-- dump date 20120504_140852 -- class Genbank::misc_feature -- table misc_feature_note -- id note 658172000001 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 658172000002 putative active site [active] 658172000003 Ap4A binding site [chemical binding]; other site 658172000004 nudix motif; other site 658172000005 putative metal binding site [ion binding]; other site 658172000006 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 658172000007 NodB motif; other site 658172000008 putative active site [active] 658172000009 putative catalytic site [active] 658172000010 Zn binding site [ion binding]; other site 658172000011 thiamine transporter ATP-binding subunit; Provisional; Region: thiQ; PRK10771 658172000012 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000013 Walker A/P-loop; other site 658172000014 ATP binding site [chemical binding]; other site 658172000015 Q-loop/lid; other site 658172000016 ABC transporter signature motif; other site 658172000017 Walker B; other site 658172000018 D-loop; other site 658172000019 H-loop/switch region; other site 658172000020 thiamine transporter membrane protein; Reviewed; Region: thiP; PRK09433 658172000021 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 658172000022 dimer interface [polypeptide binding]; other site 658172000023 conserved gate region; other site 658172000024 putative PBP binding loops; other site 658172000025 ABC-ATPase subunit interface; other site 658172000026 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 658172000027 dimer interface [polypeptide binding]; other site 658172000028 conserved gate region; other site 658172000029 putative PBP binding loops; other site 658172000030 ABC-ATPase subunit interface; other site 658172000031 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 658172000032 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 658172000033 Oligomerisation domain; Region: Oligomerisation; cl00519 658172000034 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000035 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 658172000036 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 658172000037 dimerization interface [polypeptide binding]; other site 658172000038 putative ATP binding site [chemical binding]; other site 658172000039 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 658172000040 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 658172000041 active site 658172000042 substrate binding site [chemical binding]; other site 658172000043 cosubstrate binding site; other site 658172000044 catalytic site [active] 658172000045 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 658172000046 TadE-like protein; Region: TadE; cl10688 658172000047 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 658172000048 TadE-like protein; Region: TadE; cl10688 658172000049 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 658172000050 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 658172000051 active site 658172000052 HIGH motif; other site 658172000053 nucleotide binding site [chemical binding]; other site 658172000054 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 658172000055 KMSKS motif; other site 658172000056 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 658172000057 Predicted permeases [General function prediction only]; Region: RarD; COG2962 658172000058 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 658172000059 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 658172000060 ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to...; Region: ABCC_ATM1_transporter; cd03253 658172000061 Walker A/P-loop; other site 658172000062 ATP binding site [chemical binding]; other site 658172000063 Q-loop/lid; other site 658172000064 ABC transporter signature motif; other site 658172000065 Walker B; other site 658172000066 D-loop; other site 658172000067 H-loop/switch region; other site 658172000068 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 658172000069 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 658172000070 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 658172000071 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 658172000072 putative active site [active] 658172000073 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 658172000074 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 658172000075 putative acyl-acceptor binding pocket; other site 658172000076 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000077 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 658172000078 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 658172000079 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 658172000080 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 658172000081 HSP70 interaction site [polypeptide binding]; other site 658172000082 BolA-like protein; Region: BolA; cl00386 658172000083 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 658172000084 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 658172000085 DNA binding site [nucleotide binding] 658172000086 Int/Topo IB signature motif; other site 658172000087 active site 658172000088 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 658172000089 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 658172000090 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 658172000091 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 658172000092 K+-transporting ATPase, c chain; Region: KdpC; cl00944 658172000093 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 658172000094 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 658172000095 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 658172000096 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 658172000097 catalytic residue [active] 658172000098 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 658172000099 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 658172000100 binding surface 658172000101 TPR motif; other site 658172000102 Bacitracin resistance protein BacA; Region: BacA; cl00858 658172000103 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 658172000104 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 658172000105 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 658172000106 N-terminal domain interface [polypeptide binding]; other site 658172000107 dimer interface [polypeptide binding]; other site 658172000108 substrate binding pocket (H-site) [chemical binding]; other site 658172000109 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 658172000110 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 658172000111 putative NAD(P) binding site [chemical binding]; other site 658172000112 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 658172000113 NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars; Region: ABC_NrtD_SsuB_transporters; cd03293 658172000114 Walker A/P-loop; other site 658172000115 ATP binding site [chemical binding]; other site 658172000116 Q-loop/lid; other site 658172000117 ABC transporter signature motif; other site 658172000118 Walker B; other site 658172000119 D-loop; other site 658172000120 H-loop/switch region; other site 658172000121 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; cl15413 658172000122 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 658172000123 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 658172000124 dimer interface [polypeptide binding]; other site 658172000125 conserved gate region; other site 658172000126 putative PBP binding loops; other site 658172000127 ABC-ATPase subunit interface; other site 658172000128 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; cl00427 658172000129 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 658172000130 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 658172000131 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 658172000132 GIY-YIG motif/motif A; other site 658172000133 active site 658172000134 catalytic site [active] 658172000135 putative DNA binding site [nucleotide binding]; other site 658172000136 metal binding site [ion binding]; metal-binding site 658172000137 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 658172000138 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 658172000139 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000140 DEAD-like helicases superfamily; Region: DEXDc; smart00487 658172000141 ATP binding site [chemical binding]; other site 658172000142 putative Mg++ binding site [ion binding]; other site 658172000143 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 658172000144 nucleotide binding region [chemical binding]; other site 658172000145 ATP-binding site [chemical binding]; other site 658172000146 DbpA RNA binding domain; Region: DbpA; pfam03880 658172000147 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 658172000148 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 658172000149 pyridoxal 5'-phosphate binding site [chemical binding]; other site 658172000150 homodimer interface [polypeptide binding]; other site 658172000151 catalytic residue [active] 658172000152 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 658172000153 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 658172000154 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 658172000155 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 658172000156 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 658172000157 substrate-cofactor binding pocket; other site 658172000158 pyridoxal 5'-phosphate binding site [chemical binding]; other site 658172000159 catalytic residue [active] 658172000160 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 658172000161 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 658172000162 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 658172000163 active site 658172000164 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000165 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 658172000166 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 658172000167 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 658172000168 active site 658172000169 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 658172000170 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 658172000171 active site 658172000172 metal binding site [ion binding]; metal-binding site 658172000173 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 658172000174 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 658172000175 RNA binding surface [nucleotide binding]; other site 658172000176 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 658172000177 active site 658172000178 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 658172000179 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 658172000180 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 658172000181 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 658172000182 DNA binding residues [nucleotide binding] 658172000183 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 658172000184 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 658172000185 GDP-binding site [chemical binding]; other site 658172000186 ACT binding site; other site 658172000187 IMP binding site; other site 658172000188 F0F1 ATP synthase subunit epsilon; Provisional; Region: atpC; PRK14736 658172000189 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 658172000190 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 658172000191 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 658172000192 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 658172000193 alpha subunit interaction interface [polypeptide binding]; other site 658172000194 Walker A motif; other site 658172000195 ATP binding site [chemical binding]; other site 658172000196 Walker B motif; other site 658172000197 inhibitor binding site; inhibition site 658172000198 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 658172000199 ATP synthase; Region: ATP-synt; cl00365 658172000200 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 658172000201 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 658172000202 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 658172000203 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 658172000204 beta subunit interaction interface [polypeptide binding]; other site 658172000205 Walker A motif; other site 658172000206 ATP binding site [chemical binding]; other site 658172000207 Walker B motif; other site 658172000208 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 658172000209 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 658172000210 Plant ATP synthase F0; Region: YMF19; cl07975 658172000211 primosome assembly protein PriA; Validated; Region: PRK05580 658172000212 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 658172000213 ATP binding site [chemical binding]; other site 658172000214 putative Mg++ binding site [ion binding]; other site 658172000215 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000216 Helix-turn-helix domains; Region: HTH; cl00088 658172000217 Rrf2 family protein; Region: rrf2_super; TIGR00738 658172000218 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 658172000219 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 658172000220 putative dimer interface [polypeptide binding]; other site 658172000221 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 658172000222 Flavoprotein; Region: Flavoprotein; cl08021 658172000223 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 658172000224 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 658172000225 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 658172000226 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 658172000227 ATP binding site [chemical binding]; other site 658172000228 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 658172000229 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 658172000230 S-adenosylmethionine binding site [chemical binding]; other site 658172000231 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 658172000232 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 658172000233 DNA binding site [nucleotide binding] 658172000234 catalytic residue [active] 658172000235 H2TH interface [polypeptide binding]; other site 658172000236 putative catalytic residues [active] 658172000237 turnover-facilitating residue; other site 658172000238 intercalation triad [nucleotide binding]; other site 658172000239 8OG recognition residue [nucleotide binding]; other site 658172000240 putative reading head residues; other site 658172000241 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 658172000242 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 658172000243 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 658172000244 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 658172000245 DnaA N-terminal domain; Region: DnaA_N; pfam11638 658172000246 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 658172000247 Walker A motif; other site 658172000248 ATP binding site [chemical binding]; other site 658172000249 Walker B motif; other site 658172000250 arginine finger; other site 658172000251 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 658172000252 DnaA box-binding interface [nucleotide binding]; other site 658172000253 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 658172000254 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 658172000255 FeS/SAM binding site; other site 658172000256 HemN C-terminal domain; Region: HemN_C; pfam06969 658172000257 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 658172000258 active site 658172000259 dimerization interface [polypeptide binding]; other site 658172000260 ribonuclease PH; Reviewed; Region: rph; PRK00173 658172000261 Ribonuclease PH; Region: RNase_PH_bact; cd11362 658172000262 hexamer interface [polypeptide binding]; other site 658172000263 active site 658172000264 Creatinine amidohydrolase; Region: Creatininase; cl00618 658172000265 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 658172000266 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; cl15754 658172000267 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 658172000268 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 658172000269 Ligand binding site [chemical binding]; other site 658172000270 Electron transfer flavoprotein domain; Region: ETF; pfam01012 658172000271 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 658172000272 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 658172000273 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 658172000274 argininosuccinate lyase; Provisional; Region: PRK00855 658172000275 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 658172000276 active sites [active] 658172000277 tetramer interface [polypeptide binding]; other site 658172000278 diaminopimelate decarboxylase; Region: lysA; TIGR01048 658172000279 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 658172000280 active site 658172000281 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 658172000282 substrate binding site [chemical binding]; other site 658172000283 catalytic residues [active] 658172000284 dimer interface [polypeptide binding]; other site 658172000285 FliP family; Region: FliP; cl00593 658172000286 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 658172000287 Flagellar L-ring protein; Region: FlgH; cl00905 658172000288 MgtE intracellular N domain; Region: MgtE_N; cl15244 658172000289 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 658172000290 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 658172000291 SAF domain; Region: SAF; cl00555 658172000292 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 658172000293 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 658172000294 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 658172000295 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK12782 658172000296 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 658172000297 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 658172000298 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06003 658172000299 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 658172000300 flagellum-specific ATP synthase; Validated; Region: fliI; PRK06002 658172000301 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000302 Walker A motif; other site 658172000303 ATP binding site [chemical binding]; other site 658172000304 Walker B motif; other site 658172000305 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12642 658172000306 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 658172000307 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 658172000308 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 658172000309 Flagellar motor switch protein [Cell motility and secretion]; Region: FliM; COG1868 658172000310 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 658172000311 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 658172000312 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 658172000313 MgtE intracellular N domain; Region: MgtE_N; cl15244 658172000314 FliG C-terminal domain; Region: FliG_C; pfam01706 658172000315 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 658172000316 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 658172000317 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 658172000318 DNA binding residues [nucleotide binding] 658172000319 dimerization interface [polypeptide binding]; other site 658172000320 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 658172000321 DNA binding residues [nucleotide binding] 658172000322 dimerization interface [polypeptide binding]; other site 658172000323 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 658172000324 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 658172000325 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 658172000326 glutathione synthetase; Provisional; Region: PRK05246 658172000327 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 658172000328 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172000329 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 658172000330 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 658172000331 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 658172000332 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 658172000333 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 658172000334 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 658172000335 protein binding site [polypeptide binding]; other site 658172000336 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 658172000337 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 658172000338 dimer interface [polypeptide binding]; other site 658172000339 phosphorylation site [posttranslational modification] 658172000340 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 658172000341 ATP binding site [chemical binding]; other site 658172000342 Mg2+ binding site [ion binding]; other site 658172000343 G-X-G motif; other site 658172000344 heat shock protein GrpE; Provisional; Region: PRK14140 658172000345 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 658172000346 dimer interface [polypeptide binding]; other site 658172000347 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 658172000348 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 658172000349 PhoU domain; Region: PhoU; pfam01895 658172000350 PhoU domain; Region: PhoU; pfam01895 658172000351 phosphate transporter ATP-binding protein; Provisional; Region: PRK14235 658172000352 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 658172000353 Walker A/P-loop; other site 658172000354 ATP binding site [chemical binding]; other site 658172000355 Q-loop/lid; other site 658172000356 ABC transporter signature motif; other site 658172000357 Walker B; other site 658172000358 D-loop; other site 658172000359 H-loop/switch region; other site 658172000360 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 658172000361 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 658172000362 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 658172000363 dimer interface [polypeptide binding]; other site 658172000364 conserved gate region; other site 658172000365 putative PBP binding loops; other site 658172000366 ABC-ATPase subunit interface; other site 658172000367 Phosphate ATP-binding cassette transporter; Region: DUF3708; pfam12501 658172000368 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 658172000369 dimer interface [polypeptide binding]; other site 658172000370 conserved gate region; other site 658172000371 putative PBP binding loops; other site 658172000372 ABC-ATPase subunit interface; other site 658172000373 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 658172000374 Intracellular septation protein A; Region: IspA; cl01098 658172000375 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 658172000376 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 658172000377 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 658172000378 P loop; other site 658172000379 GTP binding site [chemical binding]; other site 658172000380 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 658172000381 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 658172000382 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 658172000383 signal recognition particle protein; Provisional; Region: PRK10867 658172000384 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 658172000385 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 658172000386 P loop; other site 658172000387 GTP binding site [chemical binding]; other site 658172000388 Signal peptide binding domain; Region: SRP_SPB; pfam02978 658172000389 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 658172000390 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 658172000391 RimM N-terminal domain; Region: RimM; pfam01782 658172000392 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 658172000393 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 658172000394 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 658172000395 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000396 6-phosphogluconate dehydrogenase; Validated; Region: PRK09287 658172000397 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 658172000398 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 658172000399 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 658172000400 metal binding site [ion binding]; metal-binding site 658172000401 high-affinity zinc transporter ATPase; Reviewed; Region: znuC; PRK09544 658172000402 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000403 Walker A/P-loop; other site 658172000404 ATP binding site [chemical binding]; other site 658172000405 Q-loop/lid; other site 658172000406 ABC transporter signature motif; other site 658172000407 Walker B; other site 658172000408 D-loop; other site 658172000409 H-loop/switch region; other site 658172000410 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 658172000411 ABC-ATPase subunit interface; other site 658172000412 dimer interface [polypeptide binding]; other site 658172000413 putative PBP binding regions; other site 658172000414 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 658172000415 Ferritin-like domain; Region: Ferritin; pfam00210 658172000416 ferroxidase diiron center [ion binding]; other site 658172000417 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 658172000418 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 658172000419 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 658172000420 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 658172000421 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 658172000422 ATP binding site [chemical binding]; other site 658172000423 Walker A motif; other site 658172000424 hexamer interface [polypeptide binding]; other site 658172000425 Walker B motif; other site 658172000426 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 658172000427 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000428 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 658172000429 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 658172000430 Type IV pili component [Cell motility and secretion]; Region: COG5461; cl02279 658172000431 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 658172000432 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 658172000433 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 658172000434 SAF domain; Region: SAF; cl00555 658172000435 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 658172000436 Flp/Fap pilin component; Region: Flp_Fap; cl01585 658172000437 Flp/Fap pilin component; Region: Flp_Fap; cl01585 658172000438 Flp/Fap pilin component; Region: Flp_Fap; cl01585 658172000439 Flp/Fap pilin component; Region: Flp_Fap; cl01585 658172000440 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 658172000441 Trm112p-like protein; Region: Trm112p; cl01066 658172000442 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 658172000443 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 658172000444 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 658172000445 dimer interface [polypeptide binding]; other site 658172000446 active site 658172000447 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 658172000448 catalytic residues [active] 658172000449 substrate binding site [chemical binding]; other site 658172000450 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 658172000451 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000452 NAD(P) binding pocket [chemical binding]; other site 658172000453 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 658172000454 Fe-S cluster binding site [ion binding]; other site 658172000455 active site 658172000456 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 658172000457 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 658172000458 Walker A/P-loop; other site 658172000459 ATP binding site [chemical binding]; other site 658172000460 Q-loop/lid; other site 658172000461 ABC transporter signature motif; other site 658172000462 Walker B; other site 658172000463 D-loop; other site 658172000464 H-loop/switch region; other site 658172000465 OstA-like protein; Region: OstA; cl00844 658172000466 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 658172000467 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 658172000468 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 658172000469 tandem repeat interface [polypeptide binding]; other site 658172000470 oligomer interface [polypeptide binding]; other site 658172000471 active site residues [active] 658172000472 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 658172000473 IHF - DNA interface [nucleotide binding]; other site 658172000474 IHF dimer interface [polypeptide binding]; other site 658172000475 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 658172000476 lipoprotein signal peptidase; Provisional; Region: PRK14787 658172000477 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 658172000478 MutS domain I; Region: MutS_I; pfam01624 658172000479 MutS domain II; Region: MutS_II; pfam05188 658172000480 MutS family domain IV; Region: MutS_IV; pfam05190 658172000481 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 658172000482 Walker A/P-loop; other site 658172000483 ATP binding site [chemical binding]; other site 658172000484 Q-loop/lid; other site 658172000485 ABC transporter signature motif; other site 658172000486 Walker B; other site 658172000487 D-loop; other site 658172000488 H-loop/switch region; other site 658172000489 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 658172000490 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 658172000491 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 658172000492 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 658172000493 Transglycosylase; Region: Transgly; cl07896 658172000494 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 658172000495 peptide chain release factor 2; Validated; Region: prfB; PRK00578 658172000496 RF-1 domain; Region: RF-1; cl02875 658172000497 RF-1 domain; Region: RF-1; cl02875 658172000498 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 658172000499 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 658172000500 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 658172000501 substrate binding pocket [chemical binding]; other site 658172000502 chain length determination region; other site 658172000503 substrate-Mg2+ binding site; other site 658172000504 catalytic residues [active] 658172000505 aspartate-rich region 1; other site 658172000506 active site lid residues [active] 658172000507 aspartate-rich region 2; other site 658172000508 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 658172000509 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000510 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 658172000511 dimer interface [polypeptide binding]; other site 658172000512 motif 1; other site 658172000513 active site 658172000514 motif 2; other site 658172000515 motif 3; other site 658172000516 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 658172000517 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 658172000518 catalytic residues [active] 658172000519 structural protein; Region: PHA01972 658172000520 hypothetical protein; Region: PHA00661 658172000521 hypothetical protein; Region: PHA00662 658172000522 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 658172000523 Terminase-like family; Region: Terminase_6; pfam03237 658172000524 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 658172000525 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 658172000526 non-specific DNA binding site [nucleotide binding]; other site 658172000527 salt bridge; other site 658172000528 sequence-specific DNA binding site [nucleotide binding]; other site 658172000529 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 658172000530 BRO family, N-terminal domain; Region: Bro-N; cl10591 658172000531 TIR domain; Region: TIR_2; cl15770 658172000532 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 658172000533 Primase C terminal 2 (PriCT-2); Region: PriCT_2; pfam08707 658172000534 D5 N terminal like; Region: D5_N; cl07360 658172000535 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 658172000536 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 658172000537 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 658172000538 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 658172000539 BRO family, N-terminal domain; Region: Bro-N; cl10591 658172000540 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 658172000541 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 658172000542 active site 658172000543 substrate binding site [chemical binding]; other site 658172000544 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 658172000545 active site 658172000546 DNA binding site [nucleotide binding] 658172000547 catalytic site [active] 658172000548 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 658172000549 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 658172000550 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 658172000551 ATP binding site [chemical binding]; other site 658172000552 putative Mg++ binding site [ion binding]; other site 658172000553 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000554 nucleotide binding region [chemical binding]; other site 658172000555 ATP-binding site [chemical binding]; other site 658172000556 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; cl03295 658172000557 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 658172000558 catalytic site [active] 658172000559 G-X2-G-X-G-K; other site 658172000560 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 658172000561 DNA binding site [nucleotide binding] 658172000562 Int/Topo IB signature motif; other site 658172000563 active site 658172000564 catalytic residues [active] 658172000565 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 658172000566 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 658172000567 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 658172000568 FAD binding domain; Region: FAD_binding_4; pfam01565 658172000569 recombination protein RecR; Reviewed; Region: recR; PRK00076 658172000570 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 658172000571 putative active site [active] 658172000572 putative metal-binding site [ion binding]; other site 658172000573 tetramer interface [polypeptide binding]; other site 658172000574 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 658172000575 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 658172000576 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 658172000577 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 658172000578 Walker A motif; other site 658172000579 ATP binding site [chemical binding]; other site 658172000580 Walker B motif; other site 658172000581 arginine finger; other site 658172000582 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 658172000583 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3807 658172000584 Bacterial SH3 domain; Region: SH3_3; cl02551 658172000585 Bacterial SH3 domain; Region: SH3_3; cl02551 658172000586 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 658172000587 Ligand binding site; other site 658172000588 oligomer interface; other site 658172000589 recombination protein F; Reviewed; Region: recF; PRK00064 658172000590 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000591 Walker A/P-loop; other site 658172000592 ATP binding site [chemical binding]; other site 658172000593 Q-loop/lid; other site 658172000594 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000595 ABC transporter signature motif; other site 658172000596 Walker B; other site 658172000597 D-loop; other site 658172000598 H-loop/switch region; other site 658172000599 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 658172000600 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 658172000601 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 658172000602 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 658172000603 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 658172000604 active site 658172000605 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 658172000606 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 658172000607 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 658172000608 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 658172000609 trimer interface [polypeptide binding]; other site 658172000610 active site 658172000611 UDP-GlcNAc binding site [chemical binding]; other site 658172000612 lipid binding site [chemical binding]; lipid-binding site 658172000613 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 658172000614 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 658172000615 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 658172000616 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 658172000617 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 658172000618 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 658172000619 Surface antigen; Region: Bac_surface_Ag; cl03097 658172000620 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 658172000621 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 658172000622 active site 658172000623 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 658172000624 protein binding site [polypeptide binding]; other site 658172000625 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 658172000626 putative substrate binding region [chemical binding]; other site 658172000627 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 658172000628 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 658172000629 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 658172000630 catalytic residue [active] 658172000631 putative FPP diphosphate binding site; other site 658172000632 putative FPP binding hydrophobic cleft; other site 658172000633 dimer interface [polypeptide binding]; other site 658172000634 putative IPP diphosphate binding site; other site 658172000635 ribosome recycling factor; Reviewed; Region: frr; PRK00083 658172000636 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 658172000637 hinge region; other site 658172000638 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 658172000639 putative nucleotide binding site [chemical binding]; other site 658172000640 uridine monophosphate binding site [chemical binding]; other site 658172000641 homohexameric interface [polypeptide binding]; other site 658172000642 elongation factor Ts; Provisional; Region: tsf; PRK09377 658172000643 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 658172000644 Elongation factor TS; Region: EF_TS; pfam00889 658172000645 Elongation factor TS; Region: EF_TS; pfam00889 658172000646 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 658172000647 rRNA interaction site [nucleotide binding]; other site 658172000648 S8 interaction site; other site 658172000649 putative laminin-1 binding site; other site 658172000650 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 658172000651 HIT family signature motif; other site 658172000652 catalytic residue [active] 658172000653 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 658172000654 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 658172000655 trimer interface [polypeptide binding]; other site 658172000656 active site 658172000657 substrate binding site [chemical binding]; other site 658172000658 CoA binding site [chemical binding]; other site 658172000659 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 658172000660 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 658172000661 metal binding site [ion binding]; metal-binding site 658172000662 dimer interface [polypeptide binding]; other site 658172000663 Predicted transcriptional regulator [Transcription]; Region: COG4957 658172000664 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 658172000665 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 658172000666 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 658172000667 RNase E interface [polypeptide binding]; other site 658172000668 trimer interface [polypeptide binding]; other site 658172000669 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 658172000670 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 658172000671 RNase E interface [polypeptide binding]; other site 658172000672 trimer interface [polypeptide binding]; other site 658172000673 active site 658172000674 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 658172000675 putative nucleic acid binding region [nucleotide binding]; other site 658172000676 G-X-X-G motif; other site 658172000677 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 658172000678 RNA binding site [nucleotide binding]; other site 658172000679 domain interface; other site 658172000680 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 658172000681 16S/18S rRNA binding site [nucleotide binding]; other site 658172000682 S13e-L30e interaction site [polypeptide binding]; other site 658172000683 25S rRNA binding site [nucleotide binding]; other site 658172000684 Ribosome-binding factor A; Region: RBFA; cl00542 658172000685 translation initiation factor IF-2; Region: IF-2; TIGR00487 658172000686 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 658172000687 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 658172000688 G1 box; other site 658172000689 putative GEF interaction site [polypeptide binding]; other site 658172000690 GTP/Mg2+ binding site [chemical binding]; other site 658172000691 Switch I region; other site 658172000692 G2 box; other site 658172000693 G3 box; other site 658172000694 Switch II region; other site 658172000695 G4 box; other site 658172000696 G5 box; other site 658172000697 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 658172000698 Translation-initiation factor 2; Region: IF-2; pfam11987 658172000699 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 658172000700 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 658172000701 NusA N-terminal domain; Region: NusA_N; pfam08529 658172000702 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 658172000703 RNA binding site [nucleotide binding]; other site 658172000704 homodimer interface [polypeptide binding]; other site 658172000705 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 658172000706 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 658172000707 G-X-X-G motif; other site 658172000708 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 658172000709 ribosome maturation protein RimP; Reviewed; Region: PRK00092 658172000710 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 658172000711 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 658172000712 Sm1 motif; other site 658172000713 D3 - B interaction site; other site 658172000714 D1 - D2 interaction site; other site 658172000715 Hfq - Hfq interaction site; other site 658172000716 RNA binding pocket [nucleotide binding]; other site 658172000717 Sm2 motif; other site 658172000718 GtrA-like protein; Region: GtrA; cl00971 658172000719 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 658172000720 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 658172000721 generic binding surface II; other site 658172000722 generic binding surface I; other site 658172000723 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 658172000724 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 658172000725 MatE; Region: MatE; cl10513 658172000726 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 658172000727 active site 658172000728 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 658172000729 HIGH motif; other site 658172000730 dimer interface [polypeptide binding]; other site 658172000731 KMSKS motif; other site 658172000732 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 658172000733 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 658172000734 putative active site [active] 658172000735 putative substrate binding site [chemical binding]; other site 658172000736 ATP binding site [chemical binding]; other site 658172000737 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 658172000738 RNA/DNA hybrid binding site [nucleotide binding]; other site 658172000739 active site 658172000740 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 658172000741 putative catalytic site [active] 658172000742 putative metal binding site [ion binding]; other site 658172000743 putative phosphate binding site [ion binding]; other site 658172000744 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 658172000745 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 658172000746 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000747 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 658172000748 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 658172000749 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 658172000750 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 658172000751 catalytic residue [active] 658172000752 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 658172000753 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 658172000754 HIGH motif; other site 658172000755 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 658172000756 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 658172000757 active site 658172000758 KMSKS motif; other site 658172000759 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 658172000760 tRNA binding surface [nucleotide binding]; other site 658172000761 Lipopolysaccharide-assembly; Region: LptE; cl01125 658172000762 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 658172000763 ParB-like partition proteins; Region: parB_part; TIGR00180 658172000764 ParB-like nuclease domain; Region: ParBc; cl02129 658172000765 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 658172000766 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000767 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; cl15754 658172000768 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 658172000769 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000770 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 658172000771 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 658172000772 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 658172000773 trmE is a tRNA modification GTPase; Region: trmE; cd04164 658172000774 G1 box; other site 658172000775 GTP/Mg2+ binding site [chemical binding]; other site 658172000776 Switch I region; other site 658172000777 G2 box; other site 658172000778 Switch II region; other site 658172000779 G3 box; other site 658172000780 G4 box; other site 658172000781 G5 box; other site 658172000782 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 658172000783 transcription termination factor Rho; Provisional; Region: rho; PRK09376 658172000784 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 658172000785 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 658172000786 RNA binding site [nucleotide binding]; other site 658172000787 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 658172000788 multimer interface [polypeptide binding]; other site 658172000789 Walker A motif; other site 658172000790 ATP binding site [chemical binding]; other site 658172000791 Walker B motif; other site 658172000792 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 658172000793 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 658172000794 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 658172000795 substrate binding site [chemical binding]; other site 658172000796 active site 658172000797 Maf-like protein; Region: Maf; pfam02545 658172000798 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 658172000799 active site 658172000800 dimer interface [polypeptide binding]; other site 658172000801 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 658172000802 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 658172000803 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 658172000804 anchoring element; other site 658172000805 dimer interface [polypeptide binding]; other site 658172000806 ATP binding site [chemical binding]; other site 658172000807 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 658172000808 active site 658172000809 putative metal-binding site [ion binding]; other site 658172000810 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 658172000811 Tim44-like domain; Region: Tim44; cl09208 658172000812 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 658172000813 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 658172000814 active site 658172000815 substrate binding site [chemical binding]; other site 658172000816 catalytic site [active] 658172000817 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 658172000818 CoA-binding site [chemical binding]; other site 658172000819 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 658172000820 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 658172000821 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 658172000822 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 658172000823 catalytic residues [active] 658172000824 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 658172000825 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000826 Family description; Region: UvrD_C_2; cl15862 658172000827 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 658172000828 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 658172000829 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 658172000830 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 658172000831 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 658172000832 PAS fold; Region: PAS_7; pfam12860 658172000833 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 658172000834 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 658172000835 dimer interface [polypeptide binding]; other site 658172000836 phosphorylation site [posttranslational modification] 658172000837 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 658172000838 ATP binding site [chemical binding]; other site 658172000839 Mg2+ binding site [ion binding]; other site 658172000840 G-X-G motif; other site 658172000841 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_ATP; cd00484 658172000842 active site 658172000843 substrate-binding site [chemical binding]; other site 658172000844 metal-binding site [ion binding] 658172000845 ATP binding site [chemical binding]; other site 658172000846 pantothenate kinase; Provisional; Region: PRK05439 658172000847 Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in...; Region: PanK; cd02025 658172000848 ATP-binding site [chemical binding]; other site 658172000849 CoA-binding site [chemical binding]; other site 658172000850 Mg2+-binding site [ion binding]; other site 658172000851 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 658172000852 active site 658172000853 HslU subunit interaction site [polypeptide binding]; other site 658172000854 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 658172000855 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000856 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 658172000857 Walker A motif; other site 658172000858 ATP binding site [chemical binding]; other site 658172000859 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000860 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 658172000861 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK05963 658172000862 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 658172000863 dimer interface [polypeptide binding]; other site 658172000864 active site 658172000865 CoA binding pocket [chemical binding]; other site 658172000866 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 658172000867 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 658172000868 inhibitor-cofactor binding pocket; inhibition site 658172000869 pyridoxal 5'-phosphate binding site [chemical binding]; other site 658172000870 catalytic residue [active] 658172000871 AAA domain; Region: AAA_26; pfam13500 658172000872 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172000873 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 658172000874 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 658172000875 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 658172000876 catalytic residue [active] 658172000877 biotin synthase; Region: bioB; TIGR00433 658172000878 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 658172000879 FeS/SAM binding site; other site 658172000880 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 658172000881 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 658172000882 feedback inhibition sensing region; other site 658172000883 homohexameric interface [polypeptide binding]; other site 658172000884 nucleotide binding site [chemical binding]; other site 658172000885 N-acetyl-L-glutamate binding site [chemical binding]; other site 658172000886 Predicted GTPase [General function prediction only]; Region: COG0218 658172000887 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 658172000888 G1 box; other site 658172000889 GTP/Mg2+ binding site [chemical binding]; other site 658172000890 Switch I region; other site 658172000891 G2 box; other site 658172000892 G3 box; other site 658172000893 Switch II region; other site 658172000894 G4 box; other site 658172000895 G5 box; other site 658172000896 membrane protein insertase; Provisional; Region: PRK01318 658172000897 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 658172000898 Ribonuclease P; Region: Ribonuclease_P; cl00457 658172000899 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 658172000900 2'-deoxycytidine 5'-triphosphate deaminase; Provisional; Region: PRK07559 658172000901 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 658172000902 trimer interface [polypeptide binding]; other site 658172000903 active site 658172000904 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cl00493 658172000905 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 658172000906 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 658172000907 minor groove reading motif; other site 658172000908 helix-hairpin-helix signature motif; other site 658172000909 substrate binding pocket [chemical binding]; other site 658172000910 active site 658172000911 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 658172000912 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 658172000913 DNA binding and oxoG recognition site [nucleotide binding] 658172000914 Protein of unknown function (DUF721); Region: DUF721; cl02324 658172000915 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 658172000916 Response regulator receiver domain; Region: Response_reg; pfam00072 658172000917 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 658172000918 active site 658172000919 phosphorylation site [posttranslational modification] 658172000920 intermolecular recognition site; other site 658172000921 dimerization interface [polypeptide binding]; other site 658172000922 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 658172000923 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 658172000924 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 658172000925 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 658172000926 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 658172000927 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 658172000928 D-pathway; other site 658172000929 Putative ubiquinol binding site [chemical binding]; other site 658172000930 Low-spin heme (heme b) binding site [chemical binding]; other site 658172000931 Putative water exit pathway; other site 658172000932 Binuclear center (heme o3/CuB) [ion binding]; other site 658172000933 K-pathway; other site 658172000934 Putative proton exit pathway; other site 658172000935 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 658172000936 Subunit I/III interface [polypeptide binding]; other site 658172000937 Subunit III/IV interface [polypeptide binding]; other site 658172000938 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 658172000939 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 658172000940 RNA binding site [nucleotide binding]; other site 658172000941 Domain of unknown function (DUF329); Region: DUF329; cl01144 658172000942 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 658172000943 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 658172000944 PAS fold; Region: PAS_3; pfam08447 658172000945 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 658172000946 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 658172000947 metal binding site [ion binding]; metal-binding site 658172000948 active site 658172000949 I-site; other site 658172000950 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 658172000951 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 658172000952 Restriction endonuclease; Region: Mrr_cat; cl00516 658172000953 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000954 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 658172000955 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172000956 Fe2+ transport protein; Region: Iron_transport; cl01377 658172000957 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 658172000958 Iron permease FTR1 family; Region: FTR1; cl00475 658172000959 Predicted periplasmic lipoprotein involved in iron transport [Inorganic ion transport and metabolism]; Region: COG2822 658172000960 Imelysin; Region: Peptidase_M75; cl09159 658172000961 Dyp-type peroxidase family; Region: Dyp_perox; cl01067 658172000962 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 658172000963 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria; Region: Thr-synth_2; cd01560 658172000964 pyridoxal 5'-phosphate binding site [chemical binding]; other site 658172000965 catalytic residue [active] 658172000966 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 658172000967 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 658172000968 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 658172000969 conserved hypothetical protein YmdA/YtgF; Region: YmdA_YtgF; TIGR03319 658172000970 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06505 658172000971 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 658172000972 NAD binding site [chemical binding]; other site 658172000973 homotetramer interface [polypeptide binding]; other site 658172000974 homodimer interface [polypeptide binding]; other site 658172000975 substrate binding site [chemical binding]; other site 658172000976 active site 658172000977 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 658172000978 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 658172000979 dimer interface [polypeptide binding]; other site 658172000980 active site 658172000981 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 658172000982 active site 1 [active] 658172000983 dimer interface [polypeptide binding]; other site 658172000984 active site 2 [active] 658172000985 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4530 658172000986 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 658172000987 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 658172000988 hinge; other site 658172000989 active site 658172000990 cytidylate kinase; Provisional; Region: cmk; PRK00023 658172000991 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 658172000992 CMP-binding site; other site 658172000993 The sites determining sugar specificity; other site 658172000994 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 658172000995 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 658172000996 RNA binding site [nucleotide binding]; other site 658172000997 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 658172000998 RNA binding site [nucleotide binding]; other site 658172000999 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec3; cd05688 658172001000 RNA binding site [nucleotide binding]; other site 658172001001 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 658172001002 RNA binding site [nucleotide binding]; other site 658172001003 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of...; Region: S1_RPS1_repeat_ec5; cd05690 658172001004 RNA binding site [nucleotide binding]; other site 658172001005 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 658172001006 RNA binding site [nucleotide binding]; other site 658172001007 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 658172001008 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 658172001009 active site 658172001010 DNA polymerase III subunit beta; Validated; Region: PRK05643 658172001011 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 658172001012 putative DNA binding surface [nucleotide binding]; other site 658172001013 dimer interface [polypeptide binding]; other site 658172001014 beta-clamp/clamp loader binding surface; other site 658172001015 beta-clamp/translesion DNA polymerase binding surface; other site 658172001016 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two...; Region: OMP_decarboxylase_like; cd04725 658172001017 active site 658172001018 dimer interface [polypeptide binding]; other site 658172001019 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 658172001020 aconitate hydratase; Validated; Region: PRK09277 658172001021 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 658172001022 substrate binding site [chemical binding]; other site 658172001023 ligand binding site [chemical binding]; other site 658172001024 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 658172001025 substrate binding site [chemical binding]; other site 658172001026 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 658172001027 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 658172001028 nitrogen fixation negative regulator NifL; Region: nifL_nitrog; TIGR02938 658172001029 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 658172001030 dimer interface [polypeptide binding]; other site 658172001031 phosphorylation site [posttranslational modification] 658172001032 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 658172001033 ATP binding site [chemical binding]; other site 658172001034 Mg2+ binding site [ion binding]; other site 658172001035 G-X-G motif; other site 658172001036 Response regulator receiver domain; Region: Response_reg; pfam00072 658172001037 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 658172001038 active site 658172001039 phosphorylation site [posttranslational modification] 658172001040 intermolecular recognition site; other site 658172001041 dimerization interface [polypeptide binding]; other site 658172001042 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 658172001043 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 658172001044 active site 658172001045 HIGH motif; other site 658172001046 nucleotide binding site [chemical binding]; other site 658172001047 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 658172001048 active site 658172001049 KMSKS motif; other site 658172001050 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 658172001051 tRNA binding surface [nucleotide binding]; other site 658172001052 anticodon binding site; other site 658172001053 Predicted transcriptional regulator [Transcription]; Region: COG2932 658172001054 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 658172001055 Catalytic site [active] 658172001056 Protein of unknown function (DUF1036); Region: DUF1036; cl02296 658172001057 pyruvate kinase; Provisional; Region: PRK06247 658172001058 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 658172001059 domain interfaces; other site 658172001060 active site 658172001061 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 658172001062 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 658172001063 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 658172001064 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 658172001065 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 658172001066 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 658172001067 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 658172001068 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172001069 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 658172001070 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 658172001071 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172001072 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 658172001073 IMP binding site; other site 658172001074 dimer interface [polypeptide binding]; other site 658172001075 interdomain contacts; other site 658172001076 partial ornithine binding site; other site 658172001077 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the...; Region: PNPsynthase; cd00003 658172001078 active site 658172001079 hydrophilic channel; other site 658172001080 dimerization interface [polypeptide binding]; other site 658172001081 catalytic residues [active] 658172001082 active site lid [active] 658172001083 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 658172001084 TPR repeat; Region: TPR_11; pfam13414 658172001085 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 658172001086 binding surface 658172001087 TPR motif; other site 658172001088 TPR repeat; Region: TPR_11; pfam13414 658172001089 TPR repeat; Region: TPR_11; pfam13414 658172001090 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 658172001091 binding surface 658172001092 TPR motif; other site 658172001093 TPR repeat; Region: TPR_11; pfam13414 658172001094 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 658172001095 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 658172001096 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 658172001097 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 658172001098 active site 658172001099 catalytic residues [active] 658172001100 FMN binding site [chemical binding]; other site 658172001101 quinone interaction residues [chemical binding]; other site 658172001102 substrate binding site [chemical binding]; other site 658172001103 ornithine carbamoyltransferase; Provisional; Region: PRK00779 658172001104 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 658172001105 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001106 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 658172001107 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 658172001108 inhibitor-cofactor binding pocket; inhibition site 658172001109 pyridoxal 5'-phosphate binding site [chemical binding]; other site 658172001110 catalytic residue [active] 658172001111 GcrA cell cycle regulator; Region: GcrA; cl11564 658172001112 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 658172001113 NifU-like domain; Region: NifU; cl00484 658172001114 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 658172001115 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 658172001116 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 658172001117 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 658172001118 FeS/SAM binding site; other site 658172001119 TRAM domain; Region: TRAM; cl01282 658172001120 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 658172001121 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 658172001122 Transporter associated domain; Region: CorC_HlyC; cl08393 658172001123 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 658172001124 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 658172001125 putative active site [active] 658172001126 putative dimer interface [polypeptide binding]; other site 658172001127 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 658172001128 non-specific DNA binding site [nucleotide binding]; other site 658172001129 salt bridge; other site 658172001130 sequence-specific DNA binding site [nucleotide binding]; other site 658172001131 S-adenosylmethionine synthetase; Validated; Region: PRK05250 658172001132 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 658172001133 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 658172001134 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 658172001135 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; cl15754 658172001136 GTP-binding protein Der; Reviewed; Region: PRK00093 658172001137 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 658172001138 Switch I region; other site 658172001139 G2 box; other site 658172001140 Switch II region; other site 658172001141 G3 box; other site 658172001142 GTP/Mg2+ binding site [chemical binding]; other site 658172001143 G4 box; other site 658172001144 G5 box; other site 658172001145 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 658172001146 G1 box; other site 658172001147 GTP/Mg2+ binding site [chemical binding]; other site 658172001148 Switch I region; other site 658172001149 G2 box; other site 658172001150 G3 box; other site 658172001151 Switch II region; other site 658172001152 G4 box; other site 658172001153 G5 box; other site 658172001154 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 658172001155 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 658172001156 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 658172001157 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 658172001158 catalytic site [active] 658172001159 subunit interface [polypeptide binding]; other site 658172001160 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 658172001161 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 658172001162 dimer interface [polypeptide binding]; other site 658172001163 anticodon binding site; other site 658172001164 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the...; Region: AspRS_core; cd00777 658172001165 homodimer interface [polypeptide binding]; other site 658172001166 motif 1; other site 658172001167 active site 658172001168 motif 2; other site 658172001169 GAD domain; Region: GAD; pfam02938 658172001170 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 658172001171 active site 658172001172 motif 3; other site 658172001173 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 658172001174 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 658172001175 5S rRNA interface [nucleotide binding]; other site 658172001176 CTC domain interface [polypeptide binding]; other site 658172001177 L16 interface [polypeptide binding]; other site 658172001178 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 658172001179 Ferredoxin [Energy production and conversion]; Region: COG1146 658172001180 4Fe-4S binding domain; Region: Fer4; cl02805 658172001181 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 658172001182 Integral membrane protein TerC family; Region: TerC; cl10468 658172001183 FOG: CBS domain [General function prediction only]; Region: COG0517 658172001184 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 658172001185 Transporter associated domain; Region: CorC_HlyC; cl08393 658172001186 GMP synthase; Reviewed; Region: guaA; PRK00074 658172001187 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 658172001188 AMP/PPi binding site [chemical binding]; other site 658172001189 candidate oxyanion hole; other site 658172001190 catalytic triad [active] 658172001191 potential glutamine specificity residues [chemical binding]; other site 658172001192 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 658172001193 ATP Binding subdomain [chemical binding]; other site 658172001194 Ligand Binding sites [chemical binding]; other site 658172001195 Dimerization subdomain; other site 658172001196 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 658172001197 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 658172001198 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 658172001199 dimer interface [polypeptide binding]; other site 658172001200 phosphorylation site [posttranslational modification] 658172001201 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 658172001202 ATP binding site [chemical binding]; other site 658172001203 Mg2+ binding site [ion binding]; other site 658172001204 G-X-G motif; other site 658172001205 Membrane fusogenic activity; Region: BMFP; cl01115 658172001206 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 658172001207 Uncharacterized conserved protein [Function unknown]; Region: COG1565 658172001208 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 658172001209 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 658172001210 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 658172001211 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 658172001212 active site 658172001213 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 658172001214 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 658172001215 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 658172001216 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 658172001217 S-adenosylmethionine binding site [chemical binding]; other site 658172001218 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 658172001219 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 658172001220 purine monophosphate binding site [chemical binding]; other site 658172001221 dimer interface [polypeptide binding]; other site 658172001222 putative catalytic residues [active] 658172001223 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 658172001224 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 658172001225 active site clefts [active] 658172001226 zinc binding site [ion binding]; other site 658172001227 dimer interface [polypeptide binding]; other site 658172001228 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 658172001229 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001230 exonuclease I; Provisional; Region: sbcB; PRK11779 658172001231 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 658172001232 active site 658172001233 substrate binding site [chemical binding]; other site 658172001234 catalytic site [active] 658172001235 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 658172001236 Transcriptional regulator; Region: Transcrip_reg; cl00361 658172001237 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 658172001238 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 658172001239 putative active site [active] 658172001240 metal binding site [ion binding]; metal-binding site 658172001241 homodimer binding site [polypeptide binding]; other site 658172001242 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 658172001243 transketolase; Reviewed; Region: PRK05899 658172001244 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 658172001245 TPP-binding site [chemical binding]; other site 658172001246 dimer interface [polypeptide binding]; other site 658172001247 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 658172001248 PYR/PP interface [polypeptide binding]; other site 658172001249 dimer interface [polypeptide binding]; other site 658172001250 TPP binding site [chemical binding]; other site 658172001251 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 658172001252 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 658172001253 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001254 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 658172001255 Phosphoglycerate kinase; Region: PGK; pfam00162 658172001256 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 658172001257 substrate binding site [chemical binding]; other site 658172001258 hinge regions; other site 658172001259 ADP binding site [chemical binding]; other site 658172001260 catalytic site [active] 658172001261 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 658172001262 catalytic residue [active] 658172001263 Protein of unknown function (DUF1465); Region: DUF1465; cl11562 658172001264 Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]; Region: NadD; COG1057 658172001265 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 658172001266 active site 658172001267 (T/H)XGH motif; other site 658172001268 GTPase CgtA; Reviewed; Region: obgE; PRK12299 658172001269 GTP1/OBG; Region: GTP1_OBG; pfam01018 658172001270 Obg GTPase; Region: Obg; cd01898 658172001271 G1 box; other site 658172001272 GTP/Mg2+ binding site [chemical binding]; other site 658172001273 Switch I region; other site 658172001274 G2 box; other site 658172001275 G3 box; other site 658172001276 Switch II region; other site 658172001277 G4 box; other site 658172001278 G5 box; other site 658172001279 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 658172001280 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 658172001281 chaperone protein DnaJ; Provisional; Region: PRK10767 658172001282 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 658172001283 HSP70 interaction site [polypeptide binding]; other site 658172001284 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 658172001285 substrate binding site [polypeptide binding]; other site 658172001286 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 658172001287 Zn binding sites [ion binding]; other site 658172001288 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 658172001289 dimer interface [polypeptide binding]; other site 658172001290 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 658172001291 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 658172001292 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 658172001293 putative active site [active] 658172001294 catalytic site [active] 658172001295 putative substrate binding site [chemical binding]; other site 658172001296 Imelysin; Region: Peptidase_M75; cl09159 658172001297 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 658172001298 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 658172001299 active site 658172001300 tetramer interface; other site 658172001301 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 658172001302 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 658172001303 FAD binding pocket [chemical binding]; other site 658172001304 FAD binding motif [chemical binding]; other site 658172001305 phosphate binding motif [ion binding]; other site 658172001306 beta-alpha-beta structure motif; other site 658172001307 NAD binding pocket [chemical binding]; other site 658172001308 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 658172001309 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 658172001310 UbiA prenyltransferase family; Region: UbiA; cl00337 658172001311 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 658172001312 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 658172001313 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 658172001314 nucleoside/Zn binding site; other site 658172001315 dimer interface [polypeptide binding]; other site 658172001316 catalytic motif [active] 658172001317 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 658172001318 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 658172001319 RNA binding surface [nucleotide binding]; other site 658172001320 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 658172001321 active site 658172001322 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001323 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 658172001324 active site 658172001325 Domain of unknown function (DUF4170); Region: DUF4170; pfam13773 658172001326 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 658172001327 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 658172001328 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 658172001329 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 658172001330 Uncharacterized protein conserved in bacteria (DUF2093); Region: DUF2093; cl11535 658172001331 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 658172001332 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 658172001333 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second...; Region: TopoII_MutL_Trans; cl02783 658172001334 ATP binding site [chemical binding]; other site 658172001335 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 658172001336 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 658172001337 S-adenosylmethionine binding site [chemical binding]; other site 658172001338 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 658172001339 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 658172001340 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 658172001341 Organic solvent tolerance protein; Region: OstA_C; pfam04453 658172001342 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 658172001343 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 658172001344 multifunctional aminopeptidase A; Provisional; Region: PRK00913 658172001345 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 658172001346 interface (dimer of trimers) [polypeptide binding]; other site 658172001347 Substrate-binding/catalytic site; other site 658172001348 Zn-binding sites [ion binding]; other site 658172001349 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 658172001350 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 658172001351 active site 658172001352 multimer interface [polypeptide binding]; other site 658172001353 TadE-like protein; Region: TadE; cl10688 658172001354 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 658172001355 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 658172001356 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 658172001357 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 658172001358 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 658172001359 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 658172001360 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 658172001361 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172001362 Walker A/P-loop; other site 658172001363 ATP binding site [chemical binding]; other site 658172001364 Q-loop/lid; other site 658172001365 ABC transporter signature motif; other site 658172001366 Walker B; other site 658172001367 D-loop; other site 658172001368 H-loop/switch region; other site 658172001369 Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not...; Region: ZnMc_serralysin_like; cd04277 658172001370 active site 658172001371 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 658172001372 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 658172001373 endonuclease III; Region: ENDO3c; smart00478 658172001374 minor groove reading motif; other site 658172001375 helix-hairpin-helix signature motif; other site 658172001376 substrate binding pocket [chemical binding]; other site 658172001377 active site 658172001378 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 658172001379 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 658172001380 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 658172001381 ATP binding site [chemical binding]; other site 658172001382 Mg++ binding site [ion binding]; other site 658172001383 motif III; other site 658172001384 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 658172001385 nucleotide binding region [chemical binding]; other site 658172001386 ATP-binding site [chemical binding]; other site 658172001387 Peptidase family M23; Region: Peptidase_M23; pfam01551 658172001388 Survival protein SurE; Region: SurE; cl00448 658172001389 seryl-tRNA synthetase; Provisional; Region: PRK05431 658172001390 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 658172001391 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound...; Region: SerRS_core; cd00770 658172001392 dimer interface [polypeptide binding]; other site 658172001393 active site 658172001394 motif 1; other site 658172001395 motif 2; other site 658172001396 motif 3; other site 658172001397 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 658172001398 putative coenzyme Q binding site [chemical binding]; other site 658172001399 lipoyl synthase; Provisional; Region: PRK05481 658172001400 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 658172001401 FeS/SAM binding site; other site 658172001402 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 658172001403 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001404 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 658172001405 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 658172001406 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 658172001407 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 658172001408 E3 interaction surface; other site 658172001409 lipoyl attachment site [posttranslational modification]; other site 658172001410 e3 binding domain; Region: E3_binding; pfam02817 658172001411 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 658172001412 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 658172001413 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 658172001414 E3 interaction surface; other site 658172001415 lipoyl attachment site [posttranslational modification]; other site 658172001416 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 658172001417 alpha subunit interface [polypeptide binding]; other site 658172001418 TPP binding site [chemical binding]; other site 658172001419 heterodimer interface [polypeptide binding]; other site 658172001420 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 658172001421 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 658172001422 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 658172001423 tetramer interface [polypeptide binding]; other site 658172001424 TPP-binding site [chemical binding]; other site 658172001425 heterodimer interface [polypeptide binding]; other site 658172001426 phosphorylation loop region [posttranslational modification] 658172001427 Septum formation initiator; Region: DivIC; cl11433 658172001428 enolase; Provisional; Region: eno; PRK00077 658172001429 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 658172001430 dimer interface [polypeptide binding]; other site 658172001431 metal binding site [ion binding]; metal-binding site 658172001432 substrate binding pocket [chemical binding]; other site 658172001433 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 658172001434 NeuB family; Region: NeuB; cl00496 658172001435 LexA repressor; Validated; Region: PRK00215 658172001436 Helix-turn-helix domains; Region: HTH; cl00088 658172001437 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 658172001438 Catalytic site [active] 658172001439 potential frameshift: common BLAST hit: gi|150396364|ref|YP_001326831.1| ComEC/Rec2-related protein 658172001440 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 658172001441 dimer interface [polypeptide binding]; other site 658172001442 Citrate synthase; Region: Citrate_synt; pfam00285 658172001443 active site 658172001444 citrylCoA binding site [chemical binding]; other site 658172001445 NADH binding [chemical binding]; other site 658172001446 cationic pore residues; other site 658172001447 oxalacetate/citrate binding site [chemical binding]; other site 658172001448 coenzyme A binding site [chemical binding]; other site 658172001449 catalytic triad [active] 658172001450 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 658172001451 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 658172001452 CAP-like domain; other site 658172001453 active site 658172001454 primary dimer interface [polypeptide binding]; other site 658172001455 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 658172001456 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 658172001457 dimer interface [polypeptide binding]; other site 658172001458 allosteric magnesium binding site [ion binding]; other site 658172001459 active site 658172001460 aspartate-rich active site metal binding site; other site 658172001461 Schiff base residues; other site 658172001462 Helix-turn-helix domains; Region: HTH; cl00088 658172001463 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 658172001464 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 658172001465 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 658172001466 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 658172001467 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 658172001468 dimer interface [polypeptide binding]; other site 658172001469 glycine-pyridoxal phosphate binding site [chemical binding]; other site 658172001470 active site 658172001471 folate binding site [chemical binding]; other site 658172001472 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 658172001473 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 658172001474 catalytic motif [active] 658172001475 Zn binding site [ion binding]; other site 658172001476 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cl00161 658172001477 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 658172001478 Lumazine binding domain; Region: Lum_binding; pfam00677 658172001479 Lumazine binding domain; Region: Lum_binding; pfam00677 658172001480 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 658172001481 homopentamer interface [polypeptide binding]; other site 658172001482 active site 658172001483 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 658172001484 putative RNA binding site [nucleotide binding]; other site 658172001485 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 658172001486 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 658172001487 Cation efflux family; Region: Cation_efflux; cl00316 658172001488 NMT1-like family; Region: NMT1_2; cl15260 658172001489 choline ABC transporter, periplasmic binding protein; Region: ABC_choline_bnd; TIGR03414 658172001490 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 658172001491 dimer interface [polypeptide binding]; other site 658172001492 conserved gate region; other site 658172001493 putative PBP binding loops; other site 658172001494 ABC-ATPase subunit interface; other site 658172001495 choline ABC transporter, ATP-binding protein; Region: ABC_choXWV_ATP; TIGR03415 658172001496 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172001497 Walker A/P-loop; other site 658172001498 ATP binding site [chemical binding]; other site 658172001499 Q-loop/lid; other site 658172001500 ABC transporter signature motif; other site 658172001501 Walker B; other site 658172001502 D-loop; other site 658172001503 H-loop/switch region; other site 658172001504 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 658172001505 classical (c) SDRs; Region: SDR_c; cd05233 658172001506 NAD(P) binding site [chemical binding]; other site 658172001507 active site 658172001508 amidophosphoribosyltransferase; Provisional; Region: PRK09123 658172001509 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 658172001510 active site 658172001511 tetramer interface [polypeptide binding]; other site 658172001512 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 658172001513 active site 658172001514 Colicin V production protein; Region: Colicin_V; cl00567 658172001515 DNA repair protein RadA; Provisional; Region: PRK11823 658172001516 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172001517 Walker A motif; other site 658172001518 ATP binding site [chemical binding]; other site 658172001519 Walker B motif; other site 658172001520 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 658172001521 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 658172001522 active site 658172001523 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 658172001524 dimer interface [polypeptide binding]; other site 658172001525 substrate binding site [chemical binding]; other site 658172001526 catalytic residues [active] 658172001527 replicative DNA helicase; Provisional; Region: PRK09165 658172001528 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 658172001529 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 658172001530 Walker A motif; other site 658172001531 ATP binding site [chemical binding]; other site 658172001532 Walker B motif; other site 658172001533 DNA binding loops [nucleotide binding] 658172001534 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 658172001535 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 658172001536 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 658172001537 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 658172001538 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 658172001539 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 658172001540 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 658172001541 NAD binding site [chemical binding]; other site 658172001542 homodimer interface [polypeptide binding]; other site 658172001543 active site 658172001544 substrate binding site [chemical binding]; other site 658172001545 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 658172001546 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172001547 ATP binding site [chemical binding]; other site 658172001548 putative Mg++ binding site [ion binding]; other site 658172001549 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 658172001550 SEC-C motif; Region: SEC-C; pfam02810 658172001551 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 658172001552 heterotetramer interface [polypeptide binding]; other site 658172001553 active site pocket [active] 658172001554 cleavage site 658172001555 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 658172001556 active site 658172001557 8-oxo-dGMP binding site [chemical binding]; other site 658172001558 nudix motif; other site 658172001559 metal binding site [ion binding]; metal-binding site 658172001560 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 658172001561 TLC ATP/ADP transporter; Region: TLC; pfam03219 658172001562 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 658172001563 GTP-binding protein LepA; Provisional; Region: PRK05433 658172001564 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 658172001565 G1 box; other site 658172001566 putative GEF interaction site [polypeptide binding]; other site 658172001567 GTP/Mg2+ binding site [chemical binding]; other site 658172001568 Switch I region; other site 658172001569 G2 box; other site 658172001570 G3 box; other site 658172001571 Switch II region; other site 658172001572 G4 box; other site 658172001573 G5 box; other site 658172001574 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 658172001575 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 658172001576 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 658172001577 translation initiation factor IF-3; Region: infC; TIGR00168 658172001578 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 658172001579 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 658172001580 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 658172001581 ribosomal protein L20; Region: rpl20; CHL00068 658172001582 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 658172001583 23S rRNA binding site [nucleotide binding]; other site 658172001584 L21 binding site [polypeptide binding]; other site 658172001585 L13 binding site [polypeptide binding]; other site 658172001586 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 658172001587 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 658172001588 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 658172001589 dimer interface [polypeptide binding]; other site 658172001590 motif 1; other site 658172001591 active site 658172001592 motif 2; other site 658172001593 motif 3; other site 658172001594 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 658172001595 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 658172001596 putative tRNA-binding site [nucleotide binding]; other site 658172001597 B3/4 domain; Region: B3_4; cl11458 658172001598 tRNA synthetase B5 domain; Region: B5; cl08394 658172001599 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 658172001600 dimer interface [polypeptide binding]; other site 658172001601 motif 1; other site 658172001602 motif 3; other site 658172001603 motif 2; other site 658172001604 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 658172001605 Porin subfamily; Region: Porin_2; pfam02530 658172001606 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 658172001607 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; cl15754 658172001608 Response regulator receiver domain; Region: Response_reg; pfam00072 658172001609 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 658172001610 active site 658172001611 phosphorylation site [posttranslational modification] 658172001612 intermolecular recognition site; other site 658172001613 dimerization interface [polypeptide binding]; other site 658172001614 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 658172001615 catalytic triad [active] 658172001616 dimer interface [polypeptide binding]; other site 658172001617 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 658172001618 active site 658172001619 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 658172001620 lytic murein transglycosylase; Region: MltB_2; TIGR02283 658172001621 Transglycosylase SLT domain; Region: SLT_2; pfam13406 658172001622 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 658172001623 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001624 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 658172001625 DNA topoisomerase I subunit omega; Validated; Region: PRK07561 658172001626 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 658172001627 active site 658172001628 interdomain interaction site; other site 658172001629 putative metal-binding site [ion binding]; other site 658172001630 nucleotide binding site [chemical binding]; other site 658172001631 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 658172001632 domain I; other site 658172001633 DNA binding groove [nucleotide binding] 658172001634 phosphate binding site [ion binding]; other site 658172001635 domain II; other site 658172001636 domain III; other site 658172001637 nucleotide binding site [chemical binding]; other site 658172001638 catalytic site [active] 658172001639 domain IV; other site 658172001640 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 658172001641 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 658172001642 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 658172001643 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 658172001644 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 658172001645 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 658172001646 dihydroorotase; Validated; Region: PRK09059 658172001647 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 658172001648 active site 658172001649 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 658172001650 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 658172001651 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001652 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 658172001653 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 658172001654 active site 658172001655 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 658172001656 Flagellin and related hook-associated proteins [Cell motility and secretion]; Region: FlgL; COG1344 658172001657 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 658172001658 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 658172001659 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 658172001660 ligand binding site [chemical binding]; other site 658172001661 chemotaxis protein; Reviewed; Region: PRK12798 658172001662 Flagellar hook-length control protein FliK; Region: Flg_hook; cl15269 658172001663 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 658172001664 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 658172001665 DNA binding site [nucleotide binding] 658172001666 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 658172001667 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 658172001668 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 658172001669 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 658172001670 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07521 658172001671 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK06008 658172001672 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 658172001673 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 658172001674 Flagellar protein FlaF; Region: FlaF; cl11454 658172001675 Flagellar protein FlbT; Region: FlbT; cl11455 658172001676 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 658172001677 flagellar basal body rod modification protein; Validated; Region: flgD; PRK06792 658172001678 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 658172001679 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 658172001680 FHIPEP family; Region: FHIPEP; pfam00771 658172001681 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 658172001682 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 658172001683 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 658172001684 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 658172001685 homodimer interface [polypeptide binding]; other site 658172001686 NADP binding site [chemical binding]; other site 658172001687 substrate binding site [chemical binding]; other site 658172001688 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 658172001689 putative active site [active] 658172001690 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 658172001691 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 658172001692 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 658172001693 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 658172001694 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 658172001695 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 658172001696 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 658172001697 dimer interface [polypeptide binding]; other site 658172001698 putative radical transfer pathway; other site 658172001699 diiron center [ion binding]; other site 658172001700 tyrosyl radical; other site 658172001701 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 658172001702 Reovirus sigma C capsid protein; Region: Reo_sigmaC; pfam04582 658172001703 structural protein; Region: PHA01972 658172001704 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 658172001705 ATP cone domain; Region: ATP-cone; pfam03477 658172001706 Class I ribonucleotide reductase; Region: RNR_I; cd01679 658172001707 active site 658172001708 dimer interface [polypeptide binding]; other site 658172001709 catalytic residues [active] 658172001710 effector binding site; other site 658172001711 R2 peptide binding site; other site 658172001712 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 658172001713 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 658172001714 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 658172001715 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 658172001716 dimer interface [polypeptide binding]; other site 658172001717 active site 658172001718 CoA binding pocket [chemical binding]; other site 658172001719 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 658172001720 IHF dimer interface [polypeptide binding]; other site 658172001721 IHF - DNA interface [nucleotide binding]; other site 658172001722 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 658172001723 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 658172001724 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 658172001725 Cation efflux family; Region: Cation_efflux; cl00316 658172001726 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 658172001727 catalytic residue [active] 658172001728 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 658172001729 ATP binding site [chemical binding]; other site 658172001730 active site 658172001731 substrate binding site [chemical binding]; other site 658172001732 Domain of unknown function DUF59; Region: DUF59; cl00941 658172001733 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 658172001734 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 658172001735 Walker A motif; other site 658172001736 K+ potassium transporter; Region: K_trans; cl15781 658172001737 Integral membrane protein TerC family; Region: TerC; cl10468 658172001738 pyrophosphate--fructose-6-phosphate 1-phosphotransferase; Validated; Region: PRK06555 658172001739 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 658172001740 active site 658172001741 ADP/pyrophosphate binding site [chemical binding]; other site 658172001742 dimerization interface [polypeptide binding]; other site 658172001743 allosteric effector site; other site 658172001744 fructose-1,6-bisphosphate binding site; other site 658172001745 GTP-binding protein YchF; Reviewed; Region: PRK09601 658172001746 YchF GTPase; Region: YchF; cd01900 658172001747 G1 box; other site 658172001748 GTP/Mg2+ binding site [chemical binding]; other site 658172001749 Switch I region; other site 658172001750 G2 box; other site 658172001751 Switch II region; other site 658172001752 G3 box; other site 658172001753 G4 box; other site 658172001754 G5 box; other site 658172001755 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 658172001756 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 658172001757 putative active site [active] 658172001758 catalytic residue [active] 658172001759 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; cl15419 658172001760 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 658172001761 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 658172001762 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 658172001763 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 658172001764 ATP binding site [chemical binding]; other site 658172001765 Mg2+ binding site [ion binding]; other site 658172001766 G-X-G motif; other site 658172001767 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 658172001768 anchoring element; other site 658172001769 dimer interface [polypeptide binding]; other site 658172001770 ATP binding site [chemical binding]; other site 658172001771 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 658172001772 active site 658172001773 metal binding site [ion binding]; metal-binding site 658172001774 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 658172001775 thymidylate kinase; Validated; Region: tmk; PRK00698 658172001776 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 658172001777 TMP-binding site; other site 658172001778 ATP-binding site [chemical binding]; other site 658172001779 DNA polymerase III subunit delta'; Validated; Region: PRK09112 658172001780 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172001781 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 658172001782 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 658172001783 active site 658172001784 HIGH motif; other site 658172001785 KMSKS motif; other site 658172001786 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 658172001787 tRNA binding surface [nucleotide binding]; other site 658172001788 anticodon binding site; other site 658172001789 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 658172001790 active site 658172001791 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 658172001792 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 658172001793 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 658172001794 metal ion-dependent adhesion site (MIDAS); other site 658172001795 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 658172001796 Uncharacterized conserved protein [Function unknown]; Region: COG1432 658172001797 LabA_like proteins; Region: LabA; cd10911 658172001798 putative metal binding site [ion binding]; other site 658172001799 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 658172001800 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 658172001801 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 658172001802 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 658172001803 Catalytic site [active] 658172001804 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 658172001805 ribonuclease III; Reviewed; Region: PRK12371 658172001806 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 658172001807 dimerization interface [polypeptide binding]; other site 658172001808 active site 658172001809 metal binding site [ion binding]; metal-binding site 658172001810 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 658172001811 dsRNA binding site [nucleotide binding]; other site 658172001812 GTPase Era; Reviewed; Region: era; PRK00089 658172001813 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 658172001814 G1 box; other site 658172001815 GTP/Mg2+ binding site [chemical binding]; other site 658172001816 Switch I region; other site 658172001817 G2 box; other site 658172001818 Switch II region; other site 658172001819 G3 box; other site 658172001820 G4 box; other site 658172001821 G5 box; other site 658172001822 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 658172001823 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 658172001824 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 658172001825 Substrate binding site; other site 658172001826 Mg++ binding site; other site 658172001827 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 658172001828 active site 658172001829 substrate binding site [chemical binding]; other site 658172001830 CoA binding site [chemical binding]; other site 658172001831 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 658172001832 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 658172001833 glutaminase active site [active] 658172001834 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 658172001835 dimer interface [polypeptide binding]; other site 658172001836 active site 658172001837 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 658172001838 dimer interface [polypeptide binding]; other site 658172001839 active site 658172001840 Protein of unknown function (DUF502); Region: DUF502; cl01107 658172001841 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 658172001842 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 658172001843 generic binding surface II; other site 658172001844 ssDNA binding site; other site 658172001845 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 658172001846 ATP binding site [chemical binding]; other site 658172001847 putative Mg++ binding site [ion binding]; other site 658172001848 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 658172001849 nucleotide binding region [chemical binding]; other site 658172001850 ATP-binding site [chemical binding]; other site 658172001851 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 658172001852 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 658172001853 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 658172001854 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 658172001855 ATP binding site [chemical binding]; other site 658172001856 putative Mg++ binding site [ion binding]; other site 658172001857 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 658172001858 nucleotide binding region [chemical binding]; other site 658172001859 ATP-binding site [chemical binding]; other site 658172001860 TRCF domain; Region: TRCF; cl04088 658172001861 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 658172001862 Recombination protein O N terminal; Region: RecO_N; cl15812 658172001863 Recombination protein O C terminal; Region: RecO_C; pfam02565 658172001864 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 658172001865 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 658172001866 active site 658172001867 HIGH motif; other site 658172001868 dimer interface [polypeptide binding]; other site 658172001869 KMSKS motif; other site 658172001870 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 658172001871 RNA binding surface [nucleotide binding]; other site 658172001872 YecR-like lipoprotein; Region: YecR; cl10256 658172001873 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 658172001874 Ligand Binding Site [chemical binding]; other site 658172001875 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 658172001876 active site 658172001877 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 658172001878 HemY protein N-terminus; Region: HemY_N; pfam07219 658172001879 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 658172001880 binding surface 658172001881 TPR motif; other site 658172001882 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 658172001883 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 658172001884 active site 658172001885 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 658172001886 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl03189 658172001887 domain interfaces; other site 658172001888 active site 658172001889 UGMP family protein; Validated; Region: PRK09604 658172001890 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 658172001891 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 658172001892 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001893 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 658172001894 EVE domain; Region: EVE; cl00728 658172001895 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 658172001896 Iron-sulfur protein interface; other site 658172001897 proximal quinone binding site [chemical binding]; other site 658172001898 SdhD (CybS) interface [polypeptide binding]; other site 658172001899 proximal heme binding site [chemical binding]; other site 658172001900 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 658172001901 putative SdhC subunit interface [polypeptide binding]; other site 658172001902 putative proximal heme binding site [chemical binding]; other site 658172001903 putative Iron-sulfur protein interface [polypeptide binding]; other site 658172001904 putative proximal quinone binding site; other site 658172001905 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 658172001906 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001907 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 658172001908 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 658172001909 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cl00159 658172001910 Protease inhibitor Inh; Region: Inh; pfam02974 658172001911 Predicted ATPase [General function prediction only]; Region: COG1485 658172001912 malate dehydrogenase; Reviewed; Region: PRK06223 658172001913 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 658172001914 NAD(P) binding site [chemical binding]; other site 658172001915 dimer interface [polypeptide binding]; other site 658172001916 tetramer (dimer of dimers) interface [polypeptide binding]; other site 658172001917 substrate binding site [chemical binding]; other site 658172001918 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 658172001919 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172001920 CoA-ligase; Region: Ligase_CoA; cl02894 658172001921 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 658172001922 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001923 CoA-ligase; Region: Ligase_CoA; cl02894 658172001924 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 658172001925 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 658172001926 TPP-binding site [chemical binding]; other site 658172001927 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 658172001928 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 658172001929 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 658172001930 E3 interaction surface; other site 658172001931 lipoyl attachment site [posttranslational modification]; other site 658172001932 e3 binding domain; Region: E3_binding; pfam02817 658172001933 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 658172001934 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 658172001935 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001936 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 658172001937 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 658172001938 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 658172001939 tetramer (dimer of dimers) interface [polypeptide binding]; other site 658172001940 active site 658172001941 dimer interface [polypeptide binding]; other site 658172001942 glutathione reductase; Validated; Region: PRK06116 658172001943 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001944 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 658172001945 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 658172001946 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 658172001947 putative ABC transporter; Region: ycf24; CHL00085 658172001948 FeS assembly ATPase SufC; Region: sufC; TIGR01978 658172001949 ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under...; Region: ABC_FeS_Assembly; cd03217 658172001950 Walker A/P-loop; other site 658172001951 ATP binding site [chemical binding]; other site 658172001952 Q-loop/lid; other site 658172001953 ABC transporter signature motif; other site 658172001954 Walker B; other site 658172001955 D-loop; other site 658172001956 H-loop/switch region; other site 658172001957 Uncharacterized protein family (UPF0051); Region: UPF0051; cl03223 658172001958 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 658172001959 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 658172001960 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 658172001961 catalytic residue [active] 658172001962 Domain of unknown function DUF59; Region: DUF59; cl00941 658172001963 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 658172001964 Fe-S metabolism associated domain; Region: SufE; cl00951 658172001965 NAD synthetase; Provisional; Region: PRK13981 658172001966 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 658172001967 multimer interface [polypeptide binding]; other site 658172001968 active site 658172001969 catalytic triad [active] 658172001970 protein interface 1 [polypeptide binding]; other site 658172001971 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 658172001972 homodimer interface [polypeptide binding]; other site 658172001973 NAD binding pocket [chemical binding]; other site 658172001974 ATP binding pocket [chemical binding]; other site 658172001975 Mg binding site [ion binding]; other site 658172001976 active-site loop [active] 658172001977 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 658172001978 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 658172001979 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 658172001980 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 658172001981 active site 658172001982 dimer interface [polypeptide binding]; other site 658172001983 motif 1; other site 658172001984 motif 2; other site 658172001985 motif 3; other site 658172001986 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 658172001987 anticodon binding site; other site 658172001988 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 658172001989 DNA-binding site [nucleotide binding]; DNA binding site 658172001990 RNA-binding motif; other site 658172001991 cell division protein MraZ; Reviewed; Region: PRK00326 658172001992 MraZ protein; Region: MraZ; pfam02381 658172001993 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 658172001994 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172001995 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 658172001996 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 658172001997 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 658172001998 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 658172001999 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 658172002000 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 658172002001 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 658172002002 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 658172002003 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 658172002004 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 658172002005 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 658172002006 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 658172002007 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 658172002008 Mg++ binding site [ion binding]; other site 658172002009 putative catalytic motif [active] 658172002010 putative substrate binding site [chemical binding]; other site 658172002011 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 658172002012 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 658172002013 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 658172002014 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 658172002015 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 658172002016 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 658172002017 active site 658172002018 homodimer interface [polypeptide binding]; other site 658172002019 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 658172002020 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 658172002021 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 658172002022 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 658172002023 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 658172002024 FAD binding domain; Region: FAD_binding_4; pfam01565 658172002025 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 658172002026 hypothetical protein; Region: PHA00661 658172002027 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 658172002028 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 658172002029 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 658172002030 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 658172002031 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 658172002032 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 658172002033 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 658172002034 catalytic residue [active] 658172002035 ATP synthase A chain; Region: ATP-synt_A; cl00413 658172002036 ATP synthase subunit C; Region: ATP-synt_C; cl00466 658172002037 Plant ATP synthase F0; Region: YMF19; cl07975 658172002038 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 658172002039 Plant ATP synthase F0; Region: YMF19; cl07975 658172002040 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 658172002041 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 658172002042 metal binding site [ion binding]; metal-binding site 658172002043 active site 658172002044 I-site; other site 658172002045 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 658172002046 RNA/DNA hybrid binding site [nucleotide binding]; other site 658172002047 active site 658172002048 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 658172002049 ligand binding site [chemical binding]; other site 658172002050 active site 658172002051 UGI interface [polypeptide binding]; other site 658172002052 catalytic site [active] 658172002053 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 658172002054 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 658172002055 phosphoglucomutase; Region: PLN02307 658172002056 The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine...; Region: phosphohexomutase; cl03757 658172002057 active site 658172002058 substrate binding site [chemical binding]; other site 658172002059 metal binding site [ion binding]; metal-binding site 658172002060 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 658172002061 metal ion-dependent adhesion site (MIDAS); other site 658172002062 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 658172002063 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 658172002064 substrate binding pocket [chemical binding]; other site 658172002065 chain length determination region; other site 658172002066 substrate-Mg2+ binding site; other site 658172002067 catalytic residues [active] 658172002068 aspartate-rich region 1; other site 658172002069 active site lid residues [active] 658172002070 aspartate-rich region 2; other site 658172002071 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 658172002072 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 658172002073 substrate binding pocket [chemical binding]; other site 658172002074 membrane-bound complex binding site; other site 658172002075 hinge residues; other site 658172002076 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 658172002077 dimer interface [polypeptide binding]; other site 658172002078 conserved gate region; other site 658172002079 putative PBP binding loops; other site 658172002080 ABC-ATPase subunit interface; other site 658172002081 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 658172002082 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 658172002083 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 658172002084 excinuclease ABC subunit B; Provisional; Region: PRK05298 658172002085 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 658172002086 ATP binding site [chemical binding]; other site 658172002087 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 658172002088 nucleotide binding region [chemical binding]; other site 658172002089 ATP-binding site [chemical binding]; other site 658172002090 Ultra-violet resistance protein B; Region: UvrB; pfam12344 658172002091 UvrB/uvrC motif; Region: UVR; pfam02151 658172002092 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 658172002093 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 658172002094 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 658172002095 Protein of unknown function (DUF1217); Region: DUF1217; pfam06748 658172002096 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 658172002097 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 658172002098 non-specific DNA binding site [nucleotide binding]; other site 658172002099 salt bridge; other site 658172002100 sequence-specific DNA binding site [nucleotide binding]; other site 658172002101 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 658172002102 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 658172002103 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002104 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 658172002105 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 658172002106 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 658172002107 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 658172002108 motif II; other site 658172002109 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 658172002110 catalytic residues [active] 658172002111 HflC protein; Region: hflC; TIGR01932 658172002112 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 658172002113 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 658172002114 HflK protein; Region: hflK; TIGR01933 658172002115 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 658172002116 folate binding site [chemical binding]; other site 658172002117 NADP+ binding site [chemical binding]; other site 658172002118 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 658172002119 dimerization interface [polypeptide binding]; other site 658172002120 active site 658172002121 Stringent starvation protein B; Region: SspB; cl01120 658172002122 AsmA family; Region: AsmA; pfam05170 658172002123 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 658172002124 ligand binding site [chemical binding]; other site 658172002125 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 658172002126 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002127 Family description; Region: UvrD_C_2; cl15862 658172002128 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; cl00868 658172002129 Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase; cl00205 658172002130 homodimer interface [polypeptide binding]; other site 658172002131 substrate binding pocket [chemical binding]; other site 658172002132 catalytic residues [active] 658172002133 NADH/NADPH cofactor binding site [chemical binding]; other site 658172002134 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 658172002135 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 658172002136 homotetramer interface [polypeptide binding]; other site 658172002137 FMN binding site [chemical binding]; other site 658172002138 homodimer contacts [polypeptide binding]; other site 658172002139 putative active site [active] 658172002140 putative substrate binding site [chemical binding]; other site 658172002141 3-hydroxy-3-methylglutaryl CoA synthase, prokaryotic clade; Region: HMG-CoA-S_prok; TIGR01835 658172002142 'initiating' condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the...; Region: init_cond_enzymes; cd00827 658172002143 dimer interface [polypeptide binding]; other site 658172002144 active site 658172002145 Mevalonate kinase [Lipid metabolism]; Region: ERG12; COG1577 658172002146 Mevalonate kinase [Lipid metabolism]; Region: ERG12; COG1577 658172002147 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 658172002148 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]; Region: MVD1; COG3407 658172002149 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 658172002150 active site 658172002151 substrate binding pocket [chemical binding]; other site 658172002152 dimer interface [polypeptide binding]; other site 658172002153 orotate phosphoribosyltransferase; Validated; Region: pyrE; PRK00455 658172002154 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 658172002155 active site 658172002156 LysE type translocator; Region: LysE; cl00565 658172002157 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 658172002158 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 658172002159 GatB domain; Region: GatB_Yqey; cl11497 658172002160 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 658172002161 Amidase; Region: Amidase; cl11426 658172002162 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 658172002163 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cl00243 658172002164 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 658172002165 Terminase-like family; Region: Terminase_6; pfam03237 658172002166 Bacteriophage terminase large (ATPase) subunit and inactivated derivatives [General function prediction only]; Region: COG5565 658172002167 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 658172002168 non-specific DNA binding site [nucleotide binding]; other site 658172002169 salt bridge; other site 658172002170 sequence-specific DNA binding site [nucleotide binding]; other site 658172002171 replicative DNA helicase; Region: DnaB; TIGR00665 658172002172 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 658172002173 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 658172002174 Walker A motif; other site 658172002175 ATP binding site [chemical binding]; other site 658172002176 Walker B motif; other site 658172002177 DNA binding loops [nucleotide binding] 658172002178 Protein of unknown function (DUF1376); Region: DUF1376; cl01531 658172002179 SurA N-terminal domain; Region: SurA_N_3; cl07813 658172002180 PPIC-type PPIASE domain; Region: Rotamase; cl08278 658172002181 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 658172002182 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 658172002183 Predicted acetyltransferase [General function prediction only]; Region: COG3153 658172002184 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 658172002185 Coenzyme A binding pocket [chemical binding]; other site 658172002186 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 658172002187 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 658172002188 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 658172002189 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 658172002190 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 658172002191 NAD binding site [chemical binding]; other site 658172002192 homotetramer interface [polypeptide binding]; other site 658172002193 homodimer interface [polypeptide binding]; other site 658172002194 substrate binding site [chemical binding]; other site 658172002195 active site 658172002196 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172002197 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 658172002198 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 658172002199 FMN binding site [chemical binding]; other site 658172002200 active site 658172002201 catalytic residues [active] 658172002202 substrate binding site [chemical binding]; other site 658172002203 Domain of unknown function (DUF4145); Region: DUF4145; pfam13643 658172002204 PTS system sugar-specific permease component; Region: EIIC-GAT; cl04451 658172002205 deoxyribodipyrimidine photolyase; Provisional; Region: PRK10674 658172002206 DNA photolyase; Region: DNA_photolyase; pfam00875 658172002207 FAD binding domain of DNA photolyase; Region: FAD_binding_7; pfam03441 658172002208 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 658172002209 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 658172002210 catalytic residues [active] 658172002211 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 658172002212 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 658172002213 nucleotide binding pocket [chemical binding]; other site 658172002214 K-X-D-G motif; other site 658172002215 catalytic site [active] 658172002216 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 658172002217 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 658172002218 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 658172002219 Dimer interface [polypeptide binding]; other site 658172002220 BRCT sequence motif; other site 658172002221 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 658172002222 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 658172002223 Walker A/P-loop; other site 658172002224 ATP binding site [chemical binding]; other site 658172002225 Q-loop/lid; other site 658172002226 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 658172002227 ABC transporter signature motif; other site 658172002228 Walker B; other site 658172002229 D-loop; other site 658172002230 H-loop/switch region; other site 658172002231 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 658172002232 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 658172002233 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 658172002234 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 658172002235 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 658172002236 nucleotide binding site [chemical binding]; other site 658172002237 SulA interaction site; other site 658172002238 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 658172002239 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 658172002240 Cell division protein FtsA; Region: FtsA; cl11496 658172002241 Cell division protein FtsA; Region: FtsA; cl11496 658172002242 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 658172002243 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 658172002244 Cell division protein FtsQ; Region: FtsQ; pfam03799 658172002245 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 658172002246 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 658172002247 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172002248 Protein of unknown function (DUF4231); Region: DUF4231; pfam14015 658172002249 Protein of unknown function (DUF4065); Region: DUF4065; cl01445 658172002250 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 658172002251 non-specific DNA binding site [nucleotide binding]; other site 658172002252 salt bridge; other site 658172002253 sequence-specific DNA binding site [nucleotide binding]; other site 658172002254 putative zinc finger/helix-turn-helix protein, YgiT family; Region: CxxCG_CxxCG_HTH; TIGR03830 658172002255 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 658172002256 non-specific DNA binding site [nucleotide binding]; other site 658172002257 salt bridge; other site 658172002258 sequence-specific DNA binding site [nucleotide binding]; other site 658172002259 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 658172002260 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 658172002261 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 658172002262 active site 658172002263 NTP binding site [chemical binding]; other site 658172002264 metal binding triad [ion binding]; metal-binding site 658172002265 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 658172002266 Preprotein translocase subunit; Region: YajC; cl00806 658172002267 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 658172002268 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 658172002269 HIGH motif; other site 658172002270 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 658172002271 active site 658172002272 KMSKS motif; other site 658172002273 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 658172002274 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 658172002275 dimer interface [polypeptide binding]; other site 658172002276 putative anticodon binding site; other site 658172002277 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 658172002278 motif 1; other site 658172002279 active site 658172002280 motif 2; other site 658172002281 motif 3; other site 658172002282 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 658172002283 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 658172002284 FeS/SAM binding site; other site 658172002285 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 658172002286 Thiamine pyrophosphokinase; Region: TPK; cd07995 658172002287 active site 658172002288 dimerization interface [polypeptide binding]; other site 658172002289 thiamine binding site [chemical binding]; other site 658172002290 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 658172002291 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 658172002292 ABC transporter; Region: ABC_tran_2; pfam12848 658172002293 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 658172002294 elongation factor P; Validated; Region: PRK00529 658172002295 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 658172002296 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 658172002297 RNA binding site [nucleotide binding]; other site 658172002298 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 658172002299 RNA binding site [nucleotide binding]; other site 658172002300 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 658172002301 EF-P lysine aminoacylase GenX; Region: genX; TIGR00462 658172002302 motif 1; other site 658172002303 dimer interface [polypeptide binding]; other site 658172002304 active site 658172002305 motif 2; other site 658172002306 motif 3; other site 658172002307 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 658172002308 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 658172002309 FeS/SAM binding site; other site 658172002310 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 658172002311 catalytic center binding site [active] 658172002312 ATP binding site [chemical binding]; other site 658172002313 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 658172002314 homooctamer interface [polypeptide binding]; other site 658172002315 active site 658172002316 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 658172002317 dihydropteroate synthase; Region: DHPS; TIGR01496 658172002318 substrate binding pocket [chemical binding]; other site 658172002319 dimer interface [polypeptide binding]; other site 658172002320 inhibitor binding site; inhibition site 658172002321 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 658172002322 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002323 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 658172002324 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 658172002325 trimer interface [polypeptide binding]; other site 658172002326 active site 658172002327 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 658172002328 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172002329 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 658172002330 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 658172002331 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 658172002332 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 658172002333 substrate binding site [chemical binding]; other site 658172002334 hexamer interface [polypeptide binding]; other site 658172002335 metal binding site [ion binding]; metal-binding site 658172002336 adenylosuccinate lyase; Provisional; Region: PRK07492 658172002337 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 658172002338 tetramer interface [polypeptide binding]; other site 658172002339 active site 658172002340 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 658172002341 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 658172002342 ATP binding site [chemical binding]; other site 658172002343 active site 658172002344 substrate binding site [chemical binding]; other site 658172002345 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 658172002346 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 658172002347 putative active site [active] 658172002348 catalytic triad [active] 658172002349 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 658172002350 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 658172002351 dimerization interface [polypeptide binding]; other site 658172002352 ATP binding site [chemical binding]; other site 658172002353 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 658172002354 dimerization interface [polypeptide binding]; other site 658172002355 ATP binding site [chemical binding]; other site 658172002356 BolA-like protein; Region: BolA; cl00386 658172002357 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 658172002358 putative GSH binding site [chemical binding]; other site 658172002359 catalytic residues [active] 658172002360 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 658172002361 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 658172002362 putative substrate translocation pore; other site 658172002363 Glutaminase; Region: Glutaminase; cl00907 658172002364 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 658172002365 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 658172002366 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 658172002367 RNA binding surface [nucleotide binding]; other site 658172002368 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 658172002369 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 658172002370 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 658172002371 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 658172002372 PAS fold; Region: PAS_7; pfam12860 658172002373 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 658172002374 dimer interface [polypeptide binding]; other site 658172002375 phosphorylation site [posttranslational modification] 658172002376 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 658172002377 ATP binding site [chemical binding]; other site 658172002378 Mg2+ binding site [ion binding]; other site 658172002379 G-X-G motif; other site 658172002380 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 658172002381 CTP synthetase; Validated; Region: pyrG; PRK05380 658172002382 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 658172002383 Catalytic site [active] 658172002384 active site 658172002385 UTP binding site [chemical binding]; other site 658172002386 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 658172002387 active site 658172002388 putative oxyanion hole; other site 658172002389 catalytic triad [active] 658172002390 Preprotein translocase SecG subunit; Region: SecG; cl09123 658172002391 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 658172002392 substrate binding site [chemical binding]; other site 658172002393 dimer interface [polypeptide binding]; other site 658172002394 catalytic triad [active] 658172002395 ferrochelatase; Reviewed; Region: hemH; PRK00035 658172002396 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 658172002397 C-terminal domain interface [polypeptide binding]; other site 658172002398 active site 658172002399 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 658172002400 active site 658172002401 N-terminal domain interface [polypeptide binding]; other site 658172002402 Rhamnan synthesis protein F; Region: RgpF; cl01529 658172002403 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 658172002404 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 658172002405 UbiA prenyltransferase family; Region: UbiA; cl00337 658172002406 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 658172002407 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 658172002408 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172002409 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 658172002410 hypothetical protein; Region: PHA00662 658172002411 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 658172002412 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 658172002413 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 658172002414 active site 658172002415 Int/Topo IB signature motif; other site 658172002416 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 658172002417 catalytic triad [active] 658172002418 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 658172002419 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 658172002420 active site 658172002421 HIGH motif; other site 658172002422 nucleotide binding site [chemical binding]; other site 658172002423 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 658172002424 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 658172002425 active site 658172002426 KMSKS motif; other site 658172002427 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 658172002428 tRNA binding surface [nucleotide binding]; other site 658172002429 anticodon binding site; other site 658172002430 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 658172002431 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 658172002432 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 658172002433 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 658172002434 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: HisRS-like_core; cd00773 658172002435 dimer interface [polypeptide binding]; other site 658172002436 motif 1; other site 658172002437 active site 658172002438 motif 2; other site 658172002439 motif 3; other site 658172002440 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 658172002441 anticodon binding site; other site 658172002442 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 658172002443 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 658172002444 hinge; other site 658172002445 active site 658172002446 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13023 658172002447 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 658172002448 Protein export membrane protein; Region: SecD_SecF; cl14618 658172002449 Protein export membrane protein; Region: SecD_SecF; cl14618 658172002450 putative cation:proton antiport protein; Provisional; Region: PRK10669 658172002451 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 658172002452 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172002453 Rhamnan synthesis protein F; Region: RgpF; cl01529 658172002454 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 658172002455 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 658172002456 substrate binding site; other site 658172002457 tetramer interface; other site 658172002458 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 658172002459 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 658172002460 NADP binding site [chemical binding]; other site 658172002461 active site 658172002462 putative substrate binding site [chemical binding]; other site 658172002463 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 658172002464 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 658172002465 NAD binding site [chemical binding]; other site 658172002466 substrate binding site [chemical binding]; other site 658172002467 homodimer interface [polypeptide binding]; other site 658172002468 active site 658172002469 Cupin domain; Region: Cupin_2; cl09118 658172002470 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 658172002471 Myxococcus xanthus RfbC like proteins are required for O-antigen biosynthesis; Region: GT2_RfbC_Mx_like; cd04184 658172002472 Probable Catalytic site; other site 658172002473 metal-binding site 658172002474 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 658172002475 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 658172002476 Probable Catalytic site; other site 658172002477 metal-binding site 658172002478 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 658172002479 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 658172002480 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the...; Region: ABC_MTABC3_MDL1_MDL2; cd03249 658172002481 Walker A/P-loop; other site 658172002482 ATP binding site [chemical binding]; other site 658172002483 Q-loop/lid; other site 658172002484 ABC transporter signature motif; other site 658172002485 Walker B; other site 658172002486 D-loop; other site 658172002487 H-loop/switch region; other site 658172002488 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 658172002489 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 658172002490 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 658172002491 active site 658172002492 substrate binding site [chemical binding]; other site 658172002493 cosubstrate binding site; other site 658172002494 catalytic site [active] 658172002495 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 658172002496 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 658172002497 catalytic site [active] 658172002498 G-X2-G-X-G-K; other site 658172002499 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 658172002500 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 658172002501 active site 658172002502 phosphorylation site [posttranslational modification] 658172002503 intermolecular recognition site; other site 658172002504 dimerization interface [polypeptide binding]; other site 658172002505 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 658172002506 Walker A motif; other site 658172002507 ATP binding site [chemical binding]; other site 658172002508 Walker B motif; other site 658172002509 arginine finger; other site 658172002510 Helix-turn-helix domains; Region: HTH; cl00088 658172002511 Isoprenoid Biosynthesis enzymes, Class 1; Region: Isoprenoid_Biosyn_C1; cl00210 658172002512 substrate binding pocket [chemical binding]; other site 658172002513 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 658172002514 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 658172002515 Walker A motif; other site 658172002516 ATP binding site [chemical binding]; other site 658172002517 Walker B motif; other site 658172002518 arginine finger; other site 658172002519 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002520 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 658172002521 Walker A motif; other site 658172002522 ATP binding site [chemical binding]; other site 658172002523 Walker B motif; other site 658172002524 arginine finger; other site 658172002525 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 658172002526 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 658172002527 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 658172002528 Lipase. 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 process of becoming...; Region: Lipase; cl14883 658172002529 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 658172002530 nucleophilic elbow; other site 658172002531 catalytic triad; other site 658172002532 Zinc-finger domain; Region: zf-CHCC; cl01821 658172002533 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172002534 salicylate hydroxylase; Provisional; Region: PRK06475 658172002535 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 658172002536 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 658172002537 substrate binding pocket [chemical binding]; other site 658172002538 membrane-bound complex binding site; other site 658172002539 hinge residues; other site 658172002540 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: BatB; COG4597 658172002541 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; cl00427 658172002542 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 658172002543 dimer interface [polypeptide binding]; other site 658172002544 ABC-ATPase subunit interface; other site 658172002545 putative PBP binding loops; other site 658172002546 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 658172002547 dimer interface [polypeptide binding]; other site 658172002548 conserved gate region; other site 658172002549 putative PBP binding loops; other site 658172002550 ABC-ATPase subunit interface; other site 658172002551 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 658172002552 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP...; Region: ABC_HisP_GlnQ_permeases; cd03262 658172002553 Walker A/P-loop; other site 658172002554 ATP binding site [chemical binding]; other site 658172002555 Q-loop/lid; other site 658172002556 ABC transporter signature motif; other site 658172002557 Walker B; other site 658172002558 D-loop; other site 658172002559 H-loop/switch region; other site 658172002560 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 658172002561 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 658172002562 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 658172002563 DHH family; Region: DHH; pfam01368 658172002564 DHHA1 domain; Region: DHHA1; pfam02272 658172002565 homoserine dehydrogenase; Provisional; Region: PRK06349 658172002566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172002567 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 658172002568 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 658172002569 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 658172002570 active site 658172002571 hypothetical protein; Reviewed; Region: PRK00024 658172002572 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 658172002573 MPN+ (JAMM) motif; other site 658172002574 Zinc-binding site [ion binding]; other site 658172002575 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 658172002576 trigger factor; Provisional; Region: tig; PRK01490 658172002577 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 658172002578 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 658172002579 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 658172002580 TM-ABC transporter signature motif; other site 658172002581 Protein of unknown function (DUF1153); Region: DUF1153; pfam06627 658172002582 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 658172002583 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 658172002584 active site 658172002585 phosphorylation site [posttranslational modification] 658172002586 intermolecular recognition site; other site 658172002587 dimerization interface [polypeptide binding]; other site 658172002588 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 658172002589 DNA binding site [nucleotide binding] 658172002590 Response regulator receiver domain; Region: Response_reg; pfam00072 658172002591 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 658172002592 active site 658172002593 phosphorylation site [posttranslational modification] 658172002594 intermolecular recognition site; other site 658172002595 dimerization interface [polypeptide binding]; other site 658172002596 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5385 658172002597 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 658172002598 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 658172002599 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key...; Region: CBS_pair_IMPDH; cd04601 658172002600 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine...; Region: IMPDH; cd00381 658172002601 active site 658172002602 PilZ domain; Region: PilZ; cl01260 658172002603 PilZ domain; Region: PilZ; cl01260 658172002604 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 658172002605 GTP cyclohydrolase I; Provisional; Region: PLN03044 658172002606 active site 658172002607 Haemolytic domain; Region: Haemolytic; cl00506 658172002608 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 658172002609 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 658172002610 DNA binding site [nucleotide binding] 658172002611 Int/Topo IB signature motif; other site 658172002612 active site 658172002613 Domain of unknown function DUF59; Region: DUF59; cl00941 658172002614 Peptidase family M23; Region: Peptidase_M23; pfam01551 658172002615 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 658172002616 Clp amino terminal domain; Region: Clp_N; pfam02861 658172002617 Clp amino terminal domain; Region: Clp_N; pfam02861 658172002618 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 658172002619 Walker A motif; other site 658172002620 ATP binding site [chemical binding]; other site 658172002621 Walker B motif; other site 658172002622 arginine finger; other site 658172002623 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 658172002624 Walker A motif; other site 658172002625 ATP binding site [chemical binding]; other site 658172002626 Walker B motif; other site 658172002627 arginine finger; other site 658172002628 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 658172002629 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 658172002630 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 658172002631 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 658172002632 S-adenosylmethionine binding site [chemical binding]; other site 658172002633 peptide chain release factor 1; Validated; Region: prfA; PRK00591 658172002634 RF-1 domain; Region: RF-1; cl02875 658172002635 RF-1 domain; Region: RF-1; cl02875 658172002636 aspartate kinase; Reviewed; Region: PRK06635 658172002637 AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli; Region: AAK_AK-DapG-like; cd04246 658172002638 putative catalytic residues [active] 658172002639 putative nucleotide binding site [chemical binding]; other site 658172002640 putative aspartate binding site [chemical binding]; other site 658172002641 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 658172002642 putative allosteric regulatory site; other site 658172002643 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 658172002644 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 658172002645 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 658172002646 S-adenosylmethionine binding site [chemical binding]; other site 658172002647 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 658172002648 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 658172002649 Walker A/P-loop; other site 658172002650 ATP binding site [chemical binding]; other site 658172002651 Q-loop/lid; other site 658172002652 ABC transporter signature motif; other site 658172002653 Walker B; other site 658172002654 D-loop; other site 658172002655 H-loop/switch region; other site 658172002656 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 658172002657 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 658172002658 FtsX-like permease family; Region: FtsX; cl15850 658172002659 prolyl-tRNA synthetase; Provisional; Region: PRK12325 658172002660 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: ProRS_core_prok; cd00779 658172002661 dimer interface [polypeptide binding]; other site 658172002662 motif 1; other site 658172002663 active site 658172002664 motif 2; other site 658172002665 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches...; Region: class_II_aaRS-like_core; cl00268 658172002666 active site 658172002667 motif 3; other site 658172002668 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 658172002669 anticodon binding site; other site 658172002670 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 658172002671 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 658172002672 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 658172002673 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 658172002674 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 658172002675 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 658172002676 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 658172002677 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 658172002678 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 658172002679 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 658172002680 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 658172002681 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 658172002682 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 658172002683 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 658172002684 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 658172002685 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 658172002686 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 658172002687 4Fe-4S binding domain; Region: Fer4; cl02805 658172002688 4Fe-4S binding domain; Region: Fer4; cl02805 658172002689 NADH dehydrogenase; Region: NADHdh; cl00469 658172002690 NADH dehydrogenase subunit G; Validated; Region: PRK09130 658172002691 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 658172002692 catalytic loop [active] 658172002693 iron binding site [ion binding]; other site 658172002694 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 658172002695 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 658172002696 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 658172002697 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 658172002698 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 658172002699 SLBB domain; Region: SLBB; pfam10531 658172002700 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 658172002701 NADH dehydrogenase subunit E; Provisional; Region: PRK12373 658172002702 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 658172002703 putative dimer interface [polypeptide binding]; other site 658172002704 [2Fe-2S] cluster binding site [ion binding]; other site 658172002705 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 658172002706 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 658172002707 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 658172002708 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 658172002709 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 658172002710 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 658172002711 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 658172002712 ring oligomerisation interface [polypeptide binding]; other site 658172002713 ATP/Mg binding site [chemical binding]; other site 658172002714 stacking interactions; other site 658172002715 hinge regions; other site 658172002716 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 658172002717 oligomerisation interface [polypeptide binding]; other site 658172002718 mobile loop; other site 658172002719 roof hairpin; other site 658172002720 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 658172002721 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 658172002722 active site 658172002723 motif I; other site 658172002724 motif II; other site 658172002725 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 658172002726 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 658172002727 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 658172002728 active site 658172002729 Riboflavin kinase; Region: Flavokinase; cl03312 658172002730 glucose/galactose transporter; Region: gluP; TIGR01272 658172002731 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 658172002732 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional; Region: PRK07494 658172002733 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172002734 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 658172002735 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 658172002736 KpsF/GutQ family protein; Region: kpsF; TIGR00393 658172002737 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 658172002738 putative active site [active] 658172002739 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 658172002740 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 658172002741 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 658172002742 active site 658172002743 phosphorylation site [posttranslational modification] 658172002744 intermolecular recognition site; other site 658172002745 dimerization interface [polypeptide binding]; other site 658172002746 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 658172002747 Walker A motif; other site 658172002748 ATP binding site [chemical binding]; other site 658172002749 Walker B motif; other site 658172002750 arginine finger; other site 658172002751 Helix-turn-helix domains; Region: HTH; cl00088 658172002752 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 658172002753 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 658172002754 active site 658172002755 Zn binding site [ion binding]; other site 658172002756 malic enzyme; Reviewed; Region: PRK12862 658172002757 Malic enzyme, N-terminal domain; Region: malic; pfam00390 658172002758 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 658172002759 putative NAD(P) binding site [chemical binding]; other site 658172002760 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 658172002761 Permease; Region: Permease; cl00510 658172002762 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 658172002763 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002764 Walker A/P-loop; other site 658172002765 ATP binding site [chemical binding]; other site 658172002766 Q-loop/lid; other site 658172002767 ABC transporter signature motif; other site 658172002768 Walker B; other site 658172002769 D-loop; other site 658172002770 H-loop/switch region; other site 658172002771 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 658172002772 mce related protein; Region: MCE; pfam02470 658172002773 Protein of unknown function (DUF330); Region: DUF330; cl01135 658172002774 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 658172002775 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 658172002776 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 658172002777 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 658172002778 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 658172002779 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 658172002780 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 658172002781 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 658172002782 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 658172002783 Rpb1 - Rpb5 interaction site [polypeptide binding]; other site 658172002784 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 658172002785 DNA binding site [nucleotide binding] 658172002786 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 658172002787 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 658172002788 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 658172002789 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 658172002790 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 658172002791 RPB12 interaction site [polypeptide binding]; other site 658172002792 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl04593 658172002793 RPB11 interaction site [polypeptide binding]; other site 658172002794 RPB12 interaction site [polypeptide binding]; other site 658172002795 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 658172002796 RPB3 interaction site [polypeptide binding]; other site 658172002797 RPB1 interaction site [polypeptide binding]; other site 658172002798 RPB11 interaction site [polypeptide binding]; other site 658172002799 RPB10 interaction site [polypeptide binding]; other site 658172002800 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 658172002801 peripheral dimer interface [polypeptide binding]; other site 658172002802 core dimer interface [polypeptide binding]; other site 658172002803 L10 interface [polypeptide binding]; other site 658172002804 L11 interface [polypeptide binding]; other site 658172002805 putative EF-Tu interaction site [polypeptide binding]; other site 658172002806 putative EF-G interaction site [polypeptide binding]; other site 658172002807 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 658172002808 23S rRNA interface [nucleotide binding]; other site 658172002809 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 658172002810 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 658172002811 mRNA/rRNA interface [nucleotide binding]; other site 658172002812 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 658172002813 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 658172002814 23S rRNA interface [nucleotide binding]; other site 658172002815 L7/L12 interface [polypeptide binding]; other site 658172002816 putative thiostrepton binding site; other site 658172002817 L25 interface [polypeptide binding]; other site 658172002818 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 658172002819 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 658172002820 putative homodimer interface [polypeptide binding]; other site 658172002821 KOW motif; Region: KOW; cl00354 658172002822 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 658172002823 elongation factor Tu; Reviewed; Region: PRK00049 658172002824 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 658172002825 G1 box; other site 658172002826 GEF interaction site [polypeptide binding]; other site 658172002827 GTP/Mg2+ binding site [chemical binding]; other site 658172002828 Switch I region; other site 658172002829 G2 box; other site 658172002830 G3 box; other site 658172002831 Switch II region; other site 658172002832 G4 box; other site 658172002833 G5 box; other site 658172002834 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 658172002835 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 658172002836 Antibiotic Binding Site [chemical binding]; other site 658172002837 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 658172002838 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 658172002839 Ligand Binding Site [chemical binding]; other site 658172002840 potential frameshift: common BLAST hit: gi|15966483|ref|NP_386836.1| D-3-phosphoglycerate dehydrogenase 658172002841 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cd01494 658172002842 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 658172002843 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 658172002844 catalytic residue [active] 658172002845 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 658172002846 active site 658172002847 dimerization interface [polypeptide binding]; other site 658172002848 AIR carboxylase; Region: AIRC; cl00310 658172002849 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 658172002850 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172002851 fumarate hydratase; Reviewed; Region: fumC; PRK00485 658172002852 Class II fumarases; Region: Fumarase_classII; cd01362 658172002853 active site 658172002854 tetramer interface [polypeptide binding]; other site 658172002855 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of...; Region: AlaRS_core; cd00673 658172002856 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 658172002857 motif 1; other site 658172002858 active site 658172002859 motif 2; other site 658172002860 motif 3; other site 658172002861 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 658172002862 DHHA1 domain; Region: DHHA1; pfam02272 658172002863 recombinase A; Provisional; Region: recA; PRK09354 658172002864 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 658172002865 hexamer interface [polypeptide binding]; other site 658172002866 Walker A motif; other site 658172002867 ATP binding site [chemical binding]; other site 658172002868 Walker B motif; other site 658172002869 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002870 ABC transporter; Region: ABC_tran; pfam00005 658172002871 Q-loop/lid; other site 658172002872 ABC transporter signature motif; other site 658172002873 Walker B; other site 658172002874 D-loop; other site 658172002875 H-loop/switch region; other site 658172002876 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 658172002877 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002878 Walker A/P-loop; other site 658172002879 ATP binding site [chemical binding]; other site 658172002880 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 658172002881 potential protein location (hypothetical protein CKC_05105 [Candidatus Liberibacter solanacearum CLso-ZC1]) that overlaps RNA (tRNA-E) 658172002882 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 658172002883 structural protein; Region: PHA01972 658172002884 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 658172002885 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 658172002886 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 658172002887 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 658172002888 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 658172002889 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 658172002890 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 658172002891 active site 658172002892 nucleotide binding site [chemical binding]; other site 658172002893 HIGH motif; other site 658172002894 KMSKS motif; other site 658172002895 DNA gyrase subunit A; Validated; Region: PRK05560 658172002896 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA...; Region: TOP4c; cd00187 658172002897 CAP-like domain; other site 658172002898 active site 658172002899 primary dimer interface [polypeptide binding]; other site 658172002900 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 658172002901 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 658172002902 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 658172002903 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 658172002904 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 658172002905 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 658172002906 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 658172002907 dimer interface [polypeptide binding]; other site 658172002908 ssDNA binding site [nucleotide binding]; other site 658172002909 tetramer (dimer of dimers) interface [polypeptide binding]; other site 658172002910 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 658172002911 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 658172002912 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 658172002913 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 658172002914 glutamine synthetase; Provisional; Region: glnA; PRK09469 658172002915 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 658172002916 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 658172002917 DNA primase; Validated; Region: dnaG; PRK05667 658172002918 CHC2 zinc finger; Region: zf-CHC2; cl15369 658172002919 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 658172002920 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 658172002921 active site 658172002922 metal binding site [ion binding]; metal-binding site 658172002923 interdomain interaction site; other site 658172002924 DNA-directed DNA polymerase III (polc); Region: polc; TIGR00594 658172002925 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 658172002926 Protein of unknown function, DUF655; Region: DUF655; pfam04919 658172002927 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 658172002928 generic binding surface I; other site 658172002929 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 658172002930 DNA helicase, putative; Region: TIGR00376 658172002931 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002932 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 658172002933 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172002934 Family description; Region: UvrD_C_2; cl15862 658172002935 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 658172002936 putative active site [active] 658172002937 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 658172002938 dimer interface [polypeptide binding]; other site 658172002939 substrate binding site [chemical binding]; other site 658172002940 metal binding sites [ion binding]; metal-binding site 658172002941 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 658172002942 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 658172002943 G1 box; other site 658172002944 putative GEF interaction site [polypeptide binding]; other site 658172002945 GTP/Mg2+ binding site [chemical binding]; other site 658172002946 Switch I region; other site 658172002947 G2 box; other site 658172002948 G3 box; other site 658172002949 Switch II region; other site 658172002950 G4 box; other site 658172002951 G5 box; other site 658172002952 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 658172002953 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 658172002954 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 658172002955 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 658172002956 ANP binding site [chemical binding]; other site 658172002957 Substrate Binding Site II [chemical binding]; other site 658172002958 Substrate Binding Site I [chemical binding]; other site 658172002959 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 658172002960 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 658172002961 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 658172002962 alphaNTD - beta interaction site [polypeptide binding]; other site 658172002963 alphaNTD homodimer interface [polypeptide binding]; other site 658172002964 alphaNTD - beta' interaction site [polypeptide binding]; other site 658172002965 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 658172002966 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 658172002967 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 658172002968 adenylate kinase; Reviewed; Region: adk; PRK00279 658172002969 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 658172002970 AMP-binding site [chemical binding]; other site 658172002971 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 658172002972 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 658172002973 SecY translocase; Region: SecY; pfam00344 658172002974 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 658172002975 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 658172002976 23S rRNA binding site [nucleotide binding]; other site 658172002977 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 658172002978 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 658172002979 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 658172002980 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 658172002981 23S rRNA interface [nucleotide binding]; other site 658172002982 L21e interface [polypeptide binding]; other site 658172002983 5S rRNA interface [nucleotide binding]; other site 658172002984 L27 interface [polypeptide binding]; other site 658172002985 L5 interface [polypeptide binding]; other site 658172002986 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 658172002987 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 658172002988 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 658172002989 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 658172002990 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 658172002991 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 658172002992 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 658172002993 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 658172002994 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 658172002995 KOW motif; Region: KOW; cl00354 658172002996 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 658172002997 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 658172002998 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 658172002999 23S rRNA interface [nucleotide binding]; other site 658172003000 putative translocon interaction site; other site 658172003001 signal recognition particle (SRP54) interaction site; other site 658172003002 L23 interface [polypeptide binding]; other site 658172003003 trigger factor interaction site; other site 658172003004 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 658172003005 23S rRNA interface [nucleotide binding]; other site 658172003006 5S rRNA interface [nucleotide binding]; other site 658172003007 putative antibiotic binding site [chemical binding]; other site 658172003008 L25 interface [polypeptide binding]; other site 658172003009 L27 interface [polypeptide binding]; other site 658172003010 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 658172003011 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 658172003012 G-X-X-G motif; other site 658172003013 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 658172003014 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 658172003015 putative translocon binding site; other site 658172003016 protein-rRNA interface [nucleotide binding]; other site 658172003017 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 658172003018 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 658172003019 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 658172003020 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 658172003021 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 658172003022 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 658172003023 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 658172003024 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 658172003025 elongation factor Tu; Reviewed; Region: PRK00049 658172003026 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 658172003027 G1 box; other site 658172003028 GEF interaction site [polypeptide binding]; other site 658172003029 GTP/Mg2+ binding site [chemical binding]; other site 658172003030 Switch I region; other site 658172003031 G2 box; other site 658172003032 G3 box; other site 658172003033 Switch II region; other site 658172003034 G4 box; other site 658172003035 G5 box; other site 658172003036 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 658172003037 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 658172003038 Antibiotic Binding Site [chemical binding]; other site 658172003039 elongation factor G; Reviewed; Region: PRK00007 658172003040 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 658172003041 G1 box; other site 658172003042 putative GEF interaction site [polypeptide binding]; other site 658172003043 GTP/Mg2+ binding site [chemical binding]; other site 658172003044 Switch I region; other site 658172003045 G2 box; other site 658172003046 G3 box; other site 658172003047 Switch II region; other site 658172003048 G4 box; other site 658172003049 G5 box; other site 658172003050 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 658172003051 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 658172003052 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 658172003053 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 658172003054 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 658172003055 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 658172003056 S17 interaction site [polypeptide binding]; other site 658172003057 S8 interaction site; other site 658172003058 16S rRNA interaction site [nucleotide binding]; other site 658172003059 streptomycin interaction site [chemical binding]; other site 658172003060 23S rRNA interaction site [nucleotide binding]; other site 658172003061 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 658172003062 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 658172003063 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 658172003064 carboxyltransferase (CT) interaction site; other site 658172003065 biotinylation site [posttranslational modification]; other site 658172003066 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 658172003067 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 658172003068 ATP-grasp domain; Region: ATP-grasp_4; cl03087 658172003069 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 658172003070 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 658172003071 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 658172003072 Found in ATP-dependent protease La (LON); Region: LON; smart00464 658172003073 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 658172003074 Walker A motif; other site 658172003075 ATP binding site [chemical binding]; other site 658172003076 Walker B motif; other site 658172003077 arginine finger; other site 658172003078 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 658172003079 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 658172003080 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 658172003081 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172003082 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 658172003083 Walker A motif; other site 658172003084 ATP binding site [chemical binding]; other site 658172003085 Walker B motif; other site 658172003086 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 658172003087 Clp protease; Region: CLP_protease; pfam00574 658172003088 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 658172003089 oligomer interface [polypeptide binding]; other site 658172003090 active site residues [active] 658172003091 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 658172003092 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 658172003093 Walker A/P-loop; other site 658172003094 ATP binding site [chemical binding]; other site 658172003095 Q-loop/lid; other site 658172003096 ABC transporter signature motif; other site 658172003097 Walker B; other site 658172003098 D-loop; other site 658172003099 H-loop/switch region; other site 658172003100 ABC transporter; Region: ABC_tran_2; pfam12848 658172003101 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 658172003102 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 658172003103 potential protein location (hypothetical protein CKC_05445 [Candidatus Liberibacter solanacearum CLso-ZC1]) that overlaps RNA (tRNA-K) 658172003104 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 658172003105 SmpB-tmRNA interface; other site 658172003106 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 658172003107 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 658172003108 dimer interface [polypeptide binding]; other site 658172003109 active site 658172003110 catalytic residue [active] 658172003111 5'-3' exonuclease, N-terminal resolvase-like domain; Region: 5_3_exonuc_N; pfam02739 658172003112 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 658172003113 active site 658172003114 metal binding site 1 [ion binding]; metal-binding site 658172003115 putative 5' ssDNA interaction site; other site 658172003116 metal binding site 3; metal-binding site 658172003117 metal binding site 2 [ion binding]; metal-binding site 658172003118 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 658172003119 putative DNA binding site [nucleotide binding]; other site 658172003120 putative metal binding site [ion binding]; other site 658172003121 DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]; Region: PolA; COG0749 658172003122 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 658172003123 active site 658172003124 substrate binding site [chemical binding]; other site 658172003125 catalytic site [active] 658172003126 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 658172003127 active site 658172003128 DNA binding site [nucleotide binding] 658172003129 catalytic site [active] 658172003130 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 658172003131 catalytic core [active] 658172003132 dihydrodipicolinate reductase; Provisional; Region: PRK00048 658172003133 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172003134 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 658172003135 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 658172003136 glucokinase, proteobacterial type; Region: glk; TIGR00749 658172003137 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 658172003138 Cu(I) binding site [ion binding]; other site 658172003139 Transcriptional regulator [Transcription]; Region: LysR; COG0583 658172003140 Helix-turn-helix domains; Region: HTH; cl00088 658172003141 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 658172003142 putative effector binding pocket; other site 658172003143 dimerization interface [polypeptide binding]; other site 658172003144 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 658172003145 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 658172003146 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 658172003147 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 658172003148 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 658172003149 active site 658172003150 HIGH motif; other site 658172003151 KMSK motif region; other site 658172003152 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 658172003153 tRNA binding surface [nucleotide binding]; other site 658172003154 anticodon binding site; other site 658172003155 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 658172003156 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 658172003157 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 658172003158 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 658172003159 putative phosphate binding site [ion binding]; other site 658172003160 putative catalytic site [active] 658172003161 active site 658172003162 metal binding site A [ion binding]; metal-binding site 658172003163 DNA binding site [nucleotide binding] 658172003164 putative AP binding site [nucleotide binding]; other site 658172003165 putative metal binding site B [ion binding]; other site 658172003166 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 658172003167 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 658172003168 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 658172003169 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 658172003170 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 658172003171 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 658172003172 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 658172003173 DNA binding residues [nucleotide binding] 658172003174 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172003175 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 658172003176 23S rRNA interface [nucleotide binding]; other site 658172003177 L3 interface [polypeptide binding]; other site 658172003178 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 658172003179 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 658172003180 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 658172003181 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 658172003182 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 658172003183 dimerization interface 3.5A [polypeptide binding]; other site 658172003184 active site 658172003185 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 658172003186 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 658172003187 putative active site [active] 658172003188 substrate binding site [chemical binding]; other site 658172003189 putative cosubstrate binding site; other site 658172003190 catalytic site [active] 658172003191 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 658172003192 substrate binding site [chemical binding]; other site 658172003193 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 658172003194 active site 658172003195 catalytic residues [active] 658172003196 metal binding site [ion binding]; metal-binding site 658172003197 YceG-like family; Region: YceG; pfam02618 658172003198 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 658172003199 dimerization interface [polypeptide binding]; other site 658172003200 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 658172003201 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 658172003202 dimer interface [polypeptide binding]; other site 658172003203 active site 658172003204 Phosphopantetheine attachment site; Region: PP-binding; cl09936 658172003205 3-ketoacyl-(acyl-carrier-protein) reductase NodG; Reviewed; Region: PRK12936 658172003206 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 658172003207 NAD(P) binding site [chemical binding]; other site 658172003208 homotetramer interface [polypeptide binding]; other site 658172003209 homodimer interface [polypeptide binding]; other site 658172003210 active site 658172003211 Acyl transferase domain; Region: Acyl_transf_1; cl08282 658172003212 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 658172003213 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 658172003214 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 658172003215 metal binding site [ion binding]; metal-binding site 658172003216 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 658172003217 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 658172003218 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 658172003219 ABC-ATPase subunit interface; other site 658172003220 dimer interface [polypeptide binding]; other site 658172003221 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 658172003222 ABC-ATPase subunit interface; other site 658172003223 dimer interface [polypeptide binding]; other site 658172003224 putative PBP binding regions; other site 658172003225 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 658172003226 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 658172003227 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 658172003228 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 658172003229 active site 658172003230 substrate binding site [chemical binding]; other site 658172003231 metal binding site [ion binding]; metal-binding site 658172003232 FtsH Extracellular; Region: FtsH_ext; pfam06480 658172003233 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 658172003234 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 658172003235 Walker A motif; other site 658172003236 ATP binding site [chemical binding]; other site 658172003237 Walker B motif; other site 658172003238 arginine finger; other site 658172003239 Peptidase family M41; Region: Peptidase_M41; pfam01434 658172003240 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 658172003241 Ligand Binding Site [chemical binding]; other site 658172003242 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 658172003243 ligand binding site [chemical binding]; other site 658172003244 translocation protein TolB; Provisional; Region: tolB; PRK05137 658172003245 TolB amino-terminal domain; Region: TolB_N; cl00639 658172003246 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 658172003247 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 658172003248 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 658172003249 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 658172003250 Walker A motif; other site 658172003251 ATP binding site [chemical binding]; other site 658172003252 Walker B motif; other site 658172003253 arginine finger; other site 658172003254 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 658172003255 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 658172003256 RuvA N terminal domain; Region: RuvA_N; pfam01330 658172003257 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes...; Region: RuvC_resolvase; cd00529 658172003258 active site 658172003259 putative DNA-binding cleft [nucleotide binding]; other site 658172003260 dimer interface [polypeptide binding]; other site 658172003261 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 658172003262 active site 658172003263 DNA binding site [nucleotide binding] 658172003264 structural protein; Region: PHA01972 658172003265 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 658172003266 hypothetical protein; Region: PHA00661 658172003267 hypothetical protein; Region: PHA00662 658172003268 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 658172003269 Terminase-like family; Region: Terminase_6; pfam03237 658172003270 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 658172003271 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 658172003272 non-specific DNA binding site [nucleotide binding]; other site 658172003273 salt bridge; other site 658172003274 sequence-specific DNA binding site [nucleotide binding]; other site 658172003275 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 658172003276 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 658172003277 non-specific DNA binding site [nucleotide binding]; other site 658172003278 salt bridge; other site 658172003279 sequence-specific DNA binding site [nucleotide binding]; other site 658172003280 BRO family, N-terminal domain; Region: Bro-N; cl10591 658172003281 TIR domain; Region: TIR_2; cl15770 658172003282 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 658172003283 phage/plasmid primase, P4 family, C-terminal domain; Region: primase_Cterm; TIGR01613 658172003284 Primase C terminal 2 (PriCT-2); Region: PriCT_2; pfam08707 658172003285 D5 N terminal like; Region: D5_N; cl07360 658172003286 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cl01287 658172003287 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 658172003288 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 658172003289 BRO family, N-terminal domain; Region: Bro-N; cl10591 658172003290 Protein of unknown function (DUF2815); Region: DUF2815; pfam10991 658172003291 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 658172003292 active site 658172003293 substrate binding site [chemical binding]; other site 658172003294 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 658172003295 active site 658172003296 DNA binding site [nucleotide binding] 658172003297 catalytic site [active] 658172003298 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 658172003299 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 658172003300 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 658172003301 ATP binding site [chemical binding]; other site 658172003302 putative Mg++ binding site [ion binding]; other site 658172003303 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 658172003304 nucleotide binding region [chemical binding]; other site 658172003305 ATP-binding site [chemical binding]; other site 658172003306 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; cl03295 658172003307 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 658172003308 catalytic site [active] 658172003309 G-X2-G-X-G-K; other site 658172003310 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 658172003311 DNA binding site [nucleotide binding] 658172003312 Int/Topo IB signature motif; other site 658172003313 active site 658172003314 catalytic residues [active]