-- dump date 20111121_013409 -- class Genbank::misc_feature -- table misc_feature_note -- id note 347256000001 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 347256000002 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 347256000003 Ribonuclease P; Region: Ribonuclease_P; cl00457 347256000004 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 347256000005 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 347256000006 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 347256000007 Walker A motif; other site 347256000008 ATP binding site [chemical binding]; other site 347256000009 Walker B motif; other site 347256000010 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 347256000011 DnaA box-binding interface [nucleotide binding]; other site 347256000012 DNA polymerase III subunit beta; Validated; Region: PRK05643 347256000013 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 347256000014 putative DNA binding surface [nucleotide binding]; other site 347256000015 dimer interface [polypeptide binding]; other site 347256000016 beta-clamp/clamp loader binding surface; other site 347256000017 beta-clamp/translesion DNA polymerase binding surface; other site 347256000018 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 347256000019 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 347256000020 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 347256000021 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 347256000022 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 347256000023 active site 347256000024 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 347256000025 Microcin C7 self-immunity protein determines resistance to exogenous microcin C7; Region: Peptidase_S66_mccF_like; cd07062 347256000026 putative dimer interface [polypeptide binding]; other site 347256000027 catalytic triad [active] 347256000028 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]; Region: SSL2; COG1061 347256000029 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 347256000030 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 347256000031 MatE; Region: MatE; pfam01554 347256000032 Got1/Sft2-like family; Region: Got1; cl02130 347256000033 Clp protease ATP binding subunit; Region: clpC; CHL00095 347256000034 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 347256000035 Walker A motif; other site 347256000036 ATP binding site [chemical binding]; other site 347256000037 Walker B motif; other site 347256000038 arginine finger; other site 347256000039 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 347256000040 Walker A motif; other site 347256000041 ATP binding site [chemical binding]; other site 347256000042 Walker B motif; other site 347256000043 arginine finger; other site 347256000044 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 347256000045 ATP synthase A chain; Region: ATP-synt_A; cl00413 347256000046 ATP synthase subunit C; Region: ATP-synt_C; cl00466 347256000047 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 347256000048 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 347256000049 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 347256000050 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 347256000051 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 347256000052 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 347256000053 beta subunit interaction interface [polypeptide binding]; other site 347256000054 Walker A motif; other site 347256000055 ATP binding site [chemical binding]; other site 347256000056 Walker B motif; other site 347256000057 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 347256000058 ATP synthase; Region: ATP-synt; cl00365 347256000059 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 347256000060 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 347256000061 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 347256000062 alpha subunit interaction interface [polypeptide binding]; other site 347256000063 Walker A motif; other site 347256000064 ATP binding site [chemical binding]; other site 347256000065 Walker B motif; other site 347256000066 inhibitor binding site; inhibition site 347256000067 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 347256000068 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 347256000069 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 347256000070 putative catalytic site [active] 347256000071 putative phosphate binding site [ion binding]; other site 347256000072 putative metal binding site [ion binding]; other site 347256000073 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 347256000074 putative metal binding site [ion binding]; other site 347256000075 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 347256000076 DNA polymerase III PolC; Validated; Region: polC; PRK00448 347256000077 Cation transport protein; Region: TrkH; cl10514 347256000078 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 347256000079 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 347256000080 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 347256000081 Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH...; Region: Peptidase_C1B; cd00585 347256000082 trimer interface [polypeptide binding]; other site 347256000083 active site 347256000084 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 347256000085 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 347256000086 cofactor binding site; other site 347256000087 DNA binding site [nucleotide binding] 347256000088 substrate interaction site [chemical binding]; other site 347256000089 Eco47II restriction endonuclease; Region: RE_Eco47II; pfam09553 347256000090 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 347256000091 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 347256000092 putative acyl-acceptor binding pocket; other site 347256000093 ScpA/B protein; Region: ScpA_ScpB; cl00598 347256000094 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 347256000095 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 347256000096 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 347256000097 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 347256000098 active site 347256000099 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 347256000100 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 347256000101 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 347256000102 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 347256000103 GatB domain; Region: GatB_Yqey; cl11497 347256000104 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 347256000105 hypothetical protein; Provisional; Region: PRK09609 347256000106 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 347256000107 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347256000108 active site 347256000109 HIGH motif; other site 347256000110 nucleotide binding site [chemical binding]; other site 347256000111 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 347256000112 active site 347256000113 KMSKS motif; other site 347256000114 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 347256000115 tRNA binding surface [nucleotide binding]; other site 347256000116 anticodon binding site; other site 347256000117 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 347256000118 substrate binding site [chemical binding]; other site 347256000119 hinge regions; other site 347256000120 ADP binding site [chemical binding]; other site 347256000121 catalytic site [active] 347256000122 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 347256000123 elongation factor Tu; Reviewed; Region: PRK00049 347256000124 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 347256000125 G1 box; other site 347256000126 GEF interaction site [polypeptide binding]; other site 347256000127 GTP/Mg2+ binding site [chemical binding]; other site 347256000128 Switch I region; other site 347256000129 G2 box; other site 347256000130 G3 box; other site 347256000131 Switch II region; other site 347256000132 G4 box; other site 347256000133 G5 box; other site 347256000134 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 347256000135 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 347256000136 Antibiotic Binding Site [chemical binding]; other site 347256000137 LMP repeated region; Region: LMP; pfam04778 347256000138 LMP repeated region; Region: LMP; pfam04778 347256000139 LMP repeated region; Region: LMP; pfam04778 347256000140 LMP repeated region; Region: LMP; pfam04778 347256000141 LMP repeated region; Region: LMP; pfam04778 347256000142 Thymidine kinase; Region: TK; cl00631 347256000143 GTP-binding protein YchF; Reviewed; Region: PRK09601 347256000144 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 347256000145 G1 box; other site 347256000146 GTP/Mg2+ binding site [chemical binding]; other site 347256000147 Switch I region; other site 347256000148 G2 box; other site 347256000149 Switch II region; other site 347256000150 G3 box; other site 347256000151 G4 box; other site 347256000152 G5 box; other site 347256000153 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 347256000154 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 347256000155 ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The...; Region: ABC_ATPase; cd00267 347256000156 Walker A/P-loop; other site 347256000157 ATP binding site [chemical binding]; other site 347256000158 Q-loop/lid; other site 347256000159 ABC transporter signature motif; other site 347256000160 Walker B; other site 347256000161 D-loop; other site 347256000162 H-loop/switch region; other site 347256000163 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 347256000164 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 347256000165 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 347256000166 active site 347256000167 HIGH motif; other site 347256000168 KMSK motif region; other site 347256000169 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 347256000170 tRNA binding surface [nucleotide binding]; other site 347256000171 anticodon binding site; other site 347256000172 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347256000173 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 347256000174 active site 347256000175 HIGH motif; other site 347256000176 nucleotide binding site [chemical binding]; other site 347256000177 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347256000178 active site 347256000179 KMSKS motif; other site 347256000180 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 347256000181 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 347256000182 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 347256000183 carbamate kinase; Reviewed; Region: PRK12686 347256000184 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 347256000185 putative substrate binding site [chemical binding]; other site 347256000186 nucleotide binding site [chemical binding]; other site 347256000187 nucleotide binding site [chemical binding]; other site 347256000188 homodimer interface [polypeptide binding]; other site 347256000189 ornithine carbamoyltransferase; Validated; Region: PRK02102 347256000190 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 347256000191 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 347256000192 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 347256000193 Staphylococcal nuclease homologues; Region: SNc; smart00318 347256000194 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 347256000195 Catalytic site; other site 347256000196 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose...; Region: TBP_aldolase_IIB; cd00947 347256000197 intersubunit interface [polypeptide binding]; other site 347256000198 active site 347256000199 zinc binding site [ion binding]; other site 347256000200 Na+ binding site [ion binding]; other site 347256000201 Arginine deiminase [Amino acid transport and metabolism]; Region: ArcA; COG2235 347256000202 Amidinotransferase; Region: Amidinotransf; cl12043 347256000203 Dimeric dUTPase [Carbohydrate transport and metabolism]; Region: COG4508 347256000204 dUTPase; Region: dUTPase_2; pfam08761 347256000205 Mycoplasma MG185/MG260 protein; Region: Lipoprotein_X; pfam03305 347256000206 Putative mycoplasma lipoprotein, C-terminal region; Region: Lipoprotein_10; pfam03202 347256000207 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 347256000208 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256000209 Walker A/P-loop; other site 347256000210 ATP binding site [chemical binding]; other site 347256000211 Q-loop/lid; other site 347256000212 DNA polymerase III PolC; Validated; Region: polC; PRK00448 347256000213 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256000214 ABC transporter signature motif; other site 347256000215 Walker B; other site 347256000216 D-loop; other site 347256000217 H-loop/switch region; other site 347256000218 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 347256000219 dimer interface [polypeptide binding]; other site 347256000220 conserved gate region; other site 347256000221 putative PBP binding loops; other site 347256000222 ABC-ATPase subunit interface; other site 347256000223 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 347256000224 dimer interface [polypeptide binding]; other site 347256000225 conserved gate region; other site 347256000226 putative PBP binding loops; other site 347256000227 ABC-ATPase subunit interface; other site 347256000228 Mycoplasma MG185/MG260 protein; Region: Lipoprotein_X; pfam03305 347256000229 Putative mycoplasma lipoprotein, C-terminal region; Region: Lipoprotein_10; pfam03202 347256000230 Mycoplasma MG185/MG260 protein; Region: Lipoprotein_X; pfam03305 347256000231 Putative mycoplasma lipoprotein, C-terminal region; Region: Lipoprotein_10; pfam03202 347256000232 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 347256000233 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 347256000234 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 347256000235 RNA binding surface [nucleotide binding]; other site 347256000236 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 347256000237 metal binding site [ion binding]; metal-binding site 347256000238 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 347256000239 dsRNA binding site [nucleotide binding]; other site 347256000240 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 347256000241 dimerization interface [polypeptide binding]; other site 347256000242 putative catalytic residue [active] 347256000243 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 347256000244 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 347256000245 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 347256000246 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 347256000247 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 347256000248 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 347256000249 23S rRNA interface [nucleotide binding]; other site 347256000250 L7/L12 interface [polypeptide binding]; other site 347256000251 putative thiostrepton binding site; other site 347256000252 L25 interface [polypeptide binding]; other site 347256000253 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 347256000254 mRNA/rRNA interface [nucleotide binding]; other site 347256000255 enolase; Provisional; Region: eno; PRK00077 347256000256 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 347256000257 dimer interface [polypeptide binding]; other site 347256000258 metal binding site [ion binding]; metal-binding site 347256000259 substrate binding pocket [chemical binding]; other site 347256000260 trigger factor; Region: tig; TIGR00115 347256000261 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 347256000262 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 347256000263 preprotein translocase subunit SecA; Reviewed; Region: secA; PRK12903 347256000264 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 347256000265 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 347256000266 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_human_like; cd03428 347256000267 active site 347256000268 Ap4A binding cleft/pocket [chemical binding]; other site 347256000269 P4 phosphate binding site; other site 347256000270 nudix motif; other site 347256000271 putative P2/P3 phosphate binding site [ion binding]; other site 347256000272 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07133 347256000273 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 347256000274 Walker A motif; other site 347256000275 ATP binding site [chemical binding]; other site 347256000276 Walker B motif; other site 347256000277 arginine finger; other site 347256000278 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 347256000279 recombination protein RecR; Reviewed; Region: recR; PRK00076 347256000280 RecR protein; Region: RecR; pfam02132 347256000281 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 347256000282 active site 347256000283 metal binding site [ion binding]; metal-binding site 347256000284 thymidylate kinase; Validated; Region: tmk; PRK00698 347256000285 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 347256000286 TMP-binding site; other site 347256000287 ATP-binding site [chemical binding]; other site 347256000288 DNA polymerase III subunit delta'; Validated; Region: PRK07132 347256000289 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 347256000290 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 347256000291 Protein of unknown function DUF45; Region: DUF45; cl00636 347256000292 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 347256000293 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 347256000294 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 347256000295 active site 347256000296 dimer interface [polypeptide binding]; other site 347256000297 motif 1; other site 347256000298 motif 2; other site 347256000299 motif 3; other site 347256000300 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 347256000301 anticodon binding site; other site 347256000302 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 347256000303 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 347256000304 active site 347256000305 HIGH motif; other site 347256000306 dimer interface [polypeptide binding]; other site 347256000307 KMSKS motif; other site 347256000308 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIB_glc; cl00164 347256000309 active site turn [active] 347256000310 phosphorylation site [posttranslational modification] 347256000311 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 347256000312 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: MDN1; COG5271 347256000313 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 347256000314 active site 347256000315 catalytic residues [active] 347256000316 metal binding site [ion binding]; metal-binding site 347256000317 Domain of unknown function DUF21; Region: DUF21; pfam01595 347256000318 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 347256000319 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 347256000320 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 347256000321 dimer interface [polypeptide binding]; other site 347256000322 ssDNA binding site [nucleotide binding]; other site 347256000323 tetramer (dimer of dimers) interface [polypeptide binding]; other site 347256000324 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 347256000325 recombination factor protein RarA; Reviewed; Region: PRK13342 347256000326 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 347256000327 Walker A motif; other site 347256000328 ATP binding site [chemical binding]; other site 347256000329 Walker B motif; other site 347256000330 arginine finger; other site 347256000331 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 347256000332 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 347256000333 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 347256000334 dimer interface [polypeptide binding]; other site 347256000335 motif 1; other site 347256000336 active site 347256000337 motif 2; other site 347256000338 motif 3; other site 347256000339 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 347256000340 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 347256000341 putative tRNA-binding site [nucleotide binding]; other site 347256000342 B3/4 domain; Region: B3_4; cl11458 347256000343 tRNA synthetase B5 domain; Region: B5; cl08394 347256000344 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 347256000345 motif 1; other site 347256000346 dimer interface [polypeptide binding]; other site 347256000347 active site 347256000348 motif 3; other site 347256000349 recombinase A; Provisional; Region: recA; PRK09354 347256000350 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 347256000351 hexamer interface [polypeptide binding]; other site 347256000352 Walker A motif; other site 347256000353 ATP binding site [chemical binding]; other site 347256000354 Walker B motif; other site 347256000355 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 347256000356 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 347256000357 putative active site [active] 347256000358 metal binding site [ion binding]; metal-binding site 347256000359 homodimer binding site [polypeptide binding]; other site 347256000360 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 347256000361 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 347256000362 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 347256000363 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 347256000364 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 347256000365 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 347256000366 catalytic residue [active] 347256000367 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 347256000368 trimerization site [polypeptide binding]; other site 347256000369 active site 347256000370 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 347256000371 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 347256000372 active site 347256000373 DNA binding site [nucleotide binding] 347256000374 putative nicotinate-nucleotide adenylyltransferase; Validated; Region: nadD; PRK07152 347256000375 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 347256000376 active site 347256000377 (T/H)XGH motif; other site 347256000378 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 347256000379 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 347256000380 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 347256000381 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 347256000382 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 347256000383 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 347256000384 23S rRNA binding site [nucleotide binding]; other site 347256000385 L21 binding site [polypeptide binding]; other site 347256000386 L13 binding site [polypeptide binding]; other site 347256000387 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 347256000388 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 347256000389 Ligand Binding Site [chemical binding]; other site 347256000390 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 347256000391 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 347256000392 motif 1; other site 347256000393 active site 347256000394 motif 2; other site 347256000395 motif 3; other site 347256000396 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 347256000397 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 347256000398 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 347256000399 domain; Region: GreA_GreB_N; pfam03449 347256000400 C-term; Region: GreA_GreB; pfam01272 347256000401 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 347256000402 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 347256000403 S-adenosylmethionine binding site [chemical binding]; other site 347256000404 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 347256000405 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 347256000406 active site 347256000407 HIGH motif; other site 347256000408 KMSKS motif; other site 347256000409 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 347256000410 tRNA binding surface [nucleotide binding]; other site 347256000411 anticodon binding site; other site 347256000412 GTPase CgtA; Reviewed; Region: obgE; PRK12297 347256000413 GTP1/OBG; Region: GTP1_OBG; pfam01018 347256000414 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 347256000415 G1 box; other site 347256000416 GTP/Mg2+ binding site [chemical binding]; other site 347256000417 Switch I region; other site 347256000418 G2 box; other site 347256000419 G3 box; other site 347256000420 Switch II region; other site 347256000421 G4 box; other site 347256000422 G5 box; other site 347256000423 Domain of unknown function (DUF1967); Region: DUF1967; cl07779 347256000424 PQ loop repeat; Region: PQ-loop; cl12056 347256000425 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 347256000426 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 347256000427 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 347256000428 RNA binding surface [nucleotide binding]; other site 347256000429 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 347256000430 active site 347256000431 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 347256000432 S17 interaction site [polypeptide binding]; other site 347256000433 S8 interaction site; other site 347256000434 16S rRNA interaction site [nucleotide binding]; other site 347256000435 streptomycin interaction site [chemical binding]; other site 347256000436 23S rRNA interaction site [nucleotide binding]; other site 347256000437 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 347256000438 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 347256000439 elongation factor G; Reviewed; Region: PRK12739 347256000440 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 347256000441 G1 box; other site 347256000442 putative GEF interaction site [polypeptide binding]; other site 347256000443 GTP/Mg2+ binding site [chemical binding]; other site 347256000444 Switch I region; other site 347256000445 G2 box; other site 347256000446 G3 box; other site 347256000447 Switch II region; other site 347256000448 G4 box; other site 347256000449 G5 box; other site 347256000450 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 347256000451 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 347256000452 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 347256000453 hypothetical protein; Provisional; Region: PRK13663 347256000454 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4868 347256000455 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 347256000456 active site 347256000457 Zn binding site [ion binding]; other site 347256000458 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 347256000459 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 347256000460 dimer interface [polypeptide binding]; other site 347256000461 conserved gate region; other site 347256000462 ABC-ATPase subunit interface; other site 347256000463 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 347256000464 dimer interface [polypeptide binding]; other site 347256000465 conserved gate region; other site 347256000466 putative PBP binding loops; other site 347256000467 ABC-ATPase subunit interface; other site 347256000468 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 347256000469 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 347256000470 Walker A/P-loop; other site 347256000471 ATP binding site [chemical binding]; other site 347256000472 Q-loop/lid; other site 347256000473 ABC transporter signature motif; other site 347256000474 Walker B; other site 347256000475 D-loop; other site 347256000476 H-loop/switch region; other site 347256000477 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 347256000478 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 347256000479 Walker A/P-loop; other site 347256000480 ATP binding site [chemical binding]; other site 347256000481 Q-loop/lid; other site 347256000482 Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]; Region: GyrA; COG0188 347256000483 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 347256000484 ABC transporter signature motif; other site 347256000485 Walker B; other site 347256000486 D-loop; other site 347256000487 H-loop/switch region; other site 347256000488 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 347256000489 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 347256000490 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 347256000491 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 347256000492 active site 347256000493 peptide chain release factor 1; Validated; Region: prfA; PRK00591 347256000494 RF-1 domain; Region: RF-1; cl02875 347256000495 RF-1 domain; Region: RF-1; cl02875 347256000496 protein-(glutamine-N5) methyltransferase, release factor-specific; Region: RF_mod_PrmC; TIGR03534 347256000497 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 347256000498 S-adenosylmethionine binding site [chemical binding]; other site 347256000499 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 347256000500 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 347256000501 HSP70 interaction site [polypeptide binding]; other site 347256000502 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 347256000503 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 347256000504 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 347256000505 DNA topoisomerase I; Validated; Region: PRK05582 347256000506 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 347256000507 active site 347256000508 interdomain interaction site; other site 347256000509 putative metal-binding site [ion binding]; other site 347256000510 nucleotide binding site [chemical binding]; other site 347256000511 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 347256000512 domain I; other site 347256000513 DNA binding groove [nucleotide binding] 347256000514 phosphate binding site [ion binding]; other site 347256000515 domain II; other site 347256000516 domain III; other site 347256000517 nucleotide binding site [chemical binding]; other site 347256000518 catalytic site [active] 347256000519 domain IV; other site 347256000520 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 347256000521 LMP repeated region; Region: LMP; pfam04778 347256000522 LMP repeated region; Region: LMP; pfam04778 347256000523 LMP repeated region; Region: LMP; pfam04778 347256000524 LMP repeated region; Region: LMP; pfam04778 347256000525 LMP repeated region; Region: LMP; pfam04778 347256000526 cytidylate kinase; Provisional; Region: cmk; PRK00023 347256000527 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 347256000528 CMP-binding site; other site 347256000529 The sites determining sugar specificity; other site 347256000530 GTP-binding protein Der; Reviewed; Region: PRK00093 347256000531 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that...; Region: EngA1; cd01894 347256000532 G1 box; other site 347256000533 GTP/Mg2+ binding site [chemical binding]; other site 347256000534 Switch I region; other site 347256000535 G2 box; other site 347256000536 Switch II region; other site 347256000537 G3 box; other site 347256000538 G4 box; other site 347256000539 G5 box; other site 347256000540 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 347256000541 G1 box; other site 347256000542 GTP/Mg2+ binding site [chemical binding]; other site 347256000543 Switch I region; other site 347256000544 G2 box; other site 347256000545 G3 box; other site 347256000546 Switch II region; other site 347256000547 G4 box; other site 347256000548 G5 box; other site 347256000549 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 347256000550 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 347256000551 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 347256000552 Recombination protein U; Region: RecU; cl01314 347256000553 Domain of unknown function(DUF2779); Region: DUF2779; pfam11074 347256000554 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 347256000555 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 347256000556 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 347256000557 dimer interface [polypeptide binding]; other site 347256000558 conserved gate region; other site 347256000559 putative PBP binding loops; other site 347256000560 ABC-ATPase subunit interface; other site 347256000561 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 347256000562 Iron-containing alcohol dehydrogenase; Region: Fe-ADH; pfam00465 347256000563 active site 347256000564 NAD binding site [chemical binding]; other site 347256000565 metal binding site [ion binding]; metal-binding site 347256000566 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 347256000567 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin...; Region: TPP_enzymes; cl01629 347256000568 TPP-binding site [chemical binding]; other site 347256000569 elongation factor P; Validated; Region: PRK00529 347256000570 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 347256000571 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 347256000572 RNA binding site [nucleotide binding]; other site 347256000573 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 347256000574 RNA binding site [nucleotide binding]; other site 347256000575 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 347256000576 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 347256000577 homodimer interface [polypeptide binding]; other site 347256000578 NAD binding pocket [chemical binding]; other site 347256000579 ATP binding pocket [chemical binding]; other site 347256000580 Mg binding site [ion binding]; other site 347256000581 active-site loop [active] 347256000582 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 347256000583 dimer interface [polypeptide binding]; other site 347256000584 substrate binding site [chemical binding]; other site 347256000585 metal binding sites [ion binding]; metal-binding site 347256000586 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 347256000587 RuvA N terminal domain; Region: RuvA_N; pfam01330 347256000588 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 347256000589 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 347256000590 Walker A motif; other site 347256000591 ATP binding site [chemical binding]; other site 347256000592 Walker B motif; other site 347256000593 arginine finger; other site 347256000594 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 347256000595 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 347256000596 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 347256000597 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 347256000598 dimer interface [polypeptide binding]; other site 347256000599 active site 347256000600 motif 2; other site 347256000601 motif 3; other site 347256000602 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 347256000603 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 347256000604 dimer interface [polypeptide binding]; other site 347256000605 anticodon binding site; other site 347256000606 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 347256000607 homodimer interface [polypeptide binding]; other site 347256000608 motif 1; other site 347256000609 active site 347256000610 motif 2; other site 347256000611 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 347256000612 active site 347256000613 motif 3; other site 347256000614 ribonuclease R; Region: RNase_R; TIGR02063 347256000615 RNB domain; Region: RNB; pfam00773 347256000616 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 347256000617 SmpB-tmRNA interface; other site 347256000618 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 347256000619 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 347256000620 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 347256000621 NAD(P) binding pocket [chemical binding]; other site 347256000622 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 347256000623 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7...; Region: dNK; cd01673 347256000624 Substrate-binding site [chemical binding]; other site 347256000625 Substrate specificity [chemical binding]; other site 347256000626 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 347256000627 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13632 347256000628 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 347256000629 Walker A/P-loop; other site 347256000630 ATP binding site [chemical binding]; other site 347256000631 Q-loop/lid; other site 347256000632 ABC transporter signature motif; other site 347256000633 Walker B; other site 347256000634 D-loop; other site 347256000635 H-loop/switch region; other site 347256000636 cobalt transporter ATP-binding subunit; Provisional; Region: PRK13651 347256000637 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256000638 Walker A/P-loop; other site 347256000639 ATP binding site [chemical binding]; other site 347256000640 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This...; Region: ABC_cobalt_CbiO_domain1; cd03225 347256000641 Q-loop/lid; other site 347256000642 ABC transporter signature motif; other site 347256000643 Walker B; other site 347256000644 D-loop; other site 347256000645 H-loop/switch region; other site 347256000646 Cobalt transport protein; Region: CbiQ; cl00463 347256000647 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 347256000648 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 347256000649 nucleotide binding pocket [chemical binding]; other site 347256000650 K-X-D-G motif; other site 347256000651 catalytic site [active] 347256000652 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 347256000653 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 347256000654 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 347256000655 Dimer interface [polypeptide binding]; other site 347256000656 BRCT sequence motif; other site 347256000657 Competence protein; Region: Competence; cl00471 347256000658 Domain of unknown function DUF28; Region: DUF28; cl00361 347256000659 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 347256000660 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]; Region: GlgB; COG0296 347256000661 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 347256000662 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 347256000663 Interphotoreceptor retinoid-binding protein; serine protease family S41; Region: Peptidase_S41_IRBP; cd07563 347256000664 active site triad [active] 347256000665 DNA primase; Provisional; Region: PRK04031 347256000666 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 347256000667 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 347256000668 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 347256000669 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 347256000670 active site 347256000671 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 347256000672 endonuclease IV; Provisional; Region: PRK01060 347256000673 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-...; Region: AP2Ec; cd00019 347256000674 AP (apurinic/apyrimidinic) site pocket; other site 347256000675 DNA interaction; other site 347256000676 Metal-binding active site; metal-binding site 347256000677 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 347256000678 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 347256000679 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 347256000680 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 347256000681 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 347256000682 DNA primase, catalytic core; Region: dnaG; TIGR01391 347256000683 CHC2 zinc finger; Region: zf-CHC2; cl02597 347256000684 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 347256000685 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 347256000686 active site 347256000687 metal binding site [ion binding]; metal-binding site 347256000688 interdomain interaction site; other site 347256000689 glycyl-tRNA synthetase; Provisional; Region: PRK04173 347256000690 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 347256000691 motif 1; other site 347256000692 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the...; Region: GlyRS-like_core; cd00774 347256000693 active site 347256000694 motif 2; other site 347256000695 GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: GlyRS_anticodon; cd00858 347256000696 anticodon binding site; other site 347256000697 signal recognition particle protein; Provisional; Region: PRK10867 347256000698 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 347256000699 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 347256000700 P loop; other site 347256000701 GTP binding site [chemical binding]; other site 347256000702 Signal peptide binding domain; Region: SRP_SPB; pfam02978 347256000703 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 347256000704 YlqF. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases...; Region: YlqF; cd01856 347256000705 GTP/Mg2+ binding site [chemical binding]; other site 347256000706 G4 box; other site 347256000707 G5 box; other site 347256000708 G1 box; other site 347256000709 Switch I region; other site 347256000710 G2 box; other site 347256000711 G3 box; other site 347256000712 Switch II region; other site 347256000713 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 347256000714 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 347256000715 16S/18S rRNA binding site [nucleotide binding]; other site 347256000716 S13e-L30e interaction site [polypeptide binding]; other site 347256000717 25S rRNA binding site [nucleotide binding]; other site 347256000718 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 347256000719 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 347256000720 23S rRNA interface [nucleotide binding]; other site 347256000721 L3 interface [polypeptide binding]; other site 347256000722 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 347256000723 cell division protein FtsZ; Validated; Region: PRK09330 347256000724 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 347256000725 nucleotide binding site [chemical binding]; other site 347256000726 SulA interaction site; other site 347256000727 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 347256000728 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 347256000729 cell division protein MraZ; Reviewed; Region: PRK00326 347256000730 MraZ protein; Region: MraZ; pfam02381 347256000731 MraZ protein; Region: MraZ; pfam02381 347256000732 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 347256000733 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 347256000734 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 347256000735 Walker A/P-loop; other site 347256000736 ATP binding site [chemical binding]; other site 347256000737 Q-loop/lid; other site 347256000738 ABC transporter signature motif; other site 347256000739 Walker B; other site 347256000740 D-loop; other site 347256000741 H-loop/switch region; other site 347256000742 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 347256000743 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 347256000744 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256000745 Walker A/P-loop; other site 347256000746 ATP binding site [chemical binding]; other site 347256000747 Q-loop/lid; other site 347256000748 ABC transporter signature motif; other site 347256000749 Walker B; other site 347256000750 D-loop; other site 347256000751 H-loop/switch region; other site 347256000752 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK02193 347256000753 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 347256000754 active site 347256000755 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 347256000756 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 347256000757 active site 347256000758 motif I; other site 347256000759 motif II; other site 347256000760 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; cl11391 347256000761 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 347256000762 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 347256000763 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 347256000764 hypothetical protein; Provisional; Region: PRK07143 347256000765 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347256000766 active site 347256000767 nucleotide binding site [chemical binding]; other site 347256000768 HIGH motif; other site 347256000769 KMSKS motif; other site 347256000770 Riboflavin kinase; Region: Flavokinase; pfam01687 347256000771 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 347256000772 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 347256000773 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 347256000774 putative active site [active] 347256000775 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 347256000776 substrate binding site [chemical binding]; other site 347256000777 dimer interface [polypeptide binding]; other site 347256000778 catalytic triad [active] 347256000779 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 347256000780 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 347256000781 Amidinotransferase; Region: Amidinotransf; cl12043 347256000782 putative transposase OrfB; Reviewed; Region: PHA02517 347256000783 Integrase core domain; Region: rve; cl01316 347256000784 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 347256000785 non-specific DNA binding site [nucleotide binding]; other site 347256000786 salt bridge; other site 347256000787 sequence-specific DNA binding site [nucleotide binding]; other site 347256000788 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 347256000789 active site 347256000790 catalytic motif [active] 347256000791 Zn binding site [ion binding]; other site 347256000792 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 347256000793 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 347256000794 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 347256000795 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 347256000796 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 347256000797 active site 347256000798 HIGH motif; other site 347256000799 dimer interface [polypeptide binding]; other site 347256000800 KMSKS motif; other site 347256000801 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 347256000802 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 347256000803 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 347256000804 DNA-directed RNA polymerase subunit gamma; Provisional; Region: rpoC1; PRK02625 347256000805 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 347256000806 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 347256000807 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 347256000808 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 347256000809 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 347256000810 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 347256000811 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 347256000812 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 347256000813 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 347256000814 G-loop; other site 347256000815 DNA binding site [nucleotide binding] 347256000816 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 347256000817 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 347256000818 RPB11 interaction site [polypeptide binding]; other site 347256000819 RPB12 interaction site [polypeptide binding]; other site 347256000820 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 347256000821 RPB10 interaction site [polypeptide binding]; other site 347256000822 RPB1 interaction site [polypeptide binding]; other site 347256000823 RPB11 interaction site [polypeptide binding]; other site 347256000824 RPB3 interaction site [polypeptide binding]; other site 347256000825 RPB12 interaction site [polypeptide binding]; other site 347256000826 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 347256000827 core dimer interface [polypeptide binding]; other site 347256000828 peripheral dimer interface [polypeptide binding]; other site 347256000829 L10 interface [polypeptide binding]; other site 347256000830 L11 interface [polypeptide binding]; other site 347256000831 putative EF-Tu interaction site [polypeptide binding]; other site 347256000832 putative EF-G interaction site [polypeptide binding]; other site 347256000833 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 347256000834 23S rRNA interface [nucleotide binding]; other site 347256000835 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 347256000836 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 347256000837 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 347256000838 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 347256000839 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 347256000840 alphaNTD - beta interaction site [polypeptide binding]; other site 347256000841 alphaNTD homodimer interface [polypeptide binding]; other site 347256000842 alphaNTD - beta' interaction site [polypeptide binding]; other site 347256000843 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 347256000844 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 347256000845 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 347256000846 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 347256000847 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 347256000848 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 347256000849 rRNA binding site [nucleotide binding]; other site 347256000850 predicted 30S ribosome binding site; other site 347256000851 methionine aminopeptidase; Reviewed; Region: PRK07281 347256000852 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 347256000853 active site 347256000854 adenylate kinase; Reviewed; Region: adk; PRK00279 347256000855 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 347256000856 AMP-binding site [chemical binding]; other site 347256000857 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 347256000858 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 347256000859 SecY translocase; Region: SecY; pfam00344 347256000860 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 347256000861 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 347256000862 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 347256000863 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 347256000864 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 347256000865 5S rRNA interface [nucleotide binding]; other site 347256000866 L27 interface [polypeptide binding]; other site 347256000867 23S rRNA interface [nucleotide binding]; other site 347256000868 L5 interface [polypeptide binding]; other site 347256000869 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 347256000870 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 347256000871 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 347256000872 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 347256000873 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 347256000874 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 347256000875 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 347256000876 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 347256000877 KOW motif; Region: KOW; cl00354 347256000878 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 347256000879 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 347256000880 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; cd00427 347256000881 23S rRNA interface [nucleotide binding]; other site 347256000882 putative translocon interaction site; other site 347256000883 signal recognition particle (SRP54) interaction site; other site 347256000884 L23 interface [polypeptide binding]; other site 347256000885 trigger factor interaction site; other site 347256000886 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 347256000887 23S rRNA interface [nucleotide binding]; other site 347256000888 5S rRNA interface [nucleotide binding]; other site 347256000889 putative antibiotic binding site [chemical binding]; other site 347256000890 L25 interface [polypeptide binding]; other site 347256000891 L27 interface [polypeptide binding]; other site 347256000892 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 347256000893 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 347256000894 G-X-X-G motif; other site 347256000895 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 347256000896 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 347256000897 putative translocon binding site; other site 347256000898 protein-rRNA interface [nucleotide binding]; other site 347256000899 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 347256000900 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 347256000901 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 347256000902 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 347256000903 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 347256000904 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 347256000905 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 347256000906 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 347256000907 putative phosphoketolase; Provisional; Region: PRK05261 347256000908 Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent...; Region: TPP_PK; cd02011 347256000909 TPP-binding site; other site 347256000910 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase; Region: XFP; pfam03894 347256000911 XFP C-terminal domain; Region: XFP_C; pfam09363 347256000912 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 347256000913 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 347256000914 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 347256000915 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347256000916 active site 347256000917 HIGH motif; other site 347256000918 nucleotide binding site [chemical binding]; other site 347256000919 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 347256000920 active site 347256000921 KMSKS motif; other site 347256000922 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 347256000923 tRNA binding surface [nucleotide binding]; other site 347256000924 anticodon binding site; other site 347256000925 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 347256000926 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 347256000927 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 347256000928 HIGH motif; other site 347256000929 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 347256000930 active site 347256000931 KMSKS motif; other site 347256000932 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 347256000933 tRNA binding surface [nucleotide binding]; other site 347256000934 anticodon binding site; other site 347256000935 V-type ATP synthase subunit I; Validated; Region: PRK05771 347256000936 endonuclease subunit; Provisional; Region: 46; PHA02562 347256000937 V-type ATP synthase subunit I; Validated; Region: PRK05771 347256000938 F0F1 ATP synthase subunit beta; Provisional; Region: PRK12597 347256000939 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 347256000940 alpha subunit interaction interface [polypeptide binding]; other site 347256000941 Walker A motif; other site 347256000942 ATP binding site [chemical binding]; other site 347256000943 Walker B motif; other site 347256000944 inhibitor binding site; inhibition site 347256000945 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 347256000946 F0F1 ATP synthase subunit alpha; Validated; Region: PRK07165 347256000947 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256000948 Walker A motif; other site 347256000949 ATP binding site [chemical binding]; other site 347256000950 Walker B motif; other site 347256000951 Protein of unknown function (DUF2714); Region: DUF2714; pfam10896 347256000952 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 347256000953 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 347256000954 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256000955 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 347256000956 ABC transporter; Region: ABC_tran_2; pfam12848 347256000957 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by...; Region: ABCF_EF-3; cd03221 347256000958 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 347256000959 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256000960 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256000961 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256000962 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 347256000963 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256000964 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 347256000965 conserved cys residue [active] 347256000966 bacterial Ribonuclease HIII-like; Region: RNase_HII_bacteria_HIII_like; cd06590 347256000967 RNA/DNA hybrid binding site [nucleotide binding]; other site 347256000968 active site 347256000969 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 347256000970 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 347256000971 active site 347256000972 motif I; other site 347256000973 motif II; other site 347256000974 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; cl11391 347256000975 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 347256000976 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 347256000977 intersubunit interface [polypeptide binding]; other site 347256000978 active site 347256000979 catalytic residue [active] 347256000980 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 347256000981 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 347256000982 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 347256000983 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 347256000984 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 347256000985 Recombination protein O N terminal; Region: RecO_N; pfam11967 347256000986 Recombination protein O C terminal; Region: RecO_C; pfam02565 347256000987 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 347256000988 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 347256000989 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 347256000990 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 347256000991 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 347256000992 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 347256000993 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 347256000994 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 347256000995 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 347256000996 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 347256000997 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 347256000998 HipA-like C-terminal domain; Region: HipA_C; pfam07804 347256000999 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 347256001000 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; cl11391 347256001001 Adhesin lipoprotein; Region: Lipoprotein_7; pfam01540 347256001002 Adhesin lipoprotein; Region: Lipoprotein_7; pfam01540 347256001003 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the...; Region: HIT_like; cl00228 347256001004 nucleotide binding site/active site [active] 347256001005 HIT family signature motif; other site 347256001006 catalytic residue [active] 347256001007 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 347256001008 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 347256001009 Walker A/P-loop; other site 347256001010 ATP binding site [chemical binding]; other site 347256001011 Q-loop/lid; other site 347256001012 ABC transporter signature motif; other site 347256001013 Walker B; other site 347256001014 D-loop; other site 347256001015 H-loop/switch region; other site 347256001016 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07133 347256001017 FtsX-like permease family; Region: FtsX; pfam02687 347256001018 FtsX-like permease family; Region: FtsX; pfam02687 347256001019 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 347256001020 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 347256001021 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 347256001022 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 347256001023 magnesium-transporting ATPase; Provisional; Region: PRK15122 347256001024 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 347256001025 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; cl11391 347256001026 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 347256001027 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: COG3638 347256001028 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256001029 Walker A/P-loop; other site 347256001030 ATP binding site [chemical binding]; other site 347256001031 Q-loop/lid; other site 347256001032 ABC transporter signature motif; other site 347256001033 Walker B; other site 347256001034 D-loop; other site 347256001035 H-loop/switch region; other site 347256001036 NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Region: LDH_MDH_like; cl11406 347256001037 L-lactate dehydrogenase; Region: L-LDH-NAD; TIGR01771 347256001038 NAD(P) binding site [chemical binding]; other site 347256001039 LDH/MDH dimer interface [polypeptide binding]; other site 347256001040 substrate binding site [chemical binding]; other site 347256001041 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 347256001042 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 347256001043 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 347256001044 High affinity transport system protein p37; Region: Mycoplasma_p37; pfam06646 347256001045 High affinity transport system protein p37; Region: Mycoplasma_p37; pfam06646 347256001046 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 347256001047 dimer interface [polypeptide binding]; other site 347256001048 conserved gate region; other site 347256001049 ABC-ATPase subunit interface; other site 347256001050 ABC-type phosphate/phosphonate transport system, permease component [Inorganic ion transport and metabolism]; Region: COG3639 347256001051 S-adenosylmethionine synthetase; Validated; Region: PRK05250 347256001052 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 347256001053 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 347256001054 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 347256001055 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 347256001056 motif 1; other site 347256001057 dimer interface [polypeptide binding]; other site 347256001058 active site 347256001059 motif 2; other site 347256001060 motif 3; other site 347256001061 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 347256001062 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 347256001063 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 347256001064 oligoendopeptidase F; Region: pepF; TIGR00181 347256001065 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 347256001066 active site 347256001067 Zn binding site [ion binding]; other site 347256001068 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 347256001069 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 347256001070 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 347256001071 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 347256001072 LemA family; Region: LemA; cl00742 347256001073 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 347256001074 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 347256001075 ATP binding site [chemical binding]; other site 347256001076 Mg2+ binding site [ion binding]; other site 347256001077 G-X-G motif; other site 347256001078 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 347256001079 anchoring element; other site 347256001080 dimer interface [polypeptide binding]; other site 347256001081 ATP binding site [chemical binding]; other site 347256001082 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 347256001083 active site 347256001084 putative metal-binding site [ion binding]; other site 347256001085 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 347256001086 Phosphotransferase enzyme family; Region: APH; pfam01636 347256001087 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 347256001088 active site 347256001089 substrate binding site [chemical binding]; other site 347256001090 ATP binding site [chemical binding]; other site 347256001091 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 347256001092 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 347256001093 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 347256001094 Bacterial protein of unknown function (DUF885); Region: DUF885; pfam05960 347256001095 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 347256001096 Sulfatase; Region: Sulfatase; cl10460 347256001097 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 347256001098 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 347256001099 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 347256001100 Walker A/P-loop; other site 347256001101 ATP binding site [chemical binding]; other site 347256001102 Q-loop/lid; other site 347256001103 ABC transporter signature motif; other site 347256001104 Walker B; other site 347256001105 D-loop; other site 347256001106 H-loop/switch region; other site 347256001107 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 347256001108 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 347256001109 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256001110 Walker A/P-loop; other site 347256001111 ATP binding site [chemical binding]; other site 347256001112 Q-loop/lid; other site 347256001113 ABC transporter signature motif; other site 347256001114 Walker B; other site 347256001115 D-loop; other site 347256001116 H-loop/switch region; other site 347256001117 Acetokinase family; Region: Acetate_kinase; cl01029 347256001118 Smr domain; Region: Smr; cl02619 347256001119 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 347256001120 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 347256001121 DNA binding site [nucleotide binding] 347256001122 catalytic residue [active] 347256001123 H2TH interface [polypeptide binding]; other site 347256001124 putative catalytic residues [active] 347256001125 turnover-facilitating residue; other site 347256001126 intercalation triad [nucleotide binding]; other site 347256001127 8OG recognition residue [nucleotide binding]; other site 347256001128 putative reading head residues; other site 347256001129 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 347256001130 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 347256001131 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 347256001132 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 347256001133 Uncharacterized conserved protein [Function unknown]; Region: COG1284 347256001134 Uncharacterized conserved protein [Function unknown]; Region: COG1284 347256001135 Uncharacterized conserved protein [Function unknown]; Region: COG1284 347256001136 Uncharacterized conserved protein [Function unknown]; Region: COG1284 347256001137 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 347256001138 replicative DNA helicase; Region: DnaB; TIGR00665 347256001139 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 347256001140 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 347256001141 Walker A motif; other site 347256001142 ATP binding site [chemical binding]; other site 347256001143 Walker B motif; other site 347256001144 DNA binding loops [nucleotide binding] 347256001145 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 347256001146 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 347256001147 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 347256001148 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]; Region: COG3887 347256001149 DHH family; Region: DHH; pfam01368 347256001150 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 347256001151 G1 box; other site 347256001152 GTP/Mg2+ binding site [chemical binding]; other site 347256001153 Switch I region; other site 347256001154 G2 box; other site 347256001155 G3 box; other site 347256001156 Switch II region; other site 347256001157 G4 box; other site 347256001158 G5 box; other site 347256001159 UGMP family protein; Validated; Region: PRK09604 347256001160 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 347256001161 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 347256001162 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 347256001163 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 347256001164 oligomer interface [polypeptide binding]; other site 347256001165 active site 347256001166 metal binding site [ion binding]; metal-binding site 347256001167 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 347256001168 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 347256001169 putative homodimer interface [polypeptide binding]; other site 347256001170 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 347256001171 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 347256001172 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 347256001173 THUMP domain; Region: THUMP; cl12076 347256001174 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 347256001175 Ligand Binding Site [chemical binding]; other site 347256001176 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 347256001177 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-...; Region: LysRS_N; cd04322 347256001178 dimer interface [polypeptide binding]; other site 347256001179 putative anticodon binding site; other site 347256001180 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 347256001181 motif 1; other site 347256001182 active site 347256001183 motif 2; other site 347256001184 motif 3; other site 347256001185 GTP-binding protein LepA; Provisional; Region: PRK05433 347256001186 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 347256001187 G1 box; other site 347256001188 putative GEF interaction site [polypeptide binding]; other site 347256001189 GTP/Mg2+ binding site [chemical binding]; other site 347256001190 Switch I region; other site 347256001191 G2 box; other site 347256001192 G3 box; other site 347256001193 Switch II region; other site 347256001194 G4 box; other site 347256001195 G5 box; other site 347256001196 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 347256001197 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 347256001198 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 347256001199 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 347256001200 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 347256001201 Walker A motif; other site 347256001202 ATP binding site [chemical binding]; other site 347256001203 Walker B motif; other site 347256001204 arginine finger; other site 347256001205 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 347256001206 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 347256001207 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 347256001208 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 347256001209 dimer interface [polypeptide binding]; other site 347256001210 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 347256001211 HrcA protein C terminal domain; Region: HrcA; pfam01628 347256001212 primosomal protein DnaI; Reviewed; Region: PRK08939 347256001213 Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]; Region: DnaB; COG3611 347256001214 DNA polymerase III DnaE; Validated; Region: dnaE; PRK07135 347256001215 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 347256001216 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 347256001217 5'-3' exonuclease; Provisional; Region: PRK14976 347256001218 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 347256001219 active site 347256001220 metal binding site 1 [ion binding]; metal-binding site 347256001221 putative 5' ssDNA interaction site; other site 347256001222 metal binding site 3; metal-binding site 347256001223 metal binding site 2 [ion binding]; metal-binding site 347256001224 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 347256001225 putative DNA binding site [nucleotide binding]; other site 347256001226 putative metal binding site [ion binding]; other site 347256001227 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 347256001228 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 347256001229 catalytic residues [active] 347256001230 prolyl-tRNA synthetase; Provisional; Region: PRK08661 347256001231 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_arch_euk; cd00778 347256001232 dimer interface [polypeptide binding]; other site 347256001233 motif 1; other site 347256001234 active site 347256001235 motif 2; other site 347256001236 motif 3; other site 347256001237 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity...; Region: ProRS_anticodon_zinc; cd00862 347256001238 anticodon binding site; other site 347256001239 zinc-binding site [ion binding]; other site 347256001240 Sulfatase; Region: Sulfatase; cl10460 347256001241 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 347256001242 pyruvate kinase; Provisional; Region: PRK05826 347256001243 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 347256001244 domain interfaces; other site 347256001245 active site 347256001246 seryl-tRNA synthetase; Provisional; Region: PRK05431 347256001247 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 347256001248 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 347256001249 dimer interface [polypeptide binding]; other site 347256001250 active site 347256001251 motif 1; other site 347256001252 motif 2; other site 347256001253 motif 3; other site 347256001254 RecD/TraA family; Region: recD_rel; TIGR01448 347256001255 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 347256001256 putative active site [active] 347256001257 catalytic residue [active] 347256001258 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 347256001259 Ligand Binding Site [chemical binding]; other site 347256001260 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 347256001261 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 347256001262 Walker B motif; other site 347256001263 arginine finger; other site 347256001264 Peptidase family M41; Region: Peptidase_M41; pfam01434 347256001265 Protein of unknown function (DUF402); Region: DUF402; cl00979 347256001266 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 347256001267 DNA gyrase subunit A; Validated; Region: PRK05560 347256001268 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 347256001269 CAP-like domain; other site 347256001270 Active site [active] 347256001271 primary dimer interface [polypeptide binding]; other site 347256001272 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347256001273 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347256001274 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347256001275 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347256001276 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 347256001277 LMP repeated region; Region: LMP; pfam04778 347256001278 multifunctional aminopeptidase A; Provisional; Region: PRK00913 347256001279 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 347256001280 interface (dimer of trimers) [polypeptide binding]; other site 347256001281 Substrate-binding/catalytic site; other site 347256001282 Zn-binding sites [ion binding]; other site 347256001283 Leucyl aminopeptidase [Amino acid transport and metabolism]; Region: PepB; COG0260 347256001284 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 347256001285 interface (dimer of trimers) [polypeptide binding]; other site 347256001286 Substrate-binding/catalytic site; other site 347256001287 Zn-binding sites [ion binding]; other site 347256001288 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 347256001289 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 347256001290 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 347256001291 putative active site [active] 347256001292 substrate binding site [chemical binding]; other site 347256001293 putative cosubstrate binding site; other site 347256001294 catalytic site [active] 347256001295 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 347256001296 substrate binding site [chemical binding]; other site 347256001297 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 347256001298 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256001299 Walker A/P-loop; other site 347256001300 ATP binding site [chemical binding]; other site 347256001301 Q-loop/lid; other site 347256001302 ABC transporter signature motif; other site 347256001303 Walker B; other site 347256001304 D-loop; other site 347256001305 H-loop/switch region; other site 347256001306 Domain of unknown function (DUF205); Region: DUF205; cl00410 347256001307 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 347256001308 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 347256001309 active site 347256001310 HIGH motif; other site 347256001311 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 347256001312 active site 347256001313 KMSKS motif; other site 347256001314 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 347256001315 Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The...; Region: Peptidase_C39_like; cl00296 347256001316 putative active site [active] 347256001317 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256001318 Walker A/P-loop; other site 347256001319 ATP binding site [chemical binding]; other site 347256001320 Q-loop/lid; other site 347256001321 ABC transporter signature motif; other site 347256001322 Walker B; other site 347256001323 D-loop; other site 347256001324 H-loop/switch region; other site 347256001325 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 347256001326 GTPase Era; Reviewed; Region: era; PRK00089 347256001327 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 347256001328 G1 box; other site 347256001329 GTP/Mg2+ binding site [chemical binding]; other site 347256001330 Switch I region; other site 347256001331 G2 box; other site 347256001332 Switch II region; other site 347256001333 G3 box; other site 347256001334 G4 box; other site 347256001335 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains...; Region: KH-I; cl00098 347256001336 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 347256001337 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256001338 Walker A/P-loop; other site 347256001339 ATP binding site [chemical binding]; other site 347256001340 Q-loop/lid; other site 347256001341 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 347256001342 ABC transporter signature motif; other site 347256001343 Walker B; other site 347256001344 D-loop; other site 347256001345 H-loop/switch region; other site 347256001346 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 347256001347 dimer interface [polypeptide binding]; other site 347256001348 conserved gate region; other site 347256001349 putative PBP binding loops; other site 347256001350 ABC-ATPase subunit interface; other site 347256001351 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 347256001352 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 347256001353 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 347256001354 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (...; Region: EcAsnRS_like_N; cd04318 347256001355 putative dimer interface [polypeptide binding]; other site 347256001356 putative anticodon binding site; other site 347256001357 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well...; Region: AsxRS_core; cd00776 347256001358 homodimer interface [polypeptide binding]; other site 347256001359 motif 1; other site 347256001360 motif 2; other site 347256001361 active site 347256001362 motif 3; other site 347256001363 RDD family; Region: RDD; cl00746 347256001364 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 347256001365 UvrD/REP helicase; Region: UvrD-helicase; cl14126 347256001366 Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]; Region: PepO; COG3590 347256001367 Peptidase family M13 includes neprilysin, endothelin-converting enzyme I; Region: M13; cd08662 347256001368 active site 347256001369 Zn binding site [ion binding]; other site 347256001370 hypothetical protein; Provisional; Region: PRK13671 347256001371 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 347256001372 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 347256001373 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 347256001374 G1 box; other site 347256001375 GTP/Mg2+ binding site [chemical binding]; other site 347256001376 Switch I region; other site 347256001377 G2 box; other site 347256001378 Switch II region; other site 347256001379 G3 box; other site 347256001380 G4 box; other site 347256001381 G5 box; other site 347256001382 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 347256001383 TRAM domain; Region: TRAM; cl01282 347256001384 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 347256001385 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 347256001386 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 347256001387 MatE; Region: MatE; pfam01554 347256001388 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 347256001389 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 347256001390 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 347256001391 P loop; other site 347256001392 GTP binding site [chemical binding]; other site 347256001393 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 347256001394 putative nucleotide binding site [chemical binding]; other site 347256001395 uridine monophosphate binding site [chemical binding]; other site 347256001396 homohexameric interface [polypeptide binding]; other site 347256001397 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; cl00240 347256001398 hinge region; other site 347256001399 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 347256001400 DNA polymerase III PolC; Validated; Region: polC; PRK00448 347256001401 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 347256001402 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 347256001403 generic binding surface II; other site 347256001404 generic binding surface I; other site 347256001405 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 347256001406 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 347256001407 active site 347256001408 substrate binding site [chemical binding]; other site 347256001409 catalytic site [active] 347256001410 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 347256001411 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 347256001412 dimer interface [polypeptide binding]; other site 347256001413 glycine-pyridoxal phosphate binding site [chemical binding]; other site 347256001414 active site 347256001415 folate binding site [chemical binding]; other site 347256001416 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 347256001417 DAK2 domain; Region: Dak2; cl03685 347256001418 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 347256001419 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 347256001420 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 347256001421 dimerization interface [polypeptide binding]; other site 347256001422 active site 347256001423 metal binding site [ion binding]; metal-binding site 347256001424 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 347256001425 dsRNA binding site [nucleotide binding]; other site 347256001426 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 347256001427 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 347256001428 Walker A/P-loop; other site 347256001429 ATP binding site [chemical binding]; other site 347256001430 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 347256001431 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 347256001432 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (...; Region: ABC_SMC_barmotin; cd03278 347256001433 Q-loop/lid; other site 347256001434 ABC transporter signature motif; other site 347256001435 Walker B; other site 347256001436 D-loop; other site 347256001437 H-loop/switch region; other site 347256001438 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cl11442 347256001439 excinuclease ABC subunit B; Provisional; Region: PRK05298 347256001440 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 347256001441 ATP binding site [chemical binding]; other site 347256001442 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 347256001443 nucleotide binding region [chemical binding]; other site 347256001444 ATP-binding site [chemical binding]; other site 347256001445 Ultra-violet resistance protein B; Region: UvrB; pfam12344 347256001446 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 347256001447 AAA family ATPase, CDC48 subfamily; Region: CDC48; TIGR01243 347256001448 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 347256001449 ATP binding site [chemical binding]; other site 347256001450 Walker B motif; other site 347256001451 arginine finger; other site 347256001452 Met-10+ like-protein; Region: Met_10; pfam02475 347256001453 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 347256001454 S-adenosylmethionine binding site [chemical binding]; other site 347256001455 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 347256001456 catalytic site [active] 347256001457 G-X2-G-X-G-K; other site 347256001458 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 347256001459 Active site [active] 347256001460 Catalytic domain of Protein Kinases; Region: PKc; cd00180 347256001461 active site 347256001462 ATP binding site [chemical binding]; other site 347256001463 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 347256001464 substrate binding site [chemical binding]; other site 347256001465 activation loop (A-loop); other site 347256001466 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 347256001467 GTPase RsgA; Reviewed; Region: PRK00098 347256001468 YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence...; Region: YjeQ_engC; cd01854 347256001469 GTPase/OB domain interface [polypeptide binding]; other site 347256001470 GTPase/Zn-binding domain interface [polypeptide binding]; other site 347256001471 GTP/Mg2+ binding site [chemical binding]; other site 347256001472 G4 box; other site 347256001473 G5 box; other site 347256001474 G1 box; other site 347256001475 Switch I region; other site 347256001476 G2 box; other site 347256001477 G3 box; other site 347256001478 Switch II region; other site 347256001479 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 347256001480 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 347256001481 substrate binding site [chemical binding]; other site 347256001482 hexamer interface [polypeptide binding]; other site 347256001483 metal binding site [ion binding]; metal-binding site 347256001484 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 347256001485 FGGY family of carbohydrate kinases, C-terminal domain; Region: FGGY_C; pfam02782 347256001486 ABC-2 type transporter; Region: ABC2_membrane; cl11417 347256001487 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 347256001488 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 347256001489 Walker A/P-loop; other site 347256001490 ATP binding site [chemical binding]; other site 347256001491 Q-loop/lid; other site 347256001492 ABC transporter signature motif; other site 347256001493 Walker B; other site 347256001494 D-loop; other site 347256001495 H-loop/switch region; other site 347256001496 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 347256001497 rRNA interaction site [nucleotide binding]; other site 347256001498 S8 interaction site; other site 347256001499 elongation factor Ts; Provisional; Region: tsf; PRK09377 347256001500 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 347256001501 Elongation factor TS; Region: EF_TS; pfam00889 347256001502 Elongation factor TS; Region: EF_TS; pfam00889 347256001503 Sporulation Regulator WhiA C terminal domain; Region: HTH_WhiA; pfam02650 347256001504 Isochorismatase family; Region: Isochorismatase; pfam00857 347256001505 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 347256001506 catalytic triad [active] 347256001507 conserved cis-peptide bond; other site 347256001508 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 347256001509 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 347256001510 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 347256001511 DNA polymerase II large subunit; Provisional; Region: PRK14714 347256001512 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 347256001513 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 347256001514 M28, and M42; Region: Zinc_peptidase_like; cl14876 347256001515 dipeptidase, putative; Region: dipeptidaselike; TIGR01887 347256001516 metal binding site [ion binding]; metal-binding site 347256001517 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 347256001518 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 347256001519 CAP-like domain; other site 347256001520 Active site [active] 347256001521 primary dimer interface [polypeptide binding]; other site 347256001522 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 347256001523 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 347256001524 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 347256001525 anchoring element; other site 347256001526 dimer interface [polypeptide binding]; other site 347256001527 ATP binding site [chemical binding]; other site 347256001528 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 347256001529 active site 347256001530 metal binding site [ion binding]; metal-binding site 347256001531 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 347256001532 Histidine phosphatase superfamily (branch 2); Region: His_Phos_2; pfam00328 347256001533 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 347256001534 catalytic core [active] 347256001535 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 347256001536 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 347256001537 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 347256001538 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 347256001539 MatE; Region: MatE; pfam01554 347256001540 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 347256001541 Serine carboxypeptidase S28; Region: Peptidase_S28; pfam05577 347256001542 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 347256001543 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 347256001544 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 347256001545 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 347256001546 RNA binding site [nucleotide binding]; other site 347256001547 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 347256001548 HsdM N-terminal domain; Region: HsdM_N; pfam12161 347256001549 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 347256001550 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256001551 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256001552 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 347256001553 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256001554 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 347256001555 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 347256001556 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 347256001557 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 347256001558 ATP binding site [chemical binding]; other site 347256001559 putative Mg++ binding site [ion binding]; other site 347256001560 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 347256001561 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 347256001562 NusA N-terminal domain; Region: NusA_N; pfam08529 347256001563 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 347256001564 G-X-X-G motif; other site 347256001565 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cl00189 347256001566 putative RNA binding cleft [nucleotide binding]; other site 347256001567 translation initiation factor IF-2; Region: IF-2; TIGR00487 347256001568 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 347256001569 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 347256001570 G1 box; other site 347256001571 putative GEF interaction site [polypeptide binding]; other site 347256001572 GTP/Mg2+ binding site [chemical binding]; other site 347256001573 Switch I region; other site 347256001574 G2 box; other site 347256001575 G3 box; other site 347256001576 Switch II region; other site 347256001577 G4 box; other site 347256001578 G5 box; other site 347256001579 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 347256001580 Translation-initiation factor 2; Region: IF-2; pfam11987 347256001581 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 347256001582 Ribosome-binding factor A; Region: RBFA; cl00542 347256001583 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 347256001584 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 347256001585 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 347256001586 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 347256001587 DHH family; Region: DHH; pfam01368 347256001588 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 347256001589 DHH family; Region: DHH; pfam01368 347256001590 DHHA1 domain; Region: DHHA1; pfam02272 347256001591 nicotinate phosphoribosyltransferase; Provisional; Region: PRK07188 347256001592 Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate...; Region: PRTase_typeII; cl12019 347256001593 active site