-- dump date 20111121_013542 -- class Genbank::misc_feature -- table misc_feature_note -- id note 222891000001 ParB-like partition proteins; Region: parB_part; TIGR00180 222891000002 ParB-like nuclease domain; Region: ParBc; cl02129 222891000003 KorB domain; Region: KorB; pfam08535 222891000004 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 trans-...; Region: HisKA; cd00082 222891000005 dimer interface [polypeptide binding]; other site 222891000006 phosphorylation site [posttranslational modification] 222891000007 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 222891000008 ATP binding site [chemical binding]; other site 222891000009 Mg2+ binding site [ion binding]; other site 222891000010 G-X-G motif; other site 222891000011 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 222891000012 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 222891000013 Phage-related protein [Function unknown]; Region: COG4695; cl01923 222891000014 Phage portal protein; Region: Phage_portal; pfam04860 222891000015 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 222891000016 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 222891000017 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 222891000018 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 222891000019 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 222891000020 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 222891000021 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 222891000022 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 222891000023 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 222891000024 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 222891000025 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 222891000026 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 222891000027 dimerization interface 3.5A [polypeptide binding]; other site 222891000028 active site 222891000029 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 222891000030 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 222891000031 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 222891000032 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 222891000033 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...; Region: PurM; cd02196 222891000034 dimerization interface [polypeptide binding]; other site 222891000035 putative ATP binding site [chemical binding]; other site 222891000036 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 222891000037 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 222891000038 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 222891000039 Uncharacterized conserved small protein [Function unknown]; Region: COG5606 222891000040 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 222891000041 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 222891000042 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891000043 active site 222891000044 nucleotide binding site [chemical binding]; other site 222891000045 HIGH motif; other site 222891000046 KMSKS motif; other site 222891000047 Riboflavin kinase; Region: Flavokinase; pfam01687 222891000048 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 222891000049 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 222891000050 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891000051 Walker A/P-loop; other site 222891000052 ATP binding site [chemical binding]; other site 222891000053 Q-loop/lid; other site 222891000054 ABC transporter signature motif; other site 222891000055 Walker B; other site 222891000056 D-loop; other site 222891000057 H-loop/switch region; other site 222891000058 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 222891000059 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 222891000060 NAD binding site [chemical binding]; other site 222891000061 homotetramer interface [polypeptide binding]; other site 222891000062 homodimer interface [polypeptide binding]; other site 222891000063 substrate binding site [chemical binding]; other site 222891000064 active site 222891000065 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 222891000066 thiS-thiF/thiG interaction site; other site 222891000067 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 222891000068 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 222891000069 trimer interface [polypeptide binding]; other site 222891000070 putative metal binding site [ion binding]; other site 222891000071 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 222891000072 Iron-sulfur protein interface; other site 222891000073 proximal quinone binding site [chemical binding]; other site 222891000074 SdhD (CybS) interface [polypeptide binding]; other site 222891000075 proximal heme binding site [chemical binding]; other site 222891000076 Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR...; Region: SQR_QFR_TM; cl00881 222891000077 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 222891000078 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 222891000079 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 222891000080 active site 222891000081 HIGH motif; other site 222891000082 KMSK motif region; other site 222891000083 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 222891000084 tRNA binding surface [nucleotide binding]; other site 222891000085 anticodon binding site; other site 222891000086 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cd06181 222891000087 NADH dehydrogenase subunit G; Validated; Region: PRK09130 222891000088 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 222891000089 catalytic loop [active] 222891000090 iron binding site [ion binding]; other site 222891000091 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 222891000092 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 222891000093 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 222891000094 NADH dehydrogenase; Region: NADHdh; cl00469 222891000095 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 222891000096 BON domain; Region: BON; cl02771 222891000097 BON domain; Region: BON; cl02771 222891000098 fumarate hydratase; Reviewed; Region: fumC; PRK00485 222891000099 Class II fumarases; Region: Fumarase_classII; cd01362 222891000100 active site 222891000101 tetramer interface [polypeptide binding]; other site 222891000102 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 222891000103 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 222891000104 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 222891000105 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 222891000106 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 222891000107 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 222891000108 putative nucleic acid binding region [nucleotide binding]; other site 222891000109 G-X-X-G motif; other site 222891000110 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 222891000111 RNA binding site [nucleotide binding]; other site 222891000112 domain interface; other site 222891000113 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...; Region: Ribosomal_S15p_S13e; cd00353 222891000114 16S/18S rRNA binding site [nucleotide binding]; other site 222891000115 S13e-L30e interaction site [polypeptide binding]; other site 222891000116 25S rRNA binding site [nucleotide binding]; other site 222891000117 adenylosuccinate lyase; Provisional; Region: PRK07492 222891000118 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 222891000119 tetramer interface [polypeptide binding]; other site 222891000120 active site 222891000121 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 222891000122 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 222891000123 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 222891000124 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 222891000125 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 222891000126 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 222891000127 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 222891000128 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 222891000129 putative substrate translocation pore; other site 222891000130 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cl01321 222891000131 transcription termination factor Rho; Provisional; Region: rho; PRK09376 222891000132 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 222891000133 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...; Region: Rho_CSD; cd04459 222891000134 RNA binding site [nucleotide binding]; other site 222891000135 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...; Region: rho_factor; cd01128 222891000136 multimer interface [polypeptide binding]; other site 222891000137 Walker A motif; other site 222891000138 ATP binding site [chemical binding]; other site 222891000139 Walker B motif; other site 222891000140 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 222891000141 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...; Region: AAA; cd00009 222891000142 Walker A motif; other site 222891000143 ATP binding site [chemical binding]; other site 222891000144 Walker B motif; other site 222891000145 V-type ATP synthase subunit I; Validated; Region: PRK05771 222891000146 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 222891000147 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 222891000148 GatB domain; Region: GatB_Yqey; cl11497 222891000149 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 222891000150 nucleoside/Zn binding site; other site 222891000151 dimer interface [polypeptide binding]; other site 222891000152 catalytic motif [active] 222891000153 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 222891000154 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 222891000155 putative active site [active] 222891000156 substrate binding site [chemical binding]; other site 222891000157 putative cosubstrate binding site; other site 222891000158 catalytic site [active] 222891000159 Carboxy-terminal domain of Formyltransferase and similar domains; Region: FMT_C_like; cl14785 222891000160 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...; Region: NAD_synthase; cd00553 222891000161 homodimer interface [polypeptide binding]; other site 222891000162 NAD synthase; Region: NAD_synthase; pfam02540 222891000163 NAD binding pocket [chemical binding]; other site 222891000164 ATP binding pocket [chemical binding]; other site 222891000165 Mg binding site [ion binding]; other site 222891000166 active-site loop [active] 222891000167 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 222891000168 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 222891000169 RNA binding site [nucleotide binding]; other site 222891000170 active site 222891000171 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 222891000172 Clp amino terminal domain; Region: Clp_N; pfam02861 222891000173 Clp amino terminal domain; Region: Clp_N; pfam02861 222891000174 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...; Region: AAA; cd00009 222891000175 Walker A motif; other site 222891000176 ATP binding site [chemical binding]; other site 222891000177 Walker B motif; other site 222891000178 arginine finger; other site 222891000179 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...; Region: AAA; cd00009 222891000180 Walker A motif; other site 222891000181 ATP binding site [chemical binding]; other site 222891000182 Walker B motif; other site 222891000183 arginine finger; other site 222891000184 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 222891000185 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 222891000186 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 222891000187 homodimer interface [polypeptide binding]; other site 222891000188 oligonucleotide binding site [chemical binding]; other site 222891000189 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 222891000190 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-...; Region: QPRTase; cd01572 222891000191 dimerization interface [polypeptide binding]; other site 222891000192 active site 222891000193 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 222891000194 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 222891000195 RimM N-terminal domain; Region: RimM; pfam01782 222891000196 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]; Region: HEC1; COG5185 222891000197 RmuC family; Region: RmuC; pfam02646 222891000198 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 222891000199 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 222891000200 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891000201 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 222891000202 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 222891000203 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 222891000204 beta subunit interaction interface [polypeptide binding]; other site 222891000205 Walker A motif; other site 222891000206 ATP binding site [chemical binding]; other site 222891000207 Walker B motif; other site 222891000208 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 222891000209 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 222891000210 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 222891000211 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 222891000212 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid...; Region: MECDP_synthase; cd00554 222891000213 homotrimer interaction site [polypeptide binding]; other site 222891000214 zinc binding site [ion binding]; other site 222891000215 CDP-binding sites; other site 222891000216 LolC/E family; Region: lolCE; TIGR02212 222891000217 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 222891000218 FtsX-like permease family; Region: FtsX; pfam02687 222891000219 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...; Region: PseudoU_synth_RluCD_like; cd02869 222891000220 active site 222891000221 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 222891000222 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 222891000223 putative active site; other site 222891000224 catalytic residue [active] 222891000225 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 222891000226 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 222891000227 DNA binding site [nucleotide binding] 222891000228 Int/Topo IB signature motif; other site 222891000229 active site 222891000230 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 222891000231 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 222891000232 RNA binding surface [nucleotide binding]; other site 222891000233 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...; Region: PseudoU_synth_RluCD_like; cd02869 222891000234 active site 222891000235 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 222891000236 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...; Region: Biotinyl_lipoyl_domains; cl11404 222891000237 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 222891000238 dihydroorotase; Validated; Region: pyrC; PRK09357 222891000239 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have...; Region: metallo-dependent_hydrolases; cl00281 222891000240 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 222891000241 active site 222891000242 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 222891000243 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...; Region: AlaRS_core; cd00673 222891000244 motif 1; other site 222891000245 active site 222891000246 motif 2; other site 222891000247 motif 3; other site 222891000248 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 222891000249 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 222891000250 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 222891000251 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 222891000252 Thymidylate synthase complementing protein; Region: Thy1; cl03630 222891000253 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 222891000254 HflK protein; Region: hflK; TIGR01933 222891000255 FtsH protease regulator HflC; Provisional; Region: PRK11029 222891000256 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 222891000257 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 222891000258 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...; Region: Tryp_SPc; cl00149 222891000259 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 C-...; Region: PDZ_serine_protease; cd00987 222891000260 protein binding site [polypeptide binding]; other site 222891000261 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 C-...; Region: PDZ_serine_protease; cd00987 222891000262 protein binding site [polypeptide binding]; other site 222891000263 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 222891000264 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 222891000265 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 222891000266 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 222891000267 Smr domain; Region: Smr; cl02619 222891000268 DNA polymerase III subunit beta; Validated; Region: PRK05643 222891000269 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...; Region: beta_clamp; cd00140 222891000270 putative DNA binding surface [nucleotide binding]; other site 222891000271 dimer interface [polypeptide binding]; other site 222891000272 beta-clamp/clamp loader binding surface; other site 222891000273 beta-clamp/translesion DNA polymerase binding surface; other site 222891000274 isocitrate dehydrogenase; Region: ICDH_alpha; TIGR02924 222891000275 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 222891000276 Membrane transport protein; Region: Mem_trans; cl09117 222891000277 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 222891000278 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 222891000279 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 222891000280 active site 222891000281 HslU subunit interaction site [polypeptide binding]; other site 222891000282 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 222891000283 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...; Region: AAA; cd00009 222891000284 Walker A motif; other site 222891000285 ATP binding site [chemical binding]; other site 222891000286 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891000287 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 222891000288 substrate binding site [chemical binding]; other site 222891000289 dimer interface [polypeptide binding]; other site 222891000290 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...; Region: DHOD_2_like; cd04738 222891000291 quinone interaction residues [chemical binding]; other site 222891000292 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 222891000293 active site 222891000294 catalytic residues [active] 222891000295 FMN binding site [chemical binding]; other site 222891000296 substrate binding site [chemical binding]; other site 222891000297 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 222891000298 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a...; Region: EPT_RTPC-like; cl00288 222891000299 putative active site [active] 222891000300 Predicted membrane protein [Function unknown]; Region: COG3164 222891000301 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 222891000302 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 5-aminoimidazole-4-carboxamide-; Region: IMPCH; cd01421 222891000303 purine monophosphate binding site [chemical binding]; other site 222891000304 dimer interface [polypeptide binding]; other site 222891000305 putative catalytic residues [active] 222891000306 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 222891000307 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 222891000308 glutathione synthetase; Provisional; Region: PRK05246 222891000309 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 222891000310 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891000311 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 222891000312 FMN binding site [chemical binding]; other site 222891000313 substrate binding site [chemical binding]; other site 222891000314 putative catalytic residue [active] 222891000315 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891000316 Domain of unknown function DUF20; Region: UPF0118; cl00465 222891000317 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 222891000318 Protein export membrane protein; Region: SecD_SecF; cl14618 222891000319 amidophosphoribosyltransferase; Provisional; Region: PRK09123 222891000320 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 222891000321 active site 222891000322 tetramer interface [polypeptide binding]; other site 222891000323 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 222891000324 translation elongation factor P; Region: efp; TIGR00038 222891000325 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 222891000326 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_1; cd04470 222891000327 RNA binding site [nucleotide binding]; other site 222891000328 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 N-formylmethionyl-...; Region: S1_EF-P_repeat_2; cd05794 222891000329 RNA binding site [nucleotide binding]; other site 222891000330 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 222891000331 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891000332 Walker A/P-loop; other site 222891000333 ATP binding site [chemical binding]; other site 222891000334 Q-loop/lid; other site 222891000335 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 222891000336 S-adenosylmethionine binding site [chemical binding]; other site 222891000337 BolA-like protein; Region: BolA; cl00386 222891000338 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 222891000339 putative GSH binding site [chemical binding]; other site 222891000340 catalytic residues [active] 222891000341 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 222891000342 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...; Region: TM_PBP2; cd06261 222891000343 dimer interface [polypeptide binding]; other site 222891000344 conserved gate region; other site 222891000345 putative PBP binding loops; other site 222891000346 ABC-ATPase subunit interface; other site 222891000347 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 222891000348 primosome assembly protein PriA; Validated; Region: PRK05580 222891000349 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 222891000350 ATP binding site [chemical binding]; other site 222891000351 putative Mg++ binding site [ion binding]; other site 222891000352 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; cl14882 222891000353 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 222891000354 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 222891000355 VirB7 interaction site; other site 222891000356 VirB8 protein; Region: VirB8; cl01500 222891000357 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 222891000358 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 222891000359 dimer interface [polypeptide binding]; other site 222891000360 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 222891000361 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 222891000362 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 222891000363 active site 222891000364 HIGH motif; other site 222891000365 dimer interface [polypeptide binding]; other site 222891000366 KMSKS motif; other site 222891000367 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 222891000368 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 222891000369 23S rRNA binding site [nucleotide binding]; other site 222891000370 L21 binding site [polypeptide binding]; other site 222891000371 L13 binding site [polypeptide binding]; other site 222891000372 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 222891000373 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 222891000374 dimer interface [polypeptide binding]; other site 222891000375 motif 1; other site 222891000376 active site 222891000377 motif 2; other site 222891000378 motif 3; other site 222891000379 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 222891000380 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...; Region: SHMT; cd00378 222891000381 dimer interface [polypeptide binding]; other site 222891000382 glycine-pyridoxal phosphate binding site [chemical binding]; other site 222891000383 active site 222891000384 folate binding site [chemical binding]; other site 222891000385 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-...; Region: TMP_TenI; cd00564 222891000386 thiamine phosphate binding site [chemical binding]; other site 222891000387 active site 222891000388 pyrophosphate binding site [ion binding]; other site 222891000389 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 222891000390 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 222891000391 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891000392 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 222891000393 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 222891000394 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891000395 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 222891000396 IMP binding site; other site 222891000397 dimer interface [polypeptide binding]; other site 222891000398 interdomain contacts; other site 222891000399 partial ornithine binding site; other site 222891000400 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 222891000401 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 222891000402 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 r-...; Region: AdSS; cd03108 222891000403 adenylosuccinate synthetase; Provisional; Region: PRK01117 222891000404 GDP-binding site [chemical binding]; other site 222891000405 ACT binding site; other site 222891000406 IMP binding site; other site 222891000407 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cl00559 222891000408 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 222891000409 catalytic residues [active] 222891000410 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 222891000411 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 222891000412 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 222891000413 hypothetical protein; Reviewed; Region: PRK00024 222891000414 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 222891000415 MPN+ (JAMM) motif; other site 222891000416 Zinc-binding site [ion binding]; other site 222891000417 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 222891000418 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 222891000419 non-specific DNA binding site [nucleotide binding]; other site 222891000420 salt bridge; other site 222891000421 sequence-specific DNA binding site [nucleotide binding]; other site 222891000422 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 222891000423 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; cl14882 222891000424 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 222891000425 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 222891000426 nucleotide binding region [chemical binding]; other site 222891000427 ATP-binding site [chemical binding]; other site 222891000428 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 222891000429 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 222891000430 active site 222891000431 phosphorylation site [posttranslational modification] 222891000432 intermolecular recognition site; other site 222891000433 dimerization interface [polypeptide binding]; other site 222891000434 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...; Region: trans_reg_C; cd00383 222891000435 DNA binding site [nucleotide binding] 222891000436 AIR carboxylase; Region: AIRC; cl00310 222891000437 UGMP family protein; Validated; Region: PRK09604 222891000438 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 222891000439 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 222891000440 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 222891000441 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 222891000442 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 222891000443 substrate binding pocket [chemical binding]; other site 222891000444 chain length determination region; other site 222891000445 substrate-Mg2+ binding site; other site 222891000446 catalytic residues [active] 222891000447 aspartate-rich region 1; other site 222891000448 active site lid residues [active] 222891000449 aspartate-rich region 2; other site 222891000450 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 222891000451 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 222891000452 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; cl09826 222891000453 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional; Region: PRK11929 222891000454 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 222891000455 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 222891000456 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 222891000457 minor groove reading motif; other site 222891000458 helix-hairpin-helix signature motif; other site 222891000459 substrate binding pocket [chemical binding]; other site 222891000460 active site 222891000461 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 222891000462 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 222891000463 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 222891000464 CDP-alcohol phosphatidyltransferase 2; Region: CDP-OH_P_tran_2; pfam08009 222891000465 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 222891000466 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 222891000467 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 222891000468 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 222891000469 CoA-ligase; Region: Ligase_CoA; pfam00549 222891000470 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 222891000471 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891000472 CoA-ligase; Region: Ligase_CoA; pfam00549 222891000473 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 222891000474 dimerization interface [polypeptide binding]; other site 222891000475 ATP binding site [chemical binding]; other site 222891000476 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 222891000477 substrate binding site [chemical binding]; other site 222891000478 dimer interface [polypeptide binding]; other site 222891000479 catalytic triad [active] 222891000480 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 222891000481 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 222891000482 active site residue [active] 222891000483 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 222891000484 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 222891000485 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 222891000486 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 222891000487 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 222891000488 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...; Region: AAA; cd00009 222891000489 Walker A motif; other site 222891000490 ATP binding site [chemical binding]; other site 222891000491 Walker B motif; other site 222891000492 arginine finger; other site 222891000493 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 222891000494 DnaA box-binding interface [nucleotide binding]; other site 222891000495 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 222891000496 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 222891000497 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 222891000498 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 222891000499 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 222891000500 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 222891000501 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 222891000502 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 222891000503 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 222891000504 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 222891000505 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 222891000506 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 222891000507 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 222891000508 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 222891000509 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 222891000510 putative translocon binding site; other site 222891000511 protein-rRNA interface [nucleotide binding]; other site 222891000512 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 222891000513 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...; Region: 30S_S3_KH; cd02412 222891000514 G-X-X-G motif; other site 222891000515 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 222891000516 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 222891000517 23S rRNA interface [nucleotide binding]; other site 222891000518 5S rRNA interface [nucleotide binding]; other site 222891000519 putative antibiotic binding site [chemical binding]; other site 222891000520 L25 interface [polypeptide binding]; other site 222891000521 L27 interface [polypeptide binding]; other site 222891000522 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...; Region: Ribosomal_L29_HIP; cl09943 222891000523 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 222891000524 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 222891000525 KOW motif; Region: KOW; cl00354 222891000526 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 222891000527 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 222891000528 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 222891000529 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 222891000530 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 222891000531 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 222891000532 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 222891000533 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 222891000534 23S rRNA interface [nucleotide binding]; other site 222891000535 L21e interface [polypeptide binding]; other site 222891000536 5S rRNA interface [nucleotide binding]; other site 222891000537 L27 interface [polypeptide binding]; other site 222891000538 L5 interface [polypeptide binding]; other site 222891000539 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 222891000540 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 222891000541 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 222891000542 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 222891000543 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 222891000544 SecY translocase; Region: SecY; pfam00344 222891000545 adenylate kinase; Reviewed; Region: adk; PRK00279 222891000546 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 222891000547 AMP-binding site [chemical binding]; other site 222891000548 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 222891000549 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 222891000550 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 222891000551 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 222891000552 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 222891000553 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 222891000554 alphaNTD - beta interaction site [polypeptide binding]; other site 222891000555 alphaNTD homodimer interface [polypeptide binding]; other site 222891000556 alphaNTD - beta' interaction site [polypeptide binding]; other site 222891000557 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 222891000558 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 222891000559 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 222891000560 DNA binding residues [nucleotide binding] 222891000561 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 222891000562 tetramer interfaces [polypeptide binding]; other site 222891000563 binuclear metal-binding site [ion binding]; other site 222891000564 translation initiation factor IF-3; Region: infC; TIGR00168 222891000565 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 222891000566 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 222891000567 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 222891000568 GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information on the function of the TGS domain, but...; Region: TGS; cl03735 222891000569 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 222891000570 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 222891000571 active site 222891000572 dimer interface [polypeptide binding]; other site 222891000573 motif 1; other site 222891000574 motif 2; other site 222891000575 motif 3; other site 222891000576 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 222891000577 anticodon binding site; other site 222891000578 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 222891000579 catalytic loop [active] 222891000580 iron binding site [ion binding]; other site 222891000581 Fe-S protein assembly chaperone HscA; Region: HscA; TIGR01991 222891000582 co-chaperone HscB; Provisional; Region: hscB; PRK01356 222891000583 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 222891000584 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 222891000585 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 222891000586 trimerization site [polypeptide binding]; other site 222891000587 active site 222891000588 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 222891000589 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 222891000590 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 222891000591 catalytic residue [active] 222891000592 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 222891000593 Rrf2 family protein; Region: rrf2_super; TIGR00738 222891000594 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 222891000595 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 222891000596 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 222891000597 catalytic residue [active] 222891000598 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 222891000599 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...; Region: TM_PBP2; cl00427 222891000600 Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this...; Region: Ribosomal_L25_TL5_CTC; cd00495 222891000601 5S rRNA interface [nucleotide binding]; other site 222891000602 CTC domain interface; other site 222891000603 L16 interface [polypeptide binding]; other site 222891000604 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 222891000605 putative active site [active] 222891000606 catalytic residue [active] 222891000607 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 222891000608 Glutamate-cysteine ligase; Region: GshA; pfam08886 222891000609 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 222891000610 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 222891000611 CoA-binding site [chemical binding]; other site 222891000612 ATP-binding [chemical binding]; other site 222891000613 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 222891000614 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 222891000615 GSH binding site [chemical binding]; other site 222891000616 catalytic residues [active] 222891000617 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 222891000618 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 222891000619 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 222891000620 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 222891000621 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 222891000622 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...; Region: Sigma70_r4; cl01055 222891000623 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 222891000624 Clp amino terminal domain; Region: Clp_N; pfam02861 222891000625 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...; Region: AAA; cd00009 222891000626 Walker A motif; other site 222891000627 ATP binding site [chemical binding]; other site 222891000628 Walker B motif; other site 222891000629 arginine finger; other site 222891000630 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...; Region: AAA; cd00009 222891000631 Walker A motif; other site 222891000632 ATP binding site [chemical binding]; other site 222891000633 Walker B motif; other site 222891000634 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 222891000635 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 222891000636 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 222891000637 Walker A/P-loop; other site 222891000638 ATP binding site [chemical binding]; other site 222891000639 Q-loop/lid; other site 222891000640 ABC transporter signature motif; other site 222891000641 Walker B; other site 222891000642 D-loop; other site 222891000643 H-loop/switch region; other site 222891000644 Competence protein; Region: Competence; cl00471 222891000645 Competence protein; Region: Competence; cl00471 222891000646 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 222891000647 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 222891000648 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 222891000649 Preprotein translocase subunit; Region: YajC; cl00806 222891000650 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 222891000651 active site 222891000652 hydrophilic channel; other site 222891000653 dimerization interface [polypeptide binding]; other site 222891000654 catalytic residues [active] 222891000655 active site lid [active] 222891000656 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 222891000657 lipoyl synthase; Provisional; Region: PRK05481 222891000658 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 222891000659 FeS/SAM binding site; other site 222891000660 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 222891000661 putative coenzyme Q binding site [chemical binding]; other site 222891000662 Domain of unknown function (DUF299); Region: DUF299; cl00780 222891000663 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 222891000664 Transporter associated domain; Region: CorC_HlyC; pfam03471 222891000665 Ferredoxin [Energy production and conversion]; Region: COG1146 222891000666 4Fe-4S binding domain; Region: Fer4; cl02805 222891000667 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 222891000668 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 222891000669 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891000670 active site 222891000671 HIGH motif; other site 222891000672 nucleotide binding site [chemical binding]; other site 222891000673 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 222891000674 KMSKS motif; other site 222891000675 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 222891000676 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 222891000677 MutS domain I; Region: MutS_I; pfam01624 222891000678 MutS domain II; Region: MutS_II; pfam05188 222891000679 MutS family domain IV; Region: MutS_IV; pfam05190 222891000680 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 222891000681 Walker A/P-loop; other site 222891000682 ATP binding site [chemical binding]; other site 222891000683 Q-loop/lid; other site 222891000684 ABC transporter signature motif; other site 222891000685 Walker B; other site 222891000686 D-loop; other site 222891000687 H-loop/switch region; other site 222891000688 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...; Region: RPE; cd00429 222891000689 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 222891000690 substrate binding site [chemical binding]; other site 222891000691 hexamer interface [polypeptide binding]; other site 222891000692 metal binding site [ion binding]; metal-binding site 222891000693 methionine aminopeptidase; Reviewed; Region: PRK07281 222891000694 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 222891000695 active site 222891000696 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 222891000697 diiron binding motif [ion binding]; other site 222891000698 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 222891000699 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 222891000700 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 222891000701 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...; Region: Sigma70_r4; cl01055 222891000702 cell division protein FtsZ; Validated; Region: PRK09330 222891000703 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...; Region: FtsZ_type1; cd02201 222891000704 nucleotide binding site [chemical binding]; other site 222891000705 SulA interaction site; other site 222891000706 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site...; Region: RaiA; cd00552 222891000707 30S subunit binding site; other site 222891000708 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 222891000709 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 222891000710 active site 222891000711 HIGH motif; other site 222891000712 dimer interface [polypeptide binding]; other site 222891000713 KMSKS motif; other site 222891000714 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 222891000715 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 222891000716 heme binding site [chemical binding]; other site 222891000717 ferroxidase diiron center [ion binding]; other site 222891000718 ferroxidase pore; other site 222891000719 Found in ATP-dependent protease La (LON); Region: LON; cl01056 222891000720 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 222891000721 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...; Region: AAA; cd00009 222891000722 Walker A motif; other site 222891000723 ATP binding site [chemical binding]; other site 222891000724 Walker B motif; other site 222891000725 trehalose synthase, Pseudomonas stutzeri type; Region: TreS_stutzeri; TIGR02455 222891000726 arginine finger; other site 222891000727 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 222891000728 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-...; Region: TMP_TenI; cd00564 222891000729 thiamine phosphate binding site [chemical binding]; other site 222891000730 active site 222891000731 pyrophosphate binding site [ion binding]; other site 222891000732 Uncharacterised protein family (UPF0093); Region: UPF0093; cl00863 222891000733 glutamine synthetase; Provisional; Region: glnA; PRK09469 222891000734 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 222891000735 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 222891000736 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 222891000737 ATP cone domain; Region: ATP-cone; pfam03477 222891000738 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 222891000739 UvrD/REP helicase; Region: UvrD-helicase; cl14126 222891000740 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 222891000741 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 222891000742 active site 222891000743 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 222891000744 SecA binding site; other site 222891000745 Preprotein binding site; other site 222891000746 Tim44-like domain; Region: Tim44; cl09208 222891000747 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891000748 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 222891000749 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 trans-...; Region: HisKA; cd00082 222891000750 dimer interface [polypeptide binding]; other site 222891000751 phosphorylation site [posttranslational modification] 222891000752 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 222891000753 ATP binding site [chemical binding]; other site 222891000754 Mg2+ binding site [ion binding]; other site 222891000755 G-X-G motif; other site 222891000756 Response regulator receiver domain; Region: Response_reg; pfam00072 222891000757 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 222891000758 active site 222891000759 phosphorylation site [posttranslational modification] 222891000760 intermolecular recognition site; other site 222891000761 dimerization interface [polypeptide binding]; other site 222891000762 prolyl-tRNA synthetase; Provisional; Region: PRK12325 222891000763 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...; Region: ProRS_core_prok; cd00779 222891000764 dimer interface [polypeptide binding]; other site 222891000765 motif 1; other site 222891000766 active site 222891000767 motif 2; other site 222891000768 motif 3; other site 222891000769 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-...; Region: ProRS_anticodon_short; cd00861 222891000770 anticodon binding site; other site 222891000771 pyruvate phosphate dikinase; Provisional; Region: PRK09279 222891000772 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 222891000773 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 222891000774 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 222891000775 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 222891000776 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 222891000777 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 222891000778 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 222891000779 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...; Region: DUS_like_FMN; cd02801 222891000780 FMN binding site [chemical binding]; other site 222891000781 active site 222891000782 catalytic residues [active] 222891000783 substrate binding site [chemical binding]; other site 222891000784 Survival protein SurE; Region: SurE; cl00448 222891000785 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 222891000786 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891000787 domain; Region: Succ_DH_flav_C; pfam02910 222891000788 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 222891000789 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 222891000790 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 222891000791 NADP binding site [chemical binding]; other site 222891000792 dimer interface [polypeptide binding]; other site 222891000793 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 222891000794 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891000795 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 222891000796 porphobilinogen deaminase; Region: hemC; TIGR00212 222891000797 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 222891000798 domain interfaces; other site 222891000799 active site 222891000800 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 222891000801 NmrA-like family; Region: NmrA; pfam05368 222891000802 putative NAD(P) binding site [chemical binding]; other site 222891000803 active site 222891000804 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 222891000805 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 222891000806 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(...; Region: Pep_deformylase; cd00487 222891000807 active site 222891000808 catalytic residues [active] 222891000809 metal binding site [ion binding]; metal-binding site 222891000810 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 222891000811 dimer interface [polypeptide binding]; other site 222891000812 active site 222891000813 aspartate-rich active site metal binding site; other site 222891000814 allosteric magnesium binding site [ion binding]; other site 222891000815 Schiff base residues; other site 222891000816 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 222891000817 ATP synthase A chain; Region: ATP-synt_A; cl00413 222891000818 ATP synthase subunit C; Region: ATP-synt_C; cl00466 222891000819 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 222891000820 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 222891000821 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 222891000822 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 222891000823 homopentamer interface [polypeptide binding]; other site 222891000824 active site 222891000825 membrane protein insertase; Provisional; Region: PRK01318 222891000826 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 222891000827 Domain of unknown function DUF21; Region: DUF21; pfam01595 222891000828 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 222891000829 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 222891000830 Transporter associated domain; Region: CorC_HlyC; pfam03471 222891000831 peptide chain release factor 1; Validated; Region: prfA; PRK00591 222891000832 RF-1 domain; Region: RF-1; cl02875 222891000833 RF-1 domain; Region: RF-1; cl02875 222891000834 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 222891000835 putative acyl-acceptor binding pocket; other site 222891000836 ribosomal protein S1; Region: rpsA; TIGR00717 222891000837 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 222891000838 RNA binding site [nucleotide binding]; other site 222891000839 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 222891000840 RNA binding site [nucleotide binding]; other site 222891000841 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 222891000842 RNA binding site [nucleotide binding]; other site 222891000843 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 222891000844 RNA binding site [nucleotide binding]; other site 222891000845 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 222891000846 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 222891000847 tandem repeat interface [polypeptide binding]; other site 222891000848 oligomer interface [polypeptide binding]; other site 222891000849 active site residues [active] 222891000850 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 222891000851 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 222891000852 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891000853 Walker A/P-loop; other site 222891000854 ATP binding site [chemical binding]; other site 222891000855 Q-loop/lid; other site 222891000856 ABC transporter signature motif; other site 222891000857 Walker B; other site 222891000858 D-loop; other site 222891000859 H-loop/switch region; other site 222891000860 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 222891000861 Class I ribonucleotide reductase; Region: RNR_I; cd01679 222891000862 active site 222891000863 dimer interface [polypeptide binding]; other site 222891000864 catalytic residues [active] 222891000865 effector binding site; other site 222891000866 R2 peptide binding site; other site 222891000867 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 222891000868 nucleotide binding site/active site [active] 222891000869 HIT family signature motif; other site 222891000870 catalytic residue [active] 222891000871 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 222891000872 putative phosphate binding site [ion binding]; other site 222891000873 putative catalytic site [active] 222891000874 active site 222891000875 metal binding site A [ion binding]; metal-binding site 222891000876 DNA binding site [nucleotide binding] 222891000877 putative AP binding site [nucleotide binding]; other site 222891000878 putative metal binding site B [ion binding]; other site 222891000879 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 222891000880 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 222891000881 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 222891000882 Protein export membrane protein; Region: SecD_SecF; cl14618 222891000883 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 222891000884 Malic enzyme, N-terminal domain; Region: malic; pfam00390 222891000885 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 222891000886 putative NAD(P) binding site [chemical binding]; other site 222891000887 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 222891000888 FtsH Extracellular; Region: FtsH_ext; pfam06480 222891000889 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 222891000890 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...; Region: AAA; cd00009 222891000891 Walker A motif; other site 222891000892 ATP binding site [chemical binding]; other site 222891000893 Walker B motif; other site 222891000894 arginine finger; other site 222891000895 Peptidase family M41; Region: Peptidase_M41; pfam01434 222891000896 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 222891000897 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 222891000898 putative tRNA-binding site [nucleotide binding]; other site 222891000899 B3/4 domain; Region: B3_4; cl11458 222891000900 tRNA synthetase B5 domain; Region: B5; cl08394 222891000901 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 222891000902 dimer interface [polypeptide binding]; other site 222891000903 motif 1; other site 222891000904 motif 3; other site 222891000905 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 222891000906 Cell division protein FtsA; Region: FtsA; cl11496 222891000907 cell division protein FtsA; Region: ftsA; TIGR01174 222891000908 Cell division protein FtsA; Region: FtsA; cl11496 222891000909 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 222891000910 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 222891000911 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl00539 222891000912 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 222891000913 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 222891000914 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 222891000915 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; cl00198 222891000916 substrate binding site [chemical binding]; other site 222891000917 hinge regions; other site 222891000918 ADP binding site [chemical binding]; other site 222891000919 catalytic site [active] 222891000920 LytB protein; Region: LYTB; cl00507 222891000921 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 222891000922 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 222891000923 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...; Region: HemD; cd06578 222891000924 active site 222891000925 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 222891000926 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 222891000927 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 222891000928 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 222891000929 GTPase CgtA; Reviewed; Region: obgE; PRK12299 222891000930 GTP1/OBG; Region: GTP1_OBG; pfam01018 222891000931 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 222891000932 G1 box; other site 222891000933 GTP/Mg2+ binding site [chemical binding]; other site 222891000934 Switch I region; other site 222891000935 G2 box; other site 222891000936 G3 box; other site 222891000937 Switch II region; other site 222891000938 G4 box; other site 222891000939 classical (c) SDRs; Region: SDR_c; cd05233 222891000940 NAD(P) binding site [chemical binding]; other site 222891000941 active site 222891000942 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 222891000943 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 222891000944 DNA binding site [nucleotide binding] 222891000945 Int/Topo IB signature motif; other site 222891000946 active site 222891000947 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 222891000948 conserved cys residue [active] 222891000949 Phosphopantetheine attachment site; Region: PP-binding; cl09936 222891000950 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 222891000951 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 222891000952 dimer interface [polypeptide binding]; other site 222891000953 active site 222891000954 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 222891000955 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 222891000956 catalytic motif [active] 222891000957 Catalytic residue [active] 222891000958 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 222891000959 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 222891000960 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 222891000961 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 222891000962 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 222891000963 Zn2+ binding site [ion binding]; other site 222891000964 Mg2+ binding site [ion binding]; other site 222891000965 Recombination protein O C terminal; Region: RecO_C; pfam02565 222891000966 Stringent starvation protein B; Region: SspB; cl01120 222891000967 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 222891000968 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891000969 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 222891000970 Uncharacterised protein family UPF0102; Region: UPF0102; cl00516 222891000971 MgtE intracellular N domain; Region: MgtE_N; cl15244 222891000972 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 222891000973 Divalent cation transporter; Region: MgtE; cl00786 222891000974 Phage capsid family; Region: Phage_capsid; pfam05065 222891000975 UvrD/REP helicase; Region: UvrD-helicase; cl14126 222891000976 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 222891000977 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 222891000978 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 222891000979 Ligand Binding Site [chemical binding]; other site 222891000980 Zinc-finger domain; Region: zf-CHCC; cl01821 222891000981 Proteobacterial; Region: dnaQ_proteo; TIGR01406 222891000982 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 222891000983 active site 222891000984 substrate binding site [chemical binding]; other site 222891000985 catalytic site [active] 222891000986 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 222891000987 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 222891000988 active site 222891000989 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 222891000990 Cytochrome c; Region: Cytochrom_C; cl11414 222891000991 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 222891000992 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 222891000993 active site 222891000994 substrate binding site [chemical binding]; other site 222891000995 cosubstrate binding site; other site 222891000996 catalytic site [active] 222891000997 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...; Region: Peptidase_M17; cd00433 222891000998 interface (dimer of trimers) [polypeptide binding]; other site 222891000999 Substrate-binding/catalytic site; other site 222891001000 Zn-binding sites [ion binding]; other site 222891001001 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 222891001002 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 222891001003 dimer interface [polypeptide binding]; other site 222891001004 anticodon binding site; other site 222891001005 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 222891001006 homodimer interface [polypeptide binding]; other site 222891001007 motif 1; other site 222891001008 active site 222891001009 motif 2; other site 222891001010 GAD domain; Region: GAD; pfam02938 222891001011 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 222891001012 active site 222891001013 motif 3; other site 222891001014 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed; Region: murF; PRK10773 222891001015 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 222891001016 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...; Region: TM_PBP2; cd06261 222891001017 dimer interface [polypeptide binding]; other site 222891001018 conserved gate region; other site 222891001019 putative PBP binding loops; other site 222891001020 ABC-ATPase subunit interface; other site 222891001021 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 222891001022 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 222891001023 Walker A/P-loop; other site 222891001024 ATP binding site [chemical binding]; other site 222891001025 Q-loop/lid; other site 222891001026 ABC transporter signature motif; other site 222891001027 Walker B; other site 222891001028 D-loop; other site 222891001029 H-loop/switch region; other site 222891001030 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 222891001031 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 222891001032 ThiS interaction site; other site 222891001033 putative active site [active] 222891001034 tetramer interface [polypeptide binding]; other site 222891001035 dihydropteroate synthase; Region: DHPS; TIGR01496 222891001036 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 222891001037 substrate binding pocket [chemical binding]; other site 222891001038 dimer interface [polypeptide binding]; other site 222891001039 inhibitor binding site; inhibition site 222891001040 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 222891001041 catalytic center binding site [active] 222891001042 ATP binding site [chemical binding]; other site 222891001043 S-adenosylmethionine synthetase; Validated; Region: PRK05250 222891001044 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 222891001045 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 222891001046 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 222891001047 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 222891001048 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 222891001049 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 222891001050 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...; Region: AAA; cd00009 222891001051 Walker A motif; other site 222891001052 ATP binding site [chemical binding]; other site 222891001053 Walker B motif; other site 222891001054 arginine finger; other site 222891001055 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 222891001056 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 222891001057 heat shock protein 90; Provisional; Region: PRK05218 222891001058 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 222891001059 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 222891001060 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 222891001061 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 222891001062 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 222891001063 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 222891001064 putative active site [active] 222891001065 catalytic triad [active] 222891001066 putative dimer interface [polypeptide binding]; other site 222891001067 AsmA family; Region: AsmA; pfam05170 222891001068 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 222891001069 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 222891001070 catalytic motif [active] 222891001071 Zn binding site [ion binding]; other site 222891001072 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 5,10-...; Region: DHFR; cl00161 222891001073 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 222891001074 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 222891001075 nucleotide binding pocket [chemical binding]; other site 222891001076 K-X-D-G motif; other site 222891001077 catalytic site [active] 222891001078 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 222891001079 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 222891001080 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 222891001081 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 222891001082 Dimer interface [polypeptide binding]; other site 222891001083 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 222891001084 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 222891001085 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 222891001086 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 222891001087 catalytic site [active] 222891001088 subunit interface [polypeptide binding]; other site 222891001089 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 222891001090 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 222891001091 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 222891001092 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 222891001093 HIGH motif; other site 222891001094 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891001095 active site 222891001096 KMSKS motif; other site 222891001097 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 222891001098 tRNA binding surface [nucleotide binding]; other site 222891001099 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 222891001100 non-specific DNA binding site [nucleotide binding]; other site 222891001101 salt bridge; other site 222891001102 sequence-specific DNA binding site [nucleotide binding]; other site 222891001103 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 (...; Region: S24_LexA-like; cd06529 222891001104 Catalytic site [active] 222891001105 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 222891001106 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 222891001107 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 222891001108 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 222891001109 response regulator PleD; Reviewed; Region: pleD; PRK09581 222891001110 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 222891001111 active site 222891001112 phosphorylation site [posttranslational modification] 222891001113 intermolecular recognition site; other site 222891001114 dimerization interface [polypeptide binding]; other site 222891001115 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 222891001116 metal binding site [ion binding]; metal-binding site 222891001117 active site 222891001118 I-site; other site 222891001119 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 222891001120 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 222891001121 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 222891001122 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 222891001123 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891001124 active site 222891001125 HIGH motif; other site 222891001126 nucleotide binding site [chemical binding]; other site 222891001127 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891001128 active site 222891001129 KMSKS motif; other site 222891001130 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 222891001131 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 222891001132 dimer interface [polypeptide binding]; other site 222891001133 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 222891001134 putative radical transfer pathway; other site 222891001135 diiron center [ion binding]; other site 222891001136 tyrosyl radical; other site 222891001137 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 222891001138 NusA N-terminal domain; Region: NusA_N; pfam08529 222891001139 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...; Region: S1_NusA; cd04455 222891001140 RNA binding site [nucleotide binding]; other site 222891001141 homodimer interface [polypeptide binding]; other site 222891001142 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 222891001143 G-X-X-G motif; other site 222891001144 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 222891001145 translation initiation factor IF-2; Region: IF-2; TIGR00487 222891001146 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases...; Region: IF2_eIF5B; cd01887 222891001147 G1 box; other site 222891001148 putative GEF interaction site [polypeptide binding]; other site 222891001149 GTP/Mg2+ binding site [chemical binding]; other site 222891001150 Switch I region; other site 222891001151 G2 box; other site 222891001152 G3 box; other site 222891001153 Switch II region; other site 222891001154 G4 box; other site 222891001155 G5 box; other site 222891001156 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...; Region: IF2_mtIF2_II; cd03702 222891001157 Translation-initiation factor 2; Region: IF-2; pfam11987 222891001158 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...; Region: mtIF2_IVc; cd03692 222891001159 Ribosome-binding factor A; Region: RBFA; cl00542 222891001160 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 222891001161 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 222891001162 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 222891001163 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 222891001164 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...; Region: IMPDH; cd00381 222891001165 active site 222891001166 mce related protein; Region: MCE; cl03606 222891001167 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 222891001168 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 222891001169 putative active site [active] 222891001170 catalytic site [active] 222891001171 putative substrate binding site [chemical binding]; other site 222891001172 recombinase A; Provisional; Region: recA; PRK09354 222891001173 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 222891001174 hexamer interface [polypeptide binding]; other site 222891001175 Walker A motif; other site 222891001176 ATP binding site [chemical binding]; other site 222891001177 Walker B motif; other site 222891001178 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 trans-...; Region: HisKA; cd00082 222891001179 dimer interface [polypeptide binding]; other site 222891001180 phosphorylation site [posttranslational modification] 222891001181 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 222891001182 ATP binding site [chemical binding]; other site 222891001183 Mg2+ binding site [ion binding]; other site 222891001184 G-X-G motif; other site 222891001185 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 222891001186 chaperone protein DnaJ; Provisional; Region: PRK10767 222891001187 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...; Region: DnaJ; cd06257 222891001188 HSP70 interaction site [polypeptide binding]; other site 222891001189 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 222891001190 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 222891001191 ribosome-associated GTPase EngA; Region: GTPase_EngA; TIGR03594 222891001192 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 222891001193 G1 box; other site 222891001194 GTP/Mg2+ binding site [chemical binding]; other site 222891001195 G2 box; other site 222891001196 Switch I region; other site 222891001197 G3 box; other site 222891001198 Switch II region; other site 222891001199 G4 box; other site 222891001200 G5 box; other site 222891001201 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA2; cd01895 222891001202 G1 box; other site 222891001203 GTP/Mg2+ binding site [chemical binding]; other site 222891001204 Switch I region; other site 222891001205 G2 box; other site 222891001206 G3 box; other site 222891001207 Switch II region; other site 222891001208 G4 box; other site 222891001209 G5 box; other site 222891001210 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 222891001211 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 222891001212 HIGH motif; other site 222891001213 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 222891001214 active site 222891001215 KMSKS motif; other site 222891001216 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 222891001217 tRNA binding surface [nucleotide binding]; other site 222891001218 anticodon binding site; other site 222891001219 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 222891001220 signal recognition particle protein; Provisional; Region: PRK10867 222891001221 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 222891001222 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 222891001223 P loop; other site 222891001224 GTP binding site [chemical binding]; other site 222891001225 Signal peptide binding domain; Region: SRP_SPB; pfam02978 222891001226 RDD family; Region: RDD; cl00746 222891001227 Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]; Region: TadD; COG5010 222891001228 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 222891001229 S-adenosylmethionine binding site [chemical binding]; other site 222891001230 putative enoyl-(acyl-carrier-protein) reductase II; Region: enACPred_II; TIGR03151 222891001231 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin...; Region: NPD_like; cd04730 222891001232 FMN binding site [chemical binding]; other site 222891001233 substrate binding site [chemical binding]; other site 222891001234 putative catalytic residue [active] 222891001235 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 222891001236 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 222891001237 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 222891001238 P loop; other site 222891001239 GTP binding site [chemical binding]; other site 222891001240 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891001241 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...; Region: TMPK; cd01672 222891001242 thymidylate kinase; Validated; Region: tmk; PRK00698 222891001243 TMP-binding site; other site 222891001244 ATP-binding site [chemical binding]; other site 222891001245 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 222891001246 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 222891001247 E3 interaction surface; other site 222891001248 lipoyl attachment site [posttranslational modification]; other site 222891001249 e3 binding domain; Region: E3_binding; pfam02817 222891001250 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 222891001251 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 222891001252 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 222891001253 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 222891001254 Cu(I) binding site [ion binding]; other site 222891001255 replicative DNA helicase; Provisional; Region: PRK09165 222891001256 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 222891001257 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 222891001258 Walker A motif; other site 222891001259 ATP binding site [chemical binding]; other site 222891001260 Walker B motif; other site 222891001261 DNA binding loops [nucleotide binding] 222891001262 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 222891001263 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 222891001264 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...; Region: PseudoU_synth_RluCD_like; cd02869 222891001265 active site 222891001266 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891001267 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 222891001268 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891001269 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 222891001270 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic...; Region: PRX_Typ2cys; cd03015 222891001271 dimer interface [polypeptide binding]; other site 222891001272 decamer (pentamer of dimers) interface [polypeptide binding]; other site 222891001273 catalytic triad [active] 222891001274 peroxidatic and resolving cysteines [active] 222891001275 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 222891001276 active site 222891001277 multimer interface [polypeptide binding]; other site 222891001278 integral membrane protein MviN; Region: mviN; TIGR01695 222891001279 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 222891001280 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 222891001281 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; cl00417 222891001282 seryl-tRNA synthetase; Provisional; Region: PRK05431 222891001283 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 222891001284 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 222891001285 dimer interface [polypeptide binding]; other site 222891001286 active site 222891001287 motif 1; other site 222891001288 motif 2; other site 222891001289 motif 3; other site 222891001290 IPP transferase; Region: IPPT; cl00403 222891001291 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 222891001292 Holliday junction DNA helicase RuvA; Provisional; Region: ruvA; PRK14600 222891001293 RuvA N terminal domain; Region: RuvA_N; pfam01330 222891001294 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 222891001295 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...; Region: AAA; cd00009 222891001296 Walker A motif; other site 222891001297 ATP binding site [chemical binding]; other site 222891001298 Walker B motif; other site 222891001299 arginine finger; other site 222891001300 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 222891001301 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 222891001302 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 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of...; Region: TPP_E1_OGDC_like; cd02016 222891001303 TPP-binding site [chemical binding]; other site 222891001304 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 222891001305 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 222891001306 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 222891001307 Protein of unknown function (DUF528); Region: DUF528; cl01123 222891001308 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 222891001309 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 222891001310 RNA binding surface [nucleotide binding]; other site 222891001311 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 222891001312 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 222891001313 active site 222891001314 ATP synthase; Region: ATP-synt; cl00365 222891001315 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 222891001316 FAD binding domain; Region: FAD_binding_4; pfam01565 222891001317 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 222891001318 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 222891001319 active site 222891001320 DNA topoisomerase I; Validated; Region: PRK06599 222891001321 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...; Region: TOPRIM_TopoIA_TopoI; cd03363 222891001322 active site 222891001323 interdomain interaction site; other site 222891001324 putative metal-binding site [ion binding]; other site 222891001325 nucleotide binding site [chemical binding]; other site 222891001326 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...; Region: TOP1Ac; cd00186 222891001327 domain I; other site 222891001328 DNA binding groove [nucleotide binding] 222891001329 phosphate binding site [ion binding]; other site 222891001330 domain II; other site 222891001331 domain III; other site 222891001332 nucleotide binding site [chemical binding]; other site 222891001333 catalytic site [active] 222891001334 domain IV; other site 222891001335 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 222891001336 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 222891001337 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 222891001338 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891001339 aconitate hydratase; Validated; Region: PRK09277 222891001340 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 222891001341 substrate binding site [chemical binding]; other site 222891001342 ligand binding site [chemical binding]; other site 222891001343 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 222891001344 substrate binding site [chemical binding]; other site 222891001345 Uncharacterized conserved protein [Function unknown]; Region: COG1565 222891001346 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 222891001347 tRNA synthetases class I (I, L, M and V); Region: tRNA-synt_1; pfam00133 222891001348 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891001349 active site 222891001350 HIGH motif; other site 222891001351 nucleotide binding site [chemical binding]; other site 222891001352 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891001353 active site 222891001354 KMSKS motif; other site 222891001355 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 222891001356 tRNA binding surface [nucleotide binding]; other site 222891001357 anticodon binding site; other site 222891001358 peptide chain release factor 2; Validated; Region: prfB; PRK00578 222891001359 RF-1 domain; Region: RF-1; cl02875 222891001360 RF-1 domain; Region: RF-1; cl02875 222891001361 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 222891001362 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 222891001363 ATP binding site [chemical binding]; other site 222891001364 Mg2+ binding site [ion binding]; other site 222891001365 G-X-G motif; other site 222891001366 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 222891001367 ATP binding site [chemical binding]; other site 222891001368 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 222891001369 biotin synthetase; Region: bioB; TIGR00433 222891001370 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 222891001371 FeS/SAM binding site; other site 222891001372 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 222891001373 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 222891001374 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 222891001375 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 222891001376 catalytic residue [active] 222891001377 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 222891001378 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 222891001379 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 222891001380 S-adenosylmethionine binding site [chemical binding]; other site 222891001381 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: PLN02974 222891001382 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 222891001383 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 222891001384 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 222891001385 inhibitor-cofactor binding pocket; inhibition site 222891001386 pyridoxal 5'-phosphate binding site [chemical binding]; other site 222891001387 catalytic residue [active] 222891001388 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 222891001389 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00168 222891001390 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 222891001391 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 222891001392 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 222891001393 Subunit I/III interface [polypeptide binding]; other site 222891001394 D-pathway; other site 222891001395 Subunit I/VIIc interface [polypeptide binding]; other site 222891001396 Subunit I/IV interface [polypeptide binding]; other site 222891001397 Subunit I/II interface [polypeptide binding]; other site 222891001398 Low-spin heme (heme a) binding site [chemical binding]; other site 222891001399 Subunit I/VIIa interface [polypeptide binding]; other site 222891001400 Subunit I/VIa interface [polypeptide binding]; other site 222891001401 Dimer interface; other site 222891001402 Putative water exit pathway; other site 222891001403 Binuclear center (heme a3/CuB) [ion binding]; other site 222891001404 K-pathway; other site 222891001405 Subunit I/Vb interface [polypeptide binding]; other site 222891001406 Putative proton exit pathway; other site 222891001407 Subunit I/VIb interface; other site 222891001408 Subunit I/VIc interface [polypeptide binding]; other site 222891001409 Electron transfer pathway; other site 222891001410 Subunit I/VIIIb interface [polypeptide binding]; other site 222891001411 Subunit I/VIIb interface [polypeptide binding]; other site 222891001412 UbiA prenyltransferase family; Region: UbiA; cl00337 222891001413 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 222891001414 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 222891001415 [2Fe-2S] cluster binding site [ion binding]; other site 222891001416 cytochrome b; Provisional; Region: CYTB; MTH00191 222891001417 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cd00284 222891001418 Qi binding site; other site 222891001419 intrachain domain interface; other site 222891001420 interchain domain interface [polypeptide binding]; other site 222891001421 heme bH binding site [chemical binding]; other site 222891001422 heme bL binding site [chemical binding]; other site 222891001423 Qo binding site; other site 222891001424 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: cytochrome_b_C; cl00193 222891001425 interchain domain interface [polypeptide binding]; other site 222891001426 intrachain domain interface; other site 222891001427 Qi binding site; other site 222891001428 Qo binding site; other site 222891001429 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 222891001430 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 222891001431 Protein export membrane protein; Region: SecD_SecF; cl14618 222891001432 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 222891001433 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 222891001434 S-adenosylmethionine binding site [chemical binding]; other site 222891001435 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 222891001436 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 222891001437 dimer interface [polypeptide binding]; other site 222891001438 active site 222891001439 CoA binding pocket [chemical binding]; other site 222891001440 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 222891001441 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 222891001442 NADH-quinone oxidoreductase, E subunit; Region: nuoE_fam; TIGR01958 222891001443 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...; Region: TRX_Fd_NuoE; cd03064 222891001444 putative dimer interface [polypeptide binding]; other site 222891001445 [2Fe-2S] cluster binding site [ion binding]; other site 222891001446 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 222891001447 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 222891001448 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 222891001449 active site 222891001450 ATP binding site [chemical binding]; other site 222891001451 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 higher-...; Region: HU_IHF; cd00591 222891001452 IHF dimer interface [polypeptide binding]; other site 222891001453 IHF - DNA interface [nucleotide binding]; other site 222891001454 Domain of unknown function DUF28; Region: DUF28; cl00361 222891001455 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 222891001456 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 222891001457 ring oligomerisation interface [polypeptide binding]; other site 222891001458 ATP/Mg binding site [chemical binding]; other site 222891001459 stacking interactions; other site 222891001460 hinge regions; other site 222891001461 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...; Region: cpn10; cd00320 222891001462 oligomerisation interface [polypeptide binding]; other site 222891001463 mobile loop; other site 222891001464 roof hairpin; other site 222891001465 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 222891001466 periplasmic folding chaperone; Provisional; Region: PRK10788 222891001467 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 222891001468 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 222891001469 active site 222891001470 NTP binding site [chemical binding]; other site 222891001471 metal binding triad [ion binding]; metal-binding site 222891001472 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 222891001473 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891001474 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 222891001475 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 222891001476 Coenzyme A binding pocket [chemical binding]; other site 222891001477 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 222891001478 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl14881 222891001479 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 222891001480 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-...; Region: DHOD_e_trans_like; cd06192 222891001481 FAD binding pocket [chemical binding]; other site 222891001482 FAD binding motif [chemical binding]; other site 222891001483 phosphate binding motif [ion binding]; other site 222891001484 beta-alpha-beta structure motif; other site 222891001485 NAD binding pocket [chemical binding]; other site 222891001486 Iron coordination center [ion binding]; other site 222891001487 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 222891001488 Outer membrane protein (OmpH-like); Region: OmpH; cl08146 222891001489 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 222891001490 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 222891001491 NAD(P) binding site [chemical binding]; other site 222891001492 homotetramer interface [polypeptide binding]; other site 222891001493 homodimer interface [polypeptide binding]; other site 222891001494 active site 222891001495 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 222891001496 RNA/DNA hybrid binding site [nucleotide binding]; other site 222891001497 active site 222891001498 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 222891001499 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891001500 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 222891001501 domain; Region: GreA_GreB_N; pfam03449 222891001502 C-term; Region: GreA_GreB; pfam01272 222891001503 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 222891001504 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891001505 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891001506 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 222891001507 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 222891001508 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 222891001509 G1 box; other site 222891001510 putative GEF interaction site [polypeptide binding]; other site 222891001511 GTP/Mg2+ binding site [chemical binding]; other site 222891001512 Switch I region; other site 222891001513 G2 box; other site 222891001514 G3 box; other site 222891001515 Switch II region; other site 222891001516 G4 box; other site 222891001517 G5 box; other site 222891001518 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 222891001519 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...; Region: BipA_TypA_C; cd03710 222891001520 DNA polymerase I; Provisional; Region: PRK05755 222891001521 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 222891001522 active site 222891001523 metal binding site 1 [ion binding]; metal-binding site 222891001524 putative 5' ssDNA interaction site; other site 222891001525 metal binding site 3; metal-binding site 222891001526 metal binding site 2 [ion binding]; metal-binding site 222891001527 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 222891001528 putative DNA binding site [nucleotide binding]; other site 222891001529 putative metal binding site [ion binding]; other site 222891001530 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 222891001531 active site 222891001532 DNA binding site [nucleotide binding] 222891001533 catalytic site [active] 222891001534 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 222891001535 Subunit III/VIIa interface [polypeptide binding]; other site 222891001536 Phospholipid binding site [chemical binding]; other site 222891001537 Subunit I/III interface [polypeptide binding]; other site 222891001538 Subunit III/VIb interface [polypeptide binding]; other site 222891001539 Subunit III/VIa interface; other site 222891001540 Subunit III/Vb interface [polypeptide binding]; other site 222891001541 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 222891001542 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 222891001543 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 222891001544 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 222891001545 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 222891001546 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 222891001547 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 222891001548 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 222891001549 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 222891001550 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 222891001551 DNA binding site [nucleotide binding] 222891001552 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 222891001553 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 222891001554 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 222891001555 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 222891001556 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 222891001557 RPB11 interaction site [polypeptide binding]; other site 222891001558 RPB12 interaction site [polypeptide binding]; other site 222891001559 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 222891001560 RPB3 interaction site [polypeptide binding]; other site 222891001561 RPB1 interaction site [polypeptide binding]; other site 222891001562 RPB11 interaction site [polypeptide binding]; other site 222891001563 RPB10 interaction site [polypeptide binding]; other site 222891001564 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 222891001565 core dimer interface [polypeptide binding]; other site 222891001566 L11 interface [polypeptide binding]; other site 222891001567 putative EF-Tu interaction site [polypeptide binding]; other site 222891001568 putative EF-G interaction site [polypeptide binding]; other site 222891001569 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...; Region: Ribosomal_L10; cd05797 222891001570 23S rRNA interface [nucleotide binding]; other site 222891001571 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 222891001572 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...; Region: Ribosomal_L1; cd00403 222891001573 mRNA/rRNA interface [nucleotide binding]; other site 222891001574 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 222891001575 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 222891001576 23S rRNA interface [nucleotide binding]; other site 222891001577 L7/L12 interface [polypeptide binding]; other site 222891001578 putative thiostrepton binding site; other site 222891001579 L25 interface [polypeptide binding]; other site 222891001580 Transcription antiterminator [Transcription]; Region: NusG; COG0250 222891001581 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 222891001582 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 222891001583 elongation factor Tu; Reviewed; Region: PRK00049 222891001584 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 222891001585 G1 box; other site 222891001586 GEF interaction site [polypeptide binding]; other site 222891001587 GTP/Mg2+ binding site [chemical binding]; other site 222891001588 Switch I region; other site 222891001589 G2 box; other site 222891001590 G3 box; other site 222891001591 Switch II region; other site 222891001592 G4 box; other site 222891001593 G5 box; other site 222891001594 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 222891001595 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 222891001596 Antibiotic Binding Site [chemical binding]; other site 222891001597 elongation factor G; Reviewed; Region: PRK00007 222891001598 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved...; Region: EF-G; cd01886 222891001599 G1 box; other site 222891001600 putative GEF interaction site [polypeptide binding]; other site 222891001601 GTP/Mg2+ binding site [chemical binding]; other site 222891001602 Switch I region; other site 222891001603 G2 box; other site 222891001604 G3 box; other site 222891001605 Switch II region; other site 222891001606 G4 box; other site 222891001607 G5 box; other site 222891001608 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...; Region: EFG_mtEFG_II; cd04088 222891001609 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...; Region: EFG_mtEFG1_IV; cd01434 222891001610 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...; Region: EFG_mtEFG_C; cd03713 222891001611 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 222891001612 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 222891001613 S17 interaction site [polypeptide binding]; other site 222891001614 S8 interaction site; other site 222891001615 16S rRNA interaction site [nucleotide binding]; other site 222891001616 streptomycin interaction site [chemical binding]; other site 222891001617 23S rRNA interaction site [nucleotide binding]; other site 222891001618 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 222891001619 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 222891001620 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 222891001621 ATP binding site [chemical binding]; other site 222891001622 putative Mg++ binding site [ion binding]; other site 222891001623 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 222891001624 nucleotide binding region [chemical binding]; other site 222891001625 ATP-binding site [chemical binding]; other site 222891001626 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 222891001627 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 222891001628 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 222891001629 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 222891001630 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 222891001631 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 222891001632 substrate binding pocket [chemical binding]; other site 222891001633 chain length determination region; other site 222891001634 substrate-Mg2+ binding site; other site 222891001635 catalytic residues [active] 222891001636 aspartate-rich region 1; other site 222891001637 active site lid residues [active] 222891001638 aspartate-rich region 2; other site 222891001639 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 222891001640 Domain of unknown function DUF140; Region: DUF140; cl00510 222891001641 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 222891001642 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891001643 Walker A/P-loop; other site 222891001644 ATP binding site [chemical binding]; other site 222891001645 Q-loop/lid; other site 222891001646 ABC transporter signature motif; other site 222891001647 Walker B; other site 222891001648 D-loop; other site 222891001649 H-loop/switch region; other site 222891001650 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891001651 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 222891001652 Walker A/P-loop; other site 222891001653 ATP binding site [chemical binding]; other site 222891001654 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891001655 Q-loop/lid; other site 222891001656 ABC transporter signature motif; other site 222891001657 Walker B; other site 222891001658 D-loop; other site 222891001659 H-loop/switch region; other site 222891001660 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 222891001661 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 222891001662 RNA/DNA hybrid binding site [nucleotide binding]; other site 222891001663 active site 222891001664 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 222891001665 TPP-binding site [chemical binding]; other site 222891001666 dimer interface [polypeptide binding]; other site 222891001667 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 222891001668 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 222891001669 PYR/PP interface [polypeptide binding]; other site 222891001670 dimer interface [polypeptide binding]; other site 222891001671 TPP binding site [chemical binding]; other site 222891001672 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 222891001673 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 222891001674 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 222891001675 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 222891001676 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 222891001677 active site 222891001678 (T/H)XGH motif; other site 222891001679 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 222891001680 DHH family; Region: DHH; pfam01368 222891001681 DHHA1 domain; Region: DHHA1; pfam02272 222891001682 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 222891001683 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 222891001684 SLBB domain; Region: SLBB; pfam10531 222891001685 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 222891001686 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 222891001687 probable selenium-dependent hydroxylase accessory protein YqeC; Region: TIGR03172 222891001688 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 222891001689 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 222891001690 G1 box; other site 222891001691 Switch I region; other site 222891001692 G2 box; other site 222891001693 Switch II region; other site 222891001694 G3 box; other site 222891001695 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 222891001696 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 222891001697 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 222891001698 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 222891001699 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 222891001700 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 222891001701 Surface antigen; Region: Bac_surface_Ag; cl03097 222891001702 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 222891001703 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 222891001704 active site 222891001705 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...; Region: PDZ_metalloprotease; cd00989 222891001706 protein binding site [polypeptide binding]; other site 222891001707 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 222891001708 putative substrate binding region [chemical binding]; other site 222891001709 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14610 222891001710 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 222891001711 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 222891001712 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 222891001713 anchoring element; other site 222891001714 dimer interface [polypeptide binding]; other site 222891001715 ATP binding site [chemical binding]; other site 222891001716 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...; Region: TOPRIM_TopoIIA_GyrB; cd03366 222891001717 active site 222891001718 putative metal-binding site [ion binding]; other site 222891001719 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 222891001720 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...; Region: PRX_BCP; cd03017 222891001721 catalytic triad [active] 222891001722 Sodium:solute symporter family; Region: SSF; cl00456 222891001723 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 222891001724 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 222891001725 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...; Region: GMPK; cd00071 222891001726 catalytic site [active] 222891001727 G-X2-G-X-G-K; other site 222891001728 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 222891001729 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (...; Region: CS_ACL-C_CCL; cl00416 222891001730 Citrate synthase; Region: Citrate_synt; pfam00285 222891001731 oxalacetate binding site [chemical binding]; other site 222891001732 citrylCoA binding site [chemical binding]; other site 222891001733 coenzyme A binding site [chemical binding]; other site 222891001734 catalytic triad [active] 222891001735 Signal peptidase subunit; Region: SPC22; cl04601 222891001736 enolase; Provisional; Region: eno; PRK00077 222891001737 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 222891001738 dimer interface [polypeptide binding]; other site 222891001739 metal binding site [ion binding]; metal-binding site 222891001740 substrate binding pocket [chemical binding]; other site 222891001741 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 222891001742 dimer interface [polypeptide binding]; other site 222891001743 substrate binding site [chemical binding]; other site 222891001744 metal binding sites [ion binding]; metal-binding site 222891001745 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 222891001746 active site 222891001747 catalytic site [active] 222891001748 substrate binding site [chemical binding]; other site 222891001749 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 222891001750 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 222891001751 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 222891001752 active site 222891001753 HIGH motif; other site 222891001754 KMSKS motif; other site 222891001755 Domain of unknown function (DUF205); Region: DUF205; cl00410 222891001756 type IV secretion system component VirD4; Provisional; Region: PRK13897 222891001757 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA...; Region: TraG_VirD4; cd01126 222891001758 Walker A motif; other site 222891001759 ATP binding site [chemical binding]; other site 222891001760 Walker B motif; other site 222891001761 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 222891001762 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...; Region: VirB11-like_ATPase; cd01130 222891001763 Walker A motif; other site 222891001764 hexamer interface [polypeptide binding]; other site 222891001765 ATP binding site [chemical binding]; other site 222891001766 Walker B motif; other site 222891001767 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 222891001768 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 222891001769 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 222891001770 VirB7 interaction site; other site 222891001771 VirB8 protein; Region: VirB8; cl01500 222891001772 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 222891001773 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 222891001774 dimerization interface [polypeptide binding]; other site 222891001775 active site 222891001776 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 222891001777 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 222891001778 alpha subunit interface [polypeptide binding]; other site 222891001779 TPP binding site [chemical binding]; other site 222891001780 heterodimer interface [polypeptide binding]; other site 222891001781 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 222891001782 Cell division protein ZapA; Region: ZapA; cl01146 222891001783 trigger factor; Region: tig; TIGR00115 222891001784 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 222891001785 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 222891001786 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 222891001787 oligomer interface [polypeptide binding]; other site 222891001788 active site residues [active] 222891001789 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 222891001790 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 222891001791 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...; Region: AAA; cd00009 222891001792 Walker A motif; other site 222891001793 ATP binding site [chemical binding]; other site 222891001794 Walker B motif; other site 222891001795 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 222891001796 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 222891001797 Glycyl-tRNA synthetase beta subunit; Region: tRNA_synt_2f; pfam02092 222891001798 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 222891001799 glycyl-tRNA synthetase, tetrameric type, alpha subunit; Region: glyQ; TIGR00388 222891001800 motif 1; other site 222891001801 dimer interface [polypeptide binding]; other site 222891001802 active site 222891001803 motif 2; other site 222891001804 motif 3; other site 222891001805 aspartate aminotransferase; Provisional; Region: PRK08361 222891001806 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 222891001807 pyridoxal 5'-phosphate binding site [chemical binding]; other site 222891001808 homodimer interface [polypeptide binding]; other site 222891001809 catalytic residue [active] 222891001810 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 222891001811 dimer interface [polypeptide binding]; other site 222891001812 ssDNA binding site [nucleotide binding]; other site 222891001813 tetramer (dimer of dimers) interface [polypeptide binding]; other site 222891001814 COQ9; Region: COQ9; cl14819 222891001815 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 222891001816 active site 222891001817 intersubunit interactions; other site 222891001818 catalytic residue [active] 222891001819 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 222891001820 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 222891001821 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 222891001822 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 222891001823 alpha subunit interaction interface [polypeptide binding]; other site 222891001824 Walker A motif; other site 222891001825 ATP binding site [chemical binding]; other site 222891001826 Walker B motif; other site 222891001827 inhibitor binding site; inhibition site 222891001828 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 222891001829 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 222891001830 VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 222891001831 TrbC/VIRB2 family; Region: TrbC; cl01583 222891001832 TrbC/VIRB2 family; Region: TrbC; cl01583 222891001833 GTP-binding protein LepA; Provisional; Region: PRK05433 222891001834 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 222891001835 G1 box; other site 222891001836 putative GEF interaction site [polypeptide binding]; other site 222891001837 GTP/Mg2+ binding site [chemical binding]; other site 222891001838 Switch I region; other site 222891001839 G2 box; other site 222891001840 G3 box; other site 222891001841 Switch II region; other site 222891001842 G4 box; other site 222891001843 G5 box; other site 222891001844 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-...; Region: lepA_II; cd03699 222891001845 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 222891001846 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 222891001847 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 222891001848 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 222891001849 active site 222891001850 nucleotide binding site [chemical binding]; other site 222891001851 HIGH motif; other site 222891001852 KMSKS motif; other site 222891001853 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 222891001854 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of...; Region: ThiF_MoeB_HesA_family; cd00757 222891001855 ATP binding site [chemical binding]; other site 222891001856 substrate interface [chemical binding]; other site 222891001857 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 222891001858 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891001859 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 222891001860 histidyl-tRNA synthetase; Region: hisS; TIGR00442 222891001861 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 222891001862 dimer interface [polypeptide binding]; other site 222891001863 motif 1; other site 222891001864 active site 222891001865 motif 2; other site 222891001866 motif 3; other site 222891001867 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 222891001868 anticodon binding site; other site 222891001869 BolA-like protein; Region: BolA; cl00386 222891001870 metabolite-proton symporter; Region: 2A0106; TIGR00883 222891001871 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 222891001872 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 222891001873 Catalytic site [active] 222891001874 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 222891001875 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 222891001876 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 222891001877 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; cl14056 222891001878 ferrochelatase; Reviewed; Region: hemH; PRK00035 222891001879 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 222891001880 C-terminal domain interface [polypeptide binding]; other site 222891001881 active site 222891001882 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 222891001883 active site 222891001884 N-terminal domain interface [polypeptide binding]; other site 222891001885 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 222891001886 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 222891001887 active site 222891001888 dimer interface [polypeptide binding]; other site 222891001889 Integral membrane protein TerC family; Region: TerC; cl10468 222891001890 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 222891001891 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 222891001892 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl00513 222891001893 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 222891001894 Outer membrane efflux protein; Region: OEP; pfam02321 222891001895 Outer membrane efflux protein; Region: OEP; pfam02321 222891001896 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 222891001897 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 222891001898 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 222891001899 active site 222891001900 pyruvate dehydrogenase E1 component alpha subunit; Reviewed; Region: odpA; CHL00149 222891001901 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 222891001902 tetramer interface [polypeptide binding]; other site 222891001903 TPP-binding site [chemical binding]; other site 222891001904 heterodimer interface [polypeptide binding]; other site 222891001905 phosphorylation loop region [posttranslational modification] 222891001906 UbiA prenyltransferase family; Region: UbiA; cl00337 222891001907 Flavin Reductases; Region: FlaRed; cl00801 222891001908 phosphate transporter ATP-binding protein; Provisional; Region: PRK14236 222891001909 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 222891001910 Walker A/P-loop; other site 222891001911 ATP binding site [chemical binding]; other site 222891001912 Q-loop/lid; other site 222891001913 ABC transporter signature motif; other site 222891001914 Walker B; other site 222891001915 D-loop; other site 222891001916 H-loop/switch region; other site 222891001917 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 222891001918 SmpB-tmRNA interface; other site 222891001919 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]; Region: PurL; COG0046 222891001920 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 222891001921 dimerization interface [polypeptide binding]; other site 222891001922 ATP binding site [chemical binding]; other site 222891001923 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 222891001924 dimerization interface [polypeptide binding]; other site 222891001925 ATP binding site [chemical binding]; other site 222891001926 muropeptide transporter; Reviewed; Region: ampG; PRK11902 222891001927 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; cl11420 222891001928 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 222891001929 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 222891001930 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891001931 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 222891001932 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 222891001933 carboxyltransferase (CT) interaction site; other site 222891001934 biotinylation site [posttranslational modification]; other site 222891001935 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 222891001936 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 222891001937 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 222891001938 NifU-like domain; Region: NifU; cl00484 222891001939 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 222891001940 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...; Region: DnaJ; cd06257 222891001941 HSP70 interaction site [polypeptide binding]; other site 222891001942 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 222891001943 4Fe-4S binding domain; Region: Fer4; cl02805 222891001944 4Fe-4S binding domain; Region: Fer4; cl02805 222891001945 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 222891001946 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 222891001947 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 222891001948 homodimer interface [polypeptide binding]; other site 222891001949 NADP binding site [chemical binding]; other site 222891001950 substrate binding site [chemical binding]; other site 222891001951 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 222891001952 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 222891001953 active site 222891001954 metal binding site [ion binding]; metal-binding site 222891001955 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 222891001956 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), 8-amino-7-...; Region: KBL_like; cd06454 222891001957 substrate-cofactor binding pocket; other site 222891001958 pyridoxal 5'-phosphate binding site [chemical binding]; other site 222891001959 catalytic residue [active] 222891001960 CcmE; Region: CcmE; cl00994 222891001961 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 222891001962 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 222891001963 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 222891001964 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 222891001965 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 222891001966 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 222891001967 FeS/SAM binding site; other site 222891001968 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 222891001969 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 222891001970 23S rRNA interface [nucleotide binding]; other site 222891001971 L3 interface [polypeptide binding]; other site 222891001972 Colicin V production protein; Region: Colicin_V; cl00567 222891001973 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 222891001974 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl09110 222891001975 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 222891001976 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 222891001977 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 222891001978 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 222891001979 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 222891001980 Branched-chain amino acid transport protein; Region: Branch_AA_trans; cl00547 222891001981 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 222891001982 Major Facilitator Superfamily; Region: MFS_1; pfam07690 222891001983 putative substrate translocation pore; other site 222891001984 Mechanosensitive ion channel; Region: MS_channel; pfam00924 222891001985 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II)...; Region: Aldolase_II; cl00214 222891001986 intersubunit interface [polypeptide binding]; other site 222891001987 active site 222891001988 Zn2+ binding site [ion binding]; other site 222891001989 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 222891001990 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 222891001991 inhibitor-cofactor binding pocket; inhibition site 222891001992 pyridoxal 5'-phosphate binding site [chemical binding]; other site 222891001993 catalytic residue [active] 222891001994 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 222891001995 active site 222891001996 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 222891001997 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 222891001998 ATP binding site [chemical binding]; other site 222891001999 active site 222891002000 substrate binding site [chemical binding]; other site 222891002001 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 222891002002 Lumazine binding domain; Region: Lum_binding; pfam00677 222891002003 Lumazine binding domain; Region: Lum_binding; pfam00677 222891002004 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 222891002005 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 222891002006 cytochrome c oxidase assembly protein; Provisional; Region: PTZ00127 222891002007 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 222891002008 Ribonuclease P; Region: Ribonuclease_P; cl00457 222891002009 Ribonuclease P; Region: Ribonuclease_P; cl00457 222891002010 Domain of unknown function DUF37; Region: DUF37; cl00506 222891002011 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 222891002012 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 222891002013 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 222891002014 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 222891002015 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 222891002016 VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 222891002017 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891002018 Walker A/P-loop; other site 222891002019 ATP binding site [chemical binding]; other site 222891002020 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 222891002021 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 222891002022 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 222891002023 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 222891002024 Walker A/P-loop; other site 222891002025 ATP binding site [chemical binding]; other site 222891002026 Q-loop/lid; other site 222891002027 ABC transporter signature motif; other site 222891002028 Walker B; other site 222891002029 D-loop; other site 222891002030 H-loop/switch region; other site 222891002031 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 222891002032 active site 222891002033 nucleophile elbow; other site 222891002034 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 222891002035 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 222891002036 Surface antigen; Region: Surface_Ag_2; cl01155 222891002037 Preprotein translocase SecG subunit; Region: SecG; cl09123 222891002038 CTP synthetase; Validated; Region: pyrG; PRK05380 222891002039 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...; Region: CTGs; cd03113 222891002040 Catalytic site [active] 222891002041 Active site [active] 222891002042 UTP binding site [chemical binding]; other site 222891002043 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 222891002044 active site 222891002045 putative oxyanion hole; other site 222891002046 catalytic triad [active] 222891002047 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 rRNA-...; Region: NusB_Sun; cl00223 222891002048 putative RNA binding site [nucleotide binding]; other site 222891002049 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 222891002050 active site 222891002051 dimer interface [polypeptide binding]; other site 222891002052 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 222891002053 RNA binding site [nucleotide binding]; other site 222891002054 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 222891002055 putative catalytic residue [active] 222891002056 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 222891002057 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 222891002058 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 222891002059 GMP synthase; Reviewed; Region: guaA; PRK00074 222891002060 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 222891002061 conserved cys residue [active] 222891002062 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 222891002063 ATP Binding subdomain [chemical binding]; other site 222891002064 Ligand Binding sites [chemical binding]; other site 222891002065 Dimerization subdomain; other site 222891002066 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 222891002067 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 222891002068 Walker A motif; other site 222891002069 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 222891002070 ligand binding site [chemical binding]; other site 222891002071 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 222891002072 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 222891002073 Sulfatase; Region: Sulfatase; cl10460 222891002074 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 222891002075 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 222891002076 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 222891002077 active site 222891002078 HIGH motif; other site 222891002079 KMSKS motif; other site 222891002080 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 222891002081 tRNA binding surface [nucleotide binding]; other site 222891002082 anticodon binding site; other site 222891002083 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 222891002084 catalytic residues [active] 222891002085 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 222891002086 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 222891002087 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 222891002088 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 222891002089 recombination protein RecR; Reviewed; Region: recR; PRK00076 222891002090 RecR protein; Region: RecR; pfam02132 222891002091 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 222891002092 putative active site [active] 222891002093 putative metal-binding site [ion binding]; other site 222891002094 tetramer interface [polypeptide binding]; other site 222891002095 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 222891002096 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 222891002097 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 222891002098 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 222891002099 GTP-binding protein YchF; Reviewed; Region: PRK09601 222891002100 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 222891002101 G1 box; other site 222891002102 GTP/Mg2+ binding site [chemical binding]; other site 222891002103 Switch I region; other site 222891002104 G2 box; other site 222891002105 Switch II region; other site 222891002106 G3 box; other site 222891002107 G4 box; other site 222891002108 G5 box; other site 222891002109 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 222891002110 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 222891002111 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 222891002112 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 222891002113 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 222891002114 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 222891002115 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 222891002116 lipoprotein signal peptidase; Provisional; Region: PRK14787 222891002117 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 222891002118 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 222891002119 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 222891002120 Zn binding site [ion binding]; other site 222891002121 ribonuclease III; Reviewed; Region: rnc; PRK00102 222891002122 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 post-...; Region: RIBOc; cd00593 222891002123 dimerization interface [polypeptide binding]; other site 222891002124 active site 222891002125 metal binding site [ion binding]; metal-binding site 222891002126 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...; Region: DSRM; cd00048 222891002127 dsRNA binding site [nucleotide binding]; other site 222891002128 Domain of unknown function DUF143; Region: DUF143; cl00519 222891002129 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 222891002130 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891002131 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891002132 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 222891002133 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 222891002134 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 222891002135 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891002136 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 222891002137 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 222891002138 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 222891002139 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 222891002140 dimer interface [polypeptide binding]; other site 222891002141 active site 222891002142 catalytic residue [active] 222891002143 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria...; Region: Cytochrome_b_N; cl00859 222891002144 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 222891002145 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 222891002146 motif II; other site 222891002147 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 222891002148 VacJ like lipoprotein; Region: VacJ; cl01073 222891002149 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 222891002150 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 222891002151 Protein of unknown function (DUF2610); Region: DUF2610; pfam11020 222891002152 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 222891002153 Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner; Region: G1PDH; cd08175 222891002154 active site 222891002155 metal binding site [ion binding]; metal-binding site 222891002156 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 222891002157 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 222891002158 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 222891002159 catalytic residue [active] 222891002160 putative FPP diphosphate binding site; other site 222891002161 putative FPP binding hydrophobic cleft; other site 222891002162 dimer interface [polypeptide binding]; other site 222891002163 putative IPP diphosphate binding site; other site 222891002164 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 222891002165 hinge region; other site 222891002166 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...; Region: AAK_UMPK-PyrH-Ec; cd04254 222891002167 putative nucleotide binding site [chemical binding]; other site 222891002168 uridine monophosphate binding site [chemical binding]; other site 222891002169 homohexameric interface [polypeptide binding]; other site 222891002170 elongation factor Ts; Provisional; Region: tsf; PRK09377 222891002171 Elongation factor TS; Region: EF_TS; pfam00889 222891002172 Elongation factor TS; Region: EF_TS; pfam00889 222891002173 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 222891002174 rRNA interaction site [nucleotide binding]; other site 222891002175 S8 interaction site; other site 222891002176 putative laminin-1 binding site; other site 222891002177 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 222891002178 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 222891002179 S-adenosylmethionine binding site [chemical binding]; other site 222891002180 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)...; Region: AdoMet_MTases; cl12011 222891002181 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 222891002182 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 222891002183 E3 interaction surface; other site 222891002184 lipoyl attachment site [posttranslational modification]; other site 222891002185 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 222891002186 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 222891002187 substrate binding site [chemical binding]; other site 222891002188 dimer interface [polypeptide binding]; other site 222891002189 ATP binding site [chemical binding]; other site 222891002190 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 222891002191 active site 222891002192 putative DNA-binding cleft [nucleotide binding]; other site 222891002193 dimer interface [polypeptide binding]; other site 222891002194 malate dehydrogenase; Reviewed; Region: PRK06223 222891002195 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 222891002196 NAD(P) binding site [chemical binding]; other site 222891002197 dimer interface [polypeptide binding]; other site 222891002198 tetramer (dimer of dimers) interface [polypeptide binding]; other site 222891002199 substrate binding site [chemical binding]; other site 222891002200 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 222891002201 trimer interface [polypeptide binding]; other site 222891002202 active site 222891002203 DNA gyrase subunit A; Validated; Region: PRK05560 222891002204 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...; Region: TOP4c; cd00187 222891002205 CAP-like domain; other site 222891002206 Active site [active] 222891002207 primary dimer interface [polypeptide binding]; other site 222891002208 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 222891002209 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 222891002210 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 222891002211 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 222891002212 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 222891002213 GTPase Era; Reviewed; Region: era; PRK00089 222891002214 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit...; Region: Era; cd04163 222891002215 G1 box; other site 222891002216 GTP/Mg2+ binding site [chemical binding]; other site 222891002217 Switch I region; other site 222891002218 G2 box; other site 222891002219 Switch II region; other site 222891002220 G3 box; other site 222891002221 G4 box; other site 222891002222 G5 box; other site 222891002223 Acyl transferase domain; Region: Acyl_transf_1; cl08282 222891002224 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 222891002225 DNA primase; Validated; Region: dnaG; PRK05667 222891002226 CHC2 zinc finger; Region: zf-CHC2; cl02597 222891002227 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 222891002228 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 222891002229 active site 222891002230 metal binding site [ion binding]; metal-binding site 222891002231 interdomain interaction site; other site 222891002232 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 222891002233 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 222891002234 trimer interface [polypeptide binding]; other site 222891002235 active site 222891002236 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 222891002237 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 222891002238 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 222891002239 NAD(P) binding site [chemical binding]; other site 222891002240 active site 222891002241 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 222891002242 Terminase-like family; Region: Terminase_6; pfam03237 222891002243 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 222891002244 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...; Region: URO-D; cd00717 222891002245 substrate binding site [chemical binding]; other site 222891002246 active site 222891002247 Quinolinate synthetase A protein; Region: NadA; cl00420 222891002248 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 222891002249 active site 222891002250 (T/H)XGH motif; other site