only]; Region: COG1106 546269004732 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 546269004733 Walker B; other site 546269004734 D-loop; other site 546269004735 H-loop/switch region; other site 546269004736 Protein of unknown function (DUF419); Region: DUF419; cl15265 546269004737 Copper amine oxidase N-terminal domain; Region: Cu_amine_oxidN1; pfam07833 546269004738 Transcriptional regulators [Transcription]; Region: MarR; COG1846 546269004739 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 546269004740 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 546269004741 Amidohydrolase; Region: Amidohydro_4; pfam13147 546269004742 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 546269004743 active site 546269004744 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 546269004745 Cation transport protein; Region: TrkH; cl17365 546269004746 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 546269004747 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 546269004748 TrkA-N domain; Region: TrkA_N; pfam02254 546269004749 TrkA-C domain; Region: TrkA_C; pfam02080 546269004750 TrkA-N domain; Region: TrkA_N; pfam02254 546269004751 TrkA-C domain; Region: TrkA_C; pfam02080 546269004752 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 546269004753 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 546269004754 active site 546269004755 putative catalytic site [active] 546269004756 DNA binding site [nucleotide binding] 546269004757 putative phosphate binding site [ion binding]; other site 546269004758 metal binding site A [ion binding]; metal-binding site 546269004759 AP binding site [nucleotide binding]; other site 546269004760 metal binding site B [ion binding]; metal-binding site 546269004761 ParB-like nuclease domain; Region: ParB; smart00470 546269004762 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 546269004763 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 546269004764 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 546269004765 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 546269004766 Magnesium ion binding site [ion binding]; other site 546269004767 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 546269004768 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 546269004769 active site 546269004770 phosphorylation site [posttranslational modification] 546269004771 intermolecular recognition site; other site 546269004772 dimerization interface [polypeptide binding]; other site 546269004773 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 546269004774 DNA binding site [nucleotide binding] 546269004775 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 546269004776 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 546269004777 dimerization interface [polypeptide binding]; other site 546269004778 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 546269004779 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 546269004780 dimer interface [polypeptide binding]; other site 546269004781 phosphorylation site [posttranslational modification] 546269004782 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 546269004783 ATP binding site [chemical binding]; other site 546269004784 Mg2+ binding site [ion binding]; other site 546269004785 G-X-G motif; other site 546269004786 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 546269004787 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 546269004788 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 546269004789 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 546269004790 active site 546269004791 dimer interface [polypeptide binding]; other site 546269004792 motif 1; other site 546269004793 motif 2; other site 546269004794 motif 3; other site 546269004795 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 546269004796 anticodon binding site; other site 546269004797 Rubrerythrin [Energy production and conversion]; Region: COG1592 546269004798 Rubrerythrin, ferritin-like diiron-binding domain; Region: Rubrerythrin; cd01041 546269004799 binuclear metal center [ion binding]; other site 546269004800 Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and...; Region: rubredoxin_SM; cd00729 546269004801 iron binding site [ion binding]; other site 546269004802 hypothetical protein; Provisional; Region: PRK10621 546269004803 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 546269004804 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 546269004805 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 546269004806 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 546269004807 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 546269004808 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 546269004809 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 546269004810 S-adenosylmethionine binding site [chemical binding]; other site 546269004811 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 546269004812 ParB-like nuclease domain; Region: ParB; smart00470 546269004813 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 546269004814 active site residue [active] 546269004815 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 546269004816 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 546269004817 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 546269004818 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 546269004819 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 546269004820 active site residue [active] 546269004821 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cl00436 546269004822 CPxP motif; other site 546269004823 DsrE/DsrF/DrsH-like family; Region: DrsE_2; pfam13686 546269004824 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 546269004825 dimerization interface [polypeptide binding]; other site 546269004826 putative DNA binding site [nucleotide binding]; other site 546269004827 putative Zn2+ binding site [ion binding]; other site 546269004828 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 546269004829 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 546269004830 putative active site pocket [active] 546269004831 cleavage site 546269004832 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; pfam07155