-- dump date 20111121_015457 -- class Genbank::misc_feature -- table misc_feature_note -- id note 505682000001 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 505682000002 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 505682000003 Walker A motif; other site 505682000004 ATP binding site [chemical binding]; other site 505682000005 Walker B motif; other site 505682000006 arginine finger; other site 505682000007 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 505682000008 DnaA box-binding interface [nucleotide binding]; other site 505682000009 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 505682000010 peptide chain release factor 1; Validated; Region: prfA; PRK00591 505682000011 RF-1 domain; Region: RF-1; cl02875 505682000012 RF-1 domain; Region: RF-1; cl02875 505682000013 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 505682000014 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 505682000015 S-adenosylmethionine binding site [chemical binding]; other site 505682000016 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 505682000017 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 505682000018 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 505682000019 MgtE intracellular N domain; Region: MgtE_N; cl15244 505682000020 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-...; Region: CBS_pair_13; cd04626 505682000021 Divalent cation transporter; Region: MgtE; cl00786 505682000022 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 505682000023 23S rRNA interface [nucleotide binding]; other site 505682000024 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 505682000025 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 505682000026 core dimer interface [polypeptide binding]; other site 505682000027 peripheral dimer interface [polypeptide binding]; other site 505682000028 L10 interface [polypeptide binding]; other site 505682000029 L11 interface [polypeptide binding]; other site 505682000030 putative EF-Tu interaction site [polypeptide binding]; other site 505682000031 putative EF-G interaction site [polypeptide binding]; other site 505682000032 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 505682000033 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 505682000034 TM-ABC transporter signature motif; other site 505682000035 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (; Region: TM_PBP1_transp_TpRbsC_like; cd06580 505682000036 TM-ABC transporter signature motif; other site 505682000037 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 505682000038 Protein of unknown function (DUF1202); Region: DUF1202; pfam06717 505682000039 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 505682000040 This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and...; Region: ABC_Carb_Monos_I; cd03216 505682000041 Walker A/P-loop; other site 505682000042 ATP binding site [chemical binding]; other site 505682000043 Q-loop/lid; other site 505682000044 ABC transporter signature motif; other site 505682000045 Walker B; other site 505682000046 D-loop; other site 505682000047 H-loop/switch region; other site 505682000048 This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (; Region: ABC_Carb_Monos_II; cd03215 505682000049 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 505682000050 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 505682000051 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 505682000052 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 505682000053 active site 505682000054 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 505682000055 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 505682000056 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 505682000057 G1 box; other site 505682000058 GTP/Mg2+ binding site [chemical binding]; other site 505682000059 Switch I region; other site 505682000060 G2 box; other site 505682000061 Switch II region; other site 505682000062 G3 box; other site 505682000063 G4 box; other site 505682000064 G5 box; other site 505682000065 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 505682000066 DNA polymerase III subunit delta'; Validated; Region: PRK08058 505682000067 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682000068 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 505682000069 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 505682000070 TMP-binding site; other site 505682000071 ATP-binding site [chemical binding]; other site 505682000072 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 505682000073 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682000074 ABC-ATPase subunit interface; other site 505682000075 dimer interface [polypeptide binding]; other site 505682000076 putative PBP binding regions; other site 505682000077 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682000078 ABC-ATPase subunit interface; other site 505682000079 dimer interface [polypeptide binding]; other site 505682000080 putative PBP binding regions; other site 505682000081 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682000082 ABC-ATPase subunit interface; other site 505682000083 dimer interface [polypeptide binding]; other site 505682000084 putative PBP binding regions; other site 505682000085 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 505682000086 rRNA interaction site [nucleotide binding]; other site 505682000087 S8 interaction site; other site 505682000088 putative laminin-1 binding site; other site 505682000089 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 505682000090 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 505682000091 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 505682000092 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 505682000093 RNA binding site [nucleotide binding]; other site 505682000094 Uncharacterized phage-associated protein [Function unknown]; Region: GepA; COG3600 505682000095 Divergent AAA domain; Region: AAA_4; pfam04326 505682000096 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 505682000097 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]; Region: COG2865 505682000098 Divergent AAA domain; Region: AAA_4; pfam04326 505682000099 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 505682000100 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 505682000101 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 505682000102 16S rRNA (guanine(527)-N(7))-methyltransferase GidB; Region: gidB; TIGR00138 505682000103 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 505682000104 S-adenosylmethionine binding site [chemical binding]; other site 505682000105 PQ loop repeat; Region: PQ-loop; cl12056 505682000106 PQ loop repeat; Region: PQ-loop; cl12056 505682000107 Domain of unknown function DUF31; Region: DUF31; pfam01732 505682000108 Lipoprotein associated domain; Region: Lipoprotein_17; pfam04200 505682000109 Domain of unknown function DUF31; Region: DUF31; pfam01732 505682000110 Domain of unknown function DUF31; Region: DUF31; pfam01732 505682000111 Protein of unknown function (DUF2714); Region: DUF2714; pfam10896 505682000112 DNA-directed RNA polymerase, subunit A''; Region: RNA_pol_rpoA2; TIGR02389 505682000113 F0F1 ATP synthase subunit alpha; Validated; Region: PRK07165 505682000114 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682000115 Walker A motif; other site 505682000116 ATP binding site [chemical binding]; other site 505682000117 Walker B motif; other site 505682000118 F0F1 ATP synthase subunit beta; Provisional; Region: PRK12597 505682000119 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 505682000120 alpha subunit interaction interface [polypeptide binding]; other site 505682000121 Walker A motif; other site 505682000122 ATP binding site [chemical binding]; other site 505682000123 Walker B motif; other site 505682000124 inhibitor binding site; inhibition site 505682000125 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 505682000126 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 505682000127 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 505682000128 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 505682000129 putative active site [active] 505682000130 putative catalytic site [active] 505682000131 putative Mg binding site IVb [ion binding]; other site 505682000132 putative phosphate binding site [ion binding]; other site 505682000133 putative DNA binding site [nucleotide binding]; other site 505682000134 putative Mg binding site IVa [ion binding]; other site 505682000135 Preprotein translocase SecG subunit; Region: SecG; cl09123 505682000136 ribonuclease R; Region: RNase_R; TIGR02063 505682000137 RNB domain; Region: RNB; pfam00773 505682000138 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an...; Region: S1_RNase_R; cd04471 505682000139 RNA binding site [nucleotide binding]; other site 505682000140 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 505682000141 SmpB-tmRNA interface; other site 505682000142 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 505682000143 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 505682000144 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682000145 Walker A/P-loop; other site 505682000146 ATP binding site [chemical binding]; other site 505682000147 Q-loop/lid; other site 505682000148 ABC transporter signature motif; other site 505682000149 Walker B; other site 505682000150 D-loop; other site 505682000151 H-loop/switch region; other site 505682000152 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 505682000153 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 505682000154 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682000155 Walker A/P-loop; other site 505682000156 ATP binding site [chemical binding]; other site 505682000157 Q-loop/lid; other site 505682000158 ABC transporter signature motif; other site 505682000159 Walker B; other site 505682000160 D-loop; other site 505682000161 H-loop/switch region; other site 505682000162 Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ValS; COG0525 505682000163 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 505682000164 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 505682000165 dimer interface [polypeptide binding]; other site 505682000166 putative anticodon binding site; other site 505682000167 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 505682000168 motif 1; other site 505682000169 active site 505682000170 motif 2; other site 505682000171 motif 3; other site 505682000172 Nucleoside 2-deoxyribosyltransferase; Region: Nuc_deoxyrib_tr; cl01450 505682000173 oligoendopeptidase F; Region: pepF; TIGR00181 505682000174 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 505682000175 active site 505682000176 Zn binding site [ion binding]; other site 505682000177 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 505682000178 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 505682000179 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 505682000180 DNA-binding site [nucleotide binding]; DNA binding site 505682000181 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 505682000182 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 505682000183 Walker A/P-loop; other site 505682000184 ATP binding site [chemical binding]; other site 505682000185 Q-loop/lid; other site 505682000186 ABC transporter signature motif; other site 505682000187 Walker B; other site 505682000188 D-loop; other site 505682000189 H-loop/switch region; other site 505682000190 ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]; Region: CeuC; COG4605 505682000191 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682000192 ABC-ATPase subunit interface; other site 505682000193 dimer interface [polypeptide binding]; other site 505682000194 putative PBP binding regions; other site 505682000195 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 505682000196 Domain of unknown function DUF21; Region: DUF21; pfam01595 505682000197 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 505682000198 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1481 505682000199 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 505682000200 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 505682000201 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 505682000202 HPr kinase/phosphorylase; Provisional; Region: PRK05428 505682000203 DRTGG domain; Region: DRTGG; cl12147 505682000204 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-...; Region: HprK_C; cd01918 505682000205 Hpr binding site; other site 505682000206 active site 505682000207 homohexamer subunit interaction site [polypeptide binding]; other site 505682000208 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 505682000209 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 505682000210 Ligand Binding Site [chemical binding]; other site 505682000211 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 505682000212 putative active site [active] 505682000213 catalytic residue [active] 505682000214 DNA polymerase III subunit beta; Validated; Region: PRK05643 505682000215 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 505682000216 putative DNA binding surface [nucleotide binding]; other site 505682000217 dimer interface [polypeptide binding]; other site 505682000218 beta-clamp/clamp loader binding surface; other site 505682000219 beta-clamp/translesion DNA polymerase binding surface; other site 505682000220 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 505682000221 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 505682000222 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 505682000223 ATP binding site [chemical binding]; other site 505682000224 Mg2+ binding site [ion binding]; other site 505682000225 G-X-G motif; other site 505682000226 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 505682000227 anchoring element; other site 505682000228 dimer interface [polypeptide binding]; other site 505682000229 ATP binding site [chemical binding]; other site 505682000230 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 505682000231 active site 505682000232 putative metal-binding site [ion binding]; other site 505682000233 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 505682000234 DNA gyrase subunit A; Validated; Region: PRK05560 505682000235 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 505682000236 CAP-like domain; other site 505682000237 Active site [active] 505682000238 primary dimer interface [polypeptide binding]; other site 505682000239 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682000240 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682000241 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682000242 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682000243 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682000244 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682000245 Competence-damaged protein; Region: CinA; cl00666 505682000246 recombinase A; Provisional; Region: recA; PRK09354 505682000247 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 505682000248 hexamer interface [polypeptide binding]; other site 505682000249 Walker A motif; other site 505682000250 ATP binding site [chemical binding]; other site 505682000251 Walker B motif; other site 505682000252 hypothetical protein; Provisional; Region: PRK12705 505682000253 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 505682000254 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 505682000255 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 505682000256 Substrate-binding site [chemical binding]; other site 505682000257 Substrate specificity [chemical binding]; other site 505682000258 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05896 505682000259 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 505682000260 Walker A motif; other site 505682000261 ATP binding site [chemical binding]; other site 505682000262 Walker B motif; other site 505682000263 arginine finger; other site 505682000264 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 505682000265 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 505682000266 RecR protein; Region: RecR; pfam02132 505682000267 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 505682000268 putative active site [active] 505682000269 putative metal-binding site [ion binding]; other site 505682000270 tetramer interface [polypeptide binding]; other site 505682000271 Protein of unknown function DUF262; Region: DUF262; cl14890 505682000272 Uncharacterized conserved protein (DUF2081); Region: DUF2081; cl09179 505682000273 signal recognition particle protein; Provisional; Region: PRK10867 505682000274 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 505682000275 P loop; other site 505682000276 GTP binding site [chemical binding]; other site 505682000277 Signal peptide binding domain; Region: SRP_SPB; pfam02978 505682000278 ABC-2 type transporter; Region: ABC2_membrane; cl11417 505682000279 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 505682000280 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 505682000281 Walker A/P-loop; other site 505682000282 ATP binding site [chemical binding]; other site 505682000283 Q-loop/lid; other site 505682000284 ABC transporter signature motif; other site 505682000285 Walker B; other site 505682000286 D-loop; other site 505682000287 H-loop/switch region; other site 505682000288 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 505682000289 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 505682000290 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 505682000291 ATP binding site [chemical binding]; other site 505682000292 putative Mg++ binding site [ion binding]; other site 505682000293 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 505682000294 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 505682000295 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 505682000296 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 505682000297 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 505682000298 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 505682000299 HsdM N-terminal domain; Region: HsdM_N; pfam12161 505682000300 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 505682000301 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 505682000302 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 505682000303 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 505682000304 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 505682000305 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 505682000306 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 505682000307 Walker A motif; other site 505682000308 ATP binding site [chemical binding]; other site 505682000309 Walker B motif; other site 505682000310 arginine finger; other site 505682000311 Peptidase family M41; Region: Peptidase_M41; pfam01434 505682000312 seryl-tRNA synthetase; Provisional; Region: PRK05431 505682000313 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 505682000314 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 505682000315 dimer interface [polypeptide binding]; other site 505682000316 active site 505682000317 motif 1; other site 505682000318 motif 2; other site 505682000319 motif 3; other site 505682000320 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682000321 Walker A/P-loop; other site 505682000322 ATP binding site [chemical binding]; other site 505682000323 Q-loop/lid; other site 505682000324 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 505682000325 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682000326 ABC transporter signature motif; other site 505682000327 Walker B; other site 505682000328 D-loop; other site 505682000329 H-loop/switch region; other site 505682000330 TOBE domain; Region: TOBE_2; cl01440 505682000331 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 505682000332 dimer interface [polypeptide binding]; other site 505682000333 conserved gate region; other site 505682000334 putative PBP binding loops; other site 505682000335 ABC-ATPase subunit interface; other site 505682000336 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 505682000337 dimer interface [polypeptide binding]; other site 505682000338 conserved gate region; other site 505682000339 putative PBP binding loops; other site 505682000340 ABC-ATPase subunit interface; other site 505682000341 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 505682000342 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 505682000343 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 505682000344 active site 505682000345 catalytic site [active] 505682000346 substrate binding site [chemical binding]; other site 505682000347 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 505682000348 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 505682000349 active site 505682000350 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-...; Region: DHFR; cd00209 505682000351 folate binding site [chemical binding]; other site 505682000352 NADP+ binding site [chemical binding]; other site 505682000353 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 505682000354 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 505682000355 motif II; other site 505682000356 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 505682000357 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 505682000358 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 505682000359 active site 505682000360 HIGH motif; other site 505682000361 dimer interface [polypeptide binding]; other site 505682000362 KMSKS motif; other site 505682000363 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 505682000364 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 505682000365 Walker A/P-loop; other site 505682000366 ATP binding site [chemical binding]; other site 505682000367 Q-loop/lid; other site 505682000368 ABC transporter signature motif; other site 505682000369 Walker B; other site 505682000370 D-loop; other site 505682000371 H-loop/switch region; other site 505682000372 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 505682000373 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 505682000374 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 505682000375 excinuclease ABC subunit B; Provisional; Region: PRK05298 505682000376 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 505682000377 ATP binding site [chemical binding]; other site 505682000378 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 505682000379 nucleotide binding region [chemical binding]; other site 505682000380 ATP-binding site [chemical binding]; other site 505682000381 Ultra-violet resistance protein B; Region: UvrB; pfam12344 505682000382 NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]; Region: Lig; COG0272 505682000383 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 505682000384 nucleotide binding pocket [chemical binding]; other site 505682000385 K-X-D-G motif; other site 505682000386 catalytic site [active] 505682000387 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 505682000388 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 505682000389 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 505682000390 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; cl00038 505682000391 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 505682000392 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 505682000393 active site 505682000394 HIGH motif; other site 505682000395 nucleotide binding site [chemical binding]; other site 505682000396 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 505682000397 KMSKS motif; other site 505682000398 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 505682000399 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 505682000400 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 505682000401 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 505682000402 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 505682000403 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 505682000404 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 505682000405 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 505682000406 alpha subunit interaction interface [polypeptide binding]; other site 505682000407 Walker A motif; other site 505682000408 ATP binding site [chemical binding]; other site 505682000409 Walker B motif; other site 505682000410 inhibitor binding site; inhibition site 505682000411 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 505682000412 ATP synthase; Region: ATP-synt; cl00365 505682000413 2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate binding; Region: PLN02980 505682000414 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 505682000415 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 505682000416 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 505682000417 beta subunit interaction interface [polypeptide binding]; other site 505682000418 Walker A motif; other site 505682000419 ATP binding site [chemical binding]; other site 505682000420 Walker B motif; other site 505682000421 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 505682000422 Uncharacterized conserved protein [Function unknown]; Region: COG4933 505682000423 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 505682000424 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 505682000425 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 505682000426 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 505682000427 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 505682000428 ATP synthase subunit C; Region: ATP-synt_C; cl00466 505682000429 ATP synthase A chain; Region: ATP-synt_A; cl00413 505682000430 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 505682000431 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 505682000432 Walker A/P-loop; other site 505682000433 ATP binding site [chemical binding]; other site 505682000434 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 505682000435 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 505682000436 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 505682000437 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 505682000438 Q-loop/lid; other site 505682000439 ABC transporter signature motif; other site 505682000440 Walker B; other site 505682000441 D-loop; other site 505682000442 H-loop/switch region; other site 505682000443 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 505682000444 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 505682000445 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 505682000446 GTP binding site [chemical binding]; other site 505682000447 Putative helix-turn-helix protein, YlxM / p13 like; Region: UPF0122; pfam04297 505682000448 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 505682000449 DUF1410 domain; Region: DUF1410; pfam07198 505682000450 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 505682000451 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 505682000452 DNA binding site [nucleotide binding] 505682000453 Int/Topo IB signature motif; other site 505682000454 active site 505682000455 RecT family; Region: RecT; cl04285 505682000456 phosphodiesterase; Provisional; Region: PRK12704 505682000457 Phage terminase large subunit; Region: Terminase_3; cl12054 505682000458 Terminase-like family; Region: Terminase_6; pfam03237 505682000459 Domain of unknown function(DUF2779); Region: DUF2779; pfam11074 505682000460 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 505682000461 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 505682000462 active site 505682000463 motif I; other site 505682000464 motif II; other site 505682000465 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 505682000466 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 505682000467 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 505682000468 active site 505682000469 HIGH motif; other site 505682000470 dimer interface [polypeptide binding]; other site 505682000471 KMSKS motif; other site 505682000472 Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting...; Region: ArsC_Spx; cd03032 505682000473 putative catalytic residues [active] 505682000474 thiol/disulfide switch; other site 505682000475 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 505682000476 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 505682000477 active site turn [active] 505682000478 phosphorylation site [posttranslational modification] 505682000479 Predicted SPOUT methyltransferase; Region: SPOUT_MTase; cl00679 505682000480 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 505682000481 substrate binding site [chemical binding]; other site 505682000482 dimer interface [polypeptide binding]; other site 505682000483 catalytic triad [active] 505682000484 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 505682000485 Sulfatase; Region: Sulfatase; cl10460 505682000486 enolase; Provisional; Region: eno; PRK00077 505682000487 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 505682000488 dimer interface [polypeptide binding]; other site 505682000489 metal binding site [ion binding]; metal-binding site 505682000490 substrate binding pocket [chemical binding]; other site 505682000491 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases...; Region: PFK; cl00204 505682000492 active site 505682000493 ADP/pyrophosphate binding site [chemical binding]; other site 505682000494 dimerization interface [polypeptide binding]; other site 505682000495 allosteric effector site; other site 505682000496 fructose-1,6-bisphosphate binding site; other site 505682000497 Pyruvate kinase [Carbohydrate transport and metabolism]; Region: PykF; COG0469 505682000498 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 505682000499 domain interfaces; other site 505682000500 active site 505682000501 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 505682000502 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 505682000503 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 505682000504 RPB10 interaction site [polypeptide binding]; other site 505682000505 RPB11 interaction site [polypeptide binding]; other site 505682000506 RPB3 interaction site [polypeptide binding]; other site 505682000507 RPB12 interaction site [polypeptide binding]; other site 505682000508 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 505682000509 RPB1 interaction site [polypeptide binding]; other site 505682000510 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 505682000511 DNA-directed RNA polymerase, beta' subunit, predominant form; Region: rpoC_TIGR; TIGR02386 505682000512 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 505682000513 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 505682000514 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 505682000515 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 505682000516 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 505682000517 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 505682000518 DNA binding site [nucleotide binding] 505682000519 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 505682000520 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 505682000521 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 505682000522 putative tRNA-binding site [nucleotide binding]; other site 505682000523 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 505682000524 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 505682000525 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 505682000526 TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in...; Region: TOPRIM_RNase_M5_like; cd01027 505682000527 putative active site [active] 505682000528 putative metal binding site [ion binding]; other site 505682000529 Predicted methyltransferases [General function prediction only]; Region: COG0313 505682000530 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 505682000531 recombination factor protein RarA; Reviewed; Region: PRK13342 505682000532 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 505682000533 Walker A motif; other site 505682000534 ATP binding site [chemical binding]; other site 505682000535 Walker B motif; other site 505682000536 arginine finger; other site 505682000537 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 505682000538 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 505682000539 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 505682000540 active site 505682000541 HIGH motif; other site 505682000542 KMSKS motif; other site 505682000543 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 505682000544 tRNA binding surface [nucleotide binding]; other site 505682000545 anticodon binding site; other site 505682000546 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 505682000547 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 505682000548 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 505682000549 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 505682000550 dimer interface [polypeptide binding]; other site 505682000551 conserved gate region; other site 505682000552 putative PBP binding loops; other site 505682000553 ABC-ATPase subunit interface; other site 505682000554 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14257 505682000555 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 505682000556 Walker A/P-loop; other site 505682000557 ATP binding site [chemical binding]; other site 505682000558 Q-loop/lid; other site 505682000559 ABC transporter signature motif; other site 505682000560 Walker B; other site 505682000561 D-loop; other site 505682000562 H-loop/switch region; other site 505682000563 Phosphate uptake regulator [Inorganic ion transport and metabolism]; Region: PhoU; COG0704 505682000564 PhoU domain; Region: PhoU; pfam01895 505682000565 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 505682000566 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 505682000567 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 505682000568 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 505682000569 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 505682000570 16S/18S rRNA binding site [nucleotide binding]; other site 505682000571 S13e-L30e interaction site [polypeptide binding]; other site 505682000572 25S rRNA binding site [nucleotide binding]; other site 505682000573 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 505682000574 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 505682000575 dimerization interface [polypeptide binding]; other site 505682000576 active site 505682000577 metal binding site [ion binding]; metal-binding site 505682000578 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 505682000579 dsRNA binding site [nucleotide binding]; other site 505682000580 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 505682000581 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 505682000582 DAK2 domain; Region: Dak2; cl03685 505682000583 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 505682000584 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 505682000585 Protein of unknown function (DUF464); Region: DUF464; cl01080 505682000586 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 505682000587 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 505682000588 catalytic site [active] 505682000589 G-X2-G-X-G-K; other site 505682000590 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 505682000591 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl14056 505682000592 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 505682000593 Protein phosphatase 2C; Region: PP2C; pfam00481 505682000594 Active site [active] 505682000595 Catalytic domain of Protein Kinases; Region: PKc; cd00180 505682000596 active site 505682000597 ATP binding site [chemical binding]; other site 505682000598 Serine/Threonine protein kinases, catalytic domain; Region: S_TKc; smart00220 505682000599 substrate binding site [chemical binding]; other site 505682000600 activation loop (A-loop); other site 505682000601 Predicted GTPases [General function prediction only]; Region: COG1162 505682000602 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 505682000603 GTPase/OB domain interface [polypeptide binding]; other site 505682000604 GTPase/Zn-binding domain interface [polypeptide binding]; other site 505682000605 GTP/Mg2+ binding site [chemical binding]; other site 505682000606 G4 box; other site 505682000607 G5 box; other site 505682000608 G1 box; other site 505682000609 Switch I region; other site 505682000610 G2 box; other site 505682000611 G3 box; other site 505682000612 Switch II region; other site 505682000613 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 505682000614 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 505682000615 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]; Region: MIS1; COG2759 505682000616 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 505682000617 Potassium binding sites [ion binding]; other site 505682000618 Cesium cation binding sites [ion binding]; other site 505682000619 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 505682000620 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 505682000621 DNA binding site [nucleotide binding] 505682000622 Int/Topo IB signature motif; other site 505682000623 active site 505682000624 Transmembrane amino acid transporter protein; Region: Aa_trans; cl00524 505682000625 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 505682000626 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 505682000627 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 505682000628 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 505682000629 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 505682000630 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 505682000631 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 505682000632 23S rRNA binding site [nucleotide binding]; other site 505682000633 L21 binding site [polypeptide binding]; other site 505682000634 L13 binding site [polypeptide binding]; other site 505682000635 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 505682000636 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 505682000637 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 505682000638 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 505682000639 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 505682000640 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 505682000641 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 505682000642 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 505682000643 50S ribosomal protein L22/unknown domain fusion protein; Provisional; Region: PRK12279 505682000644 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 505682000645 putative translocon binding site; other site 505682000646 protein-rRNA interface [nucleotide binding]; other site 505682000647 Uncharacterized conserved protein [Function unknown]; Region: COG4933 505682000648 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 505682000649 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 505682000650 G-X-X-G motif; other site 505682000651 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 505682000652 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 505682000653 23S rRNA interface [nucleotide binding]; other site 505682000654 5S rRNA interface [nucleotide binding]; other site 505682000655 putative antibiotic binding site [chemical binding]; other site 505682000656 L25 interface [polypeptide binding]; other site 505682000657 L27 interface [polypeptide binding]; other site 505682000658 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where...; Region: Ribosomal_L29_HIP; cl09943 505682000659 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 505682000660 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 505682000661 KOW motif; Region: KOW; cl00354 505682000662 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 505682000663 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 505682000664 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 505682000665 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 505682000666 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 505682000667 ribosomal protein L6, bacterial type; Region: L6_bact; TIGR03654 505682000668 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 505682000669 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 505682000670 5S rRNA interface [nucleotide binding]; other site 505682000671 L27 interface [polypeptide binding]; other site 505682000672 23S rRNA interface [nucleotide binding]; other site 505682000673 L5 interface [polypeptide binding]; other site 505682000674 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 505682000675 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 505682000676 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 505682000677 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 505682000678 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 505682000679 SecY translocase; Region: SecY; pfam00344 505682000680 adenylate kinases; Region: adk; TIGR01351 505682000681 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 505682000682 AMP-binding site [chemical binding]; other site 505682000683 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 505682000684 methionine aminopeptidase; Reviewed; Region: PRK07281 505682000685 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 505682000686 active site 505682000687 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 505682000688 rRNA binding site [nucleotide binding]; other site 505682000689 predicted 30S ribosome binding site; other site 505682000690 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 505682000691 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 505682000692 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 505682000693 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 505682000694 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 505682000695 alphaNTD homodimer interface [polypeptide binding]; other site 505682000696 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 505682000697 alphaNTD - beta interaction site [polypeptide binding]; other site 505682000698 alphaNTD - beta' interaction site [polypeptide binding]; other site 505682000699 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 505682000700 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 505682000701 Uncharacterized conserved protein [Function unknown]; Region: COG1739 505682000702 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 505682000703 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 505682000704 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 505682000705 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 505682000706 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 505682000707 Uncharacterised protein family (UPF0154); Region: UPF0154; cl01536 505682000708 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 505682000709 G1 box; other site 505682000710 GTP/Mg2+ binding site [chemical binding]; other site 505682000711 Switch I region; other site 505682000712 G2 box; other site 505682000713 G3 box; other site 505682000714 Switch II region; other site 505682000715 G4 box; other site 505682000716 G5 box; other site 505682000717 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 505682000718 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 505682000719 active site 505682000720 HIGH motif; other site 505682000721 nucleotide binding site [chemical binding]; other site 505682000722 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 505682000723 active site 505682000724 KMSKS motif; other site 505682000725 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 505682000726 tRNA binding surface [nucleotide binding]; other site 505682000727 anticodon binding site; other site 505682000728 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 505682000729 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 505682000730 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life...; Region: HINT_subgroup; cd01277 505682000731 HIT family signature motif; other site 505682000732 catalytic residue [active] 505682000733 coproporphyrinogen III oxidase; Provisional; Region: PRK05904 505682000734 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster...; Region: Radical_SAM; cl14056 505682000735 HemN C-terminal region; Region: HemN_C; pfam06969 505682000736 nicotinate phosphoribosyltransferase; Provisional; Region: PRK07188 505682000737 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting...; Region: NAPRTase_B; cd01571 505682000738 active site 505682000739 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 505682000740 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 505682000741 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 505682000742 active site 505682000743 HIGH motif; other site 505682000744 KMSK motif region; other site 505682000745 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 505682000746 tRNA binding surface [nucleotide binding]; other site 505682000747 anticodon binding site; other site 505682000748 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 505682000749 substrate binding site [chemical binding]; other site 505682000750 hinge regions; other site 505682000751 ADP binding site [chemical binding]; other site 505682000752 catalytic site [active] 505682000753 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 505682000754 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 505682000755 oligomer interface [polypeptide binding]; other site 505682000756 active site 505682000757 metal binding site [ion binding]; metal-binding site 505682000758 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 505682000759 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 505682000760 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-...; Region: HU_IHF; cd00591 505682000761 IHF - DNA interface [nucleotide binding]; other site 505682000762 IHF dimer interface [polypeptide binding]; other site 505682000763 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 505682000764 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 505682000765 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 505682000766 synthetase active site [active] 505682000767 NTP binding site [chemical binding]; other site 505682000768 metal binding site [ion binding]; metal-binding site 505682000769 CTP synthetase; Validated; Region: pyrG; PRK05380 505682000770 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer...; Region: CTGs; cd03113 505682000771 Catalytic site [active] 505682000772 Active site [active] 505682000773 UTP binding site [chemical binding]; other site 505682000774 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 505682000775 active site 505682000776 putative oxyanion hole; other site 505682000777 catalytic triad [active] 505682000778 histidyl-tRNA synthetase; Region: hisS; TIGR00442 505682000779 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 505682000780 dimer interface [polypeptide binding]; other site 505682000781 motif 1; other site 505682000782 active site 505682000783 motif 2; other site 505682000784 motif 3; other site 505682000785 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible...; Region: HGTP_anticodon; cl00266 505682000786 anticodon binding site; other site 505682000787 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 505682000788 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 505682000789 dimer interface [polypeptide binding]; other site 505682000790 anticodon binding site; other site 505682000791 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 505682000792 homodimer interface [polypeptide binding]; other site 505682000793 motif 1; other site 505682000794 active site 505682000795 motif 2; other site 505682000796 GAD domain; Region: GAD; pfam02938 505682000797 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 505682000798 motif 3; other site 505682000799 Peptide methionine sulfoxide reductase; Region: PMSR; cl00366 505682000800 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 505682000801 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue...; Region: GSH_Peroxidase; cd00340 505682000802 catalytic residues [active] 505682000803 dimer interface [polypeptide binding]; other site 505682000804 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 505682000805 active site 505682000806 catalytic triad [active] 505682000807 Domain of unknown function DUF28; Region: DUF28; cl00361 505682000808 Recombination protein U; Region: RecU; cl01314 505682000809 translation elongation factor P; Region: efp; TIGR00038 505682000810 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 505682000811 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 505682000812 RNA binding site [nucleotide binding]; other site 505682000813 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 505682000814 RNA binding site [nucleotide binding]; other site 505682000815 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 505682000816 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 505682000817 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 505682000818 domain; Region: GreA_GreB_N; pfam03449 505682000819 C-term; Region: GreA_GreB; pfam01272 505682000820 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 505682000821 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 505682000822 S-adenosylmethionine binding site [chemical binding]; other site 505682000823 endonuclease IV; Provisional; Region: PRK01060 505682000824 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 505682000825 AP (apurinic/apyrimidinic) site pocket; other site 505682000826 DNA interaction; other site 505682000827 Metal-binding active site; metal-binding site 505682000828 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 505682000829 Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]; Region: DnaB; COG3611 505682000830 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 505682000831 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 505682000832 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 505682000833 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 505682000834 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 505682000835 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 505682000836 RNA binding surface [nucleotide binding]; other site 505682000837 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 505682000838 active site 505682000839 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 505682000840 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 505682000841 dimer interface [polypeptide binding]; other site 505682000842 substrate binding site [chemical binding]; other site 505682000843 metal binding sites [ion binding]; metal-binding site 505682000844 FtsX-like permease family; Region: FtsX; pfam02687 505682000845 transcription termination factor NusA; Region: NusA; TIGR01953 505682000846 NusA N-terminal domain; Region: NusA_N; pfam08529 505682000847 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 505682000848 G-X-X-G motif; other site 505682000849 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 505682000850 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 505682000851 translation initiation factor IF-2; Region: IF-2; TIGR00487 505682000852 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 505682000853 G1 box; other site 505682000854 putative GEF interaction site [polypeptide binding]; other site 505682000855 GTP/Mg2+ binding site [chemical binding]; other site 505682000856 Switch I region; other site 505682000857 G2 box; other site 505682000858 G3 box; other site 505682000859 Switch II region; other site 505682000860 G4 box; other site 505682000861 G5 box; other site 505682000862 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 505682000863 Translation-initiation factor 2; Region: IF-2; pfam11987 505682000864 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 505682000865 Ribosome-binding factor A; Region: RBFA; cl00542 505682000866 Protein of unknown function DUF45; Region: DUF45; cl00636 505682000867 GTP-binding protein LepA; Provisional; Region: PRK05433 505682000868 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 505682000869 G1 box; other site 505682000870 putative GEF interaction site [polypeptide binding]; other site 505682000871 GTP/Mg2+ binding site [chemical binding]; other site 505682000872 Switch I region; other site 505682000873 G2 box; other site 505682000874 G3 box; other site 505682000875 Switch II region; other site 505682000876 G4 box; other site 505682000877 G5 box; other site 505682000878 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 505682000879 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 505682000880 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 505682000881 LemA family; Region: LemA; cl00742 505682000882 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 505682000883 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 505682000884 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 505682000885 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 505682000886 OPT oligopeptide transporter protein; Region: OPT; cl14607 505682000887 hypothetical protein; Provisional; Region: PRK09609 505682000888 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 505682000889 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage...; Region: UMPK; cd02023 505682000890 ATP-binding site [chemical binding]; other site 505682000891 Sugar specificity; other site 505682000892 Pyrimidine base specificity; other site 505682000893 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 505682000894 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 505682000895 NAD(P) binding pocket [chemical binding]; other site 505682000896 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 505682000897 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 505682000898 substrate binding site [chemical binding]; other site 505682000899 PRLI-interacting factor K; Provisional; Region: PLN03086 505682000900 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 505682000901 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 505682000902 CMP-binding site; other site 505682000903 The sites determining sugar specificity; other site 505682000904 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 505682000905 putative acyl-acceptor binding pocket; other site 505682000906 ScpA/B protein; Region: ScpA_ScpB; cl00598 505682000907 Putative transcriptional regulators (Ypuh-like); Region: DUF387; cl00612 505682000908 trigger factor; Region: tig; TIGR00115 505682000909 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 505682000910 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 505682000911 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 505682000912 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 505682000913 Walker A motif; other site 505682000914 ATP binding site [chemical binding]; other site 505682000915 Walker B motif; other site 505682000916 arginine finger; other site 505682000917 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 505682000918 RNA polymerase sigma factor; Provisional; Region: PRK05901 505682000919 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 505682000920 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 505682000921 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; cd06171 505682000922 DNA binding residues [nucleotide binding] 505682000923 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 505682000924 Uncharacterized conserved protein [Function unknown]; Region: COG0327 505682000925 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl01309 505682000926 phage transcriptional regulator, ArpU family; Region: phage_arpU; TIGR01637 505682000927 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of...; Region: PseudoU_synth_EcTruB; cd02573 505682000928 RNA binding site [nucleotide binding]; other site 505682000929 active site 505682000930 FAD synthase [Coenzyme metabolism]; Region: RibF; COG0196 505682000931 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 505682000932 active site 505682000933 nucleotide binding site [chemical binding]; other site 505682000934 HIGH motif; other site 505682000935 KMSKS motif; other site 505682000936 Riboflavin kinase; Region: Flavokinase; pfam01687 505682000937 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682000938 ABC-ATPase subunit interface; other site 505682000939 dimer interface [polypeptide binding]; other site 505682000940 putative PBP binding regions; other site 505682000941 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682000942 ABC-ATPase subunit interface; other site 505682000943 dimer interface [polypeptide binding]; other site 505682000944 putative PBP binding regions; other site 505682000945 NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11; Region: ALDH_F11_NP-GAPDH; cd07082 505682000946 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 505682000947 tetrameric interface [polypeptide binding]; other site 505682000948 activator binding site; other site 505682000949 NADP binding site [chemical binding]; other site 505682000950 substrate binding site [chemical binding]; other site 505682000951 catalytic residues [active] 505682000952 Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II...; Region: AsnA; cd00645 505682000953 dimer interface [polypeptide binding]; other site 505682000954 active site 505682000955 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 505682000956 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 505682000957 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 505682000958 putative dimer interface [polypeptide binding]; other site 505682000959 putative anticodon binding site; other site 505682000960 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 505682000961 homodimer interface [polypeptide binding]; other site 505682000962 motif 1; other site 505682000963 motif 2; other site 505682000964 active site 505682000965 motif 3; other site 505682000966 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 505682000967 Thymidine phosphorylase [Nucleotide transport and metabolism]; Region: DeoA; COG0213 505682000968 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 505682000969 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 505682000970 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; pfam07831 505682000971 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 505682000972 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 505682000973 motif 1; other site 505682000974 active site 505682000975 motif 2; other site 505682000976 motif 3; other site 505682000977 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 505682000978 DHHA1 domain; Region: DHHA1; pfam02272 505682000979 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 505682000980 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 505682000981 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 505682000982 HIGH motif; other site 505682000983 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 505682000984 active site 505682000985 KMSKS motif; other site 505682000986 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 505682000987 tRNA binding surface [nucleotide binding]; other site 505682000988 Integrase core domain; Region: rve; cl01316 505682000989 large tegument protein UL36; Provisional; Region: PHA03247 505682000990 Gram-positive type; Region: polC_Gram_pos; TIGR01405 505682000991 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 505682000992 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 505682000993 active site 505682000994 substrate binding site [chemical binding]; other site 505682000995 catalytic site [active] 505682000996 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 505682000997 DNA-binding transcriptional regulator DsdC; Provisional; Region: PRK10086 505682000998 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 505682000999 active site 505682001000 substrate binding site [chemical binding]; other site 505682001001 ATP binding site [chemical binding]; other site 505682001002 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 505682001003 substrate binding site [chemical binding]; other site 505682001004 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 505682001005 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 505682001006 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 505682001007 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 505682001008 Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Region: GpsA; COG0240 505682001009 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 505682001010 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 505682001011 GTP-binding protein Der; Reviewed; Region: PRK00093 505682001012 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 505682001013 G1 box; other site 505682001014 GTP/Mg2+ binding site [chemical binding]; other site 505682001015 Switch I region; other site 505682001016 G2 box; other site 505682001017 Switch II region; other site 505682001018 G3 box; other site 505682001019 G4 box; other site 505682001020 G5 box; other site 505682001021 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 505682001022 G1 box; other site 505682001023 GTP/Mg2+ binding site [chemical binding]; other site 505682001024 Switch I region; other site 505682001025 G2 box; other site 505682001026 G3 box; other site 505682001027 Switch II region; other site 505682001028 G4 box; other site 505682001029 G5 box; other site 505682001030 Competence protein; Region: Competence; cl00471 505682001031 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 505682001032 MraZ protein; Region: MraZ; pfam02381 505682001033 MraZ protein; Region: MraZ; pfam02381 505682001034 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 505682001035 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 505682001036 Abi-like protein; Region: Abi_2; cl01988 505682001037 DNA helicase, putative; Region: TIGR00376 505682001038 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 505682001039 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 505682001040 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 505682001041 Walker A motif; other site 505682001042 ATP binding site [chemical binding]; other site 505682001043 Walker B motif; other site 505682001044 arginine finger; other site 505682001045 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 505682001046 Walker A motif; other site 505682001047 ATP binding site [chemical binding]; other site 505682001048 Walker B motif; other site 505682001049 arginine finger; other site 505682001050 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 505682001051 ABC-2 type transporter; Region: ABC2_membrane; cl11417 505682001052 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 505682001053 Ribonuclease HIII [DNA replication, recombination, and repair]; Region: RnhC; COG1039 505682001054 bacterial Ribonuclease HIII-like; Region: RNase_HII_bacteria_HIII_like; cd06590 505682001055 RNA/DNA hybrid binding site [nucleotide binding]; other site 505682001056 active site 505682001057 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682001058 ABC-ATPase subunit interface; other site 505682001059 dimer interface [polypeptide binding]; other site 505682001060 putative PBP binding regions; other site 505682001061 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682001062 ABC-ATPase subunit interface; other site 505682001063 dimer interface [polypeptide binding]; other site 505682001064 putative PBP binding regions; other site 505682001065 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 505682001066 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 505682001067 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 505682001068 Domain of unknown function (DUF205); Region: DUF205; cl00410 505682001069 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 505682001070 dimer interface [polypeptide binding]; other site 505682001071 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 505682001072 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 505682001073 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 505682001074 HSP70 interaction site [polypeptide binding]; other site 505682001075 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 505682001076 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 505682001077 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 505682001078 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 505682001079 active site 505682001080 HIGH motif; other site 505682001081 nucleotide binding site [chemical binding]; other site 505682001082 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 505682001083 active site 505682001084 KMSKS motif; other site 505682001085 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 505682001086 tRNA binding surface [nucleotide binding]; other site 505682001087 anticodon binding site; other site 505682001088 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 505682001089 putative glycoprotease GCP; Region: bact_gcp; TIGR03723 505682001090 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 505682001091 S-adenosylmethionine synthetase; Validated; Region: PRK05250 505682001092 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 505682001093 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 505682001094 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 505682001095 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 505682001096 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 505682001097 DNA binding site [nucleotide binding] 505682001098 catalytic residue [active] 505682001099 H2TH interface [polypeptide binding]; other site 505682001100 putative catalytic residues [active] 505682001101 turnover-facilitating residue; other site 505682001102 intercalation triad [nucleotide binding]; other site 505682001103 8OG recognition residue [nucleotide binding]; other site 505682001104 putative reading head residues; other site 505682001105 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 505682001106 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 505682001107 5'-3' exonuclease; Provisional; Region: PRK14976 505682001108 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 505682001109 active site 505682001110 metal binding site 1 [ion binding]; metal-binding site 505682001111 putative 5' ssDNA interaction site; other site 505682001112 metal binding site 3; metal-binding site 505682001113 metal binding site 2 [ion binding]; metal-binding site 505682001114 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 505682001115 putative DNA binding site [nucleotide binding]; other site 505682001116 putative metal binding site [ion binding]; other site 505682001117 DNA polymerase III DnaE; Validated; Region: dnaE; PRK05898 505682001118 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 505682001119 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 505682001120 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 505682001121 DHH family; Region: DHH; pfam01368 505682001122 DHHA1 domain; Region: DHHA1; pfam02272 505682001123 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 505682001124 THUMP domain; Region: THUMP; cl12076 505682001125 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 505682001126 Ligand Binding Site [chemical binding]; other site 505682001127 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 505682001128 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 505682001129 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cl00088 505682001130 HrcA protein C terminal domain; Region: HrcA; pfam01628 505682001131 Protein of unknown function (DUF402); Region: DUF402; cl00979 505682001132 Protein of unknown function (DUF3196); Region: DUF3196; pfam11428 505682001133 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 505682001134 Ferritin-like domain; Region: Ferritin; pfam00210 505682001135 dinuclear metal binding motif [ion binding]; other site 505682001136 UreD urease accessory protein; Region: UreD; cl00530 505682001137 Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras...; Region: Ras_like_GTPase; cl10444 505682001138 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 505682001139 UreF; Region: UreF; pfam01730 505682001140 urease accessory protein UreE; Provisional; Region: PRK14112 505682001141 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-...; Region: UreE; cd00571 505682001142 dimer interface [polypeptide binding]; other site 505682001143 catalytic residues [active] 505682001144 urease subunit alpha; Reviewed; Region: ureC; PRK13207 505682001145 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 505682001146 subunit interactions [polypeptide binding]; other site 505682001147 active site 505682001148 flap region; other site 505682001149 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_beta; cd00407 505682001150 gamma-beta subunit interface [polypeptide binding]; other site 505682001151 alpha-beta subunit interface [polypeptide binding]; other site 505682001152 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 505682001153 alpha-gamma subunit interface [polypeptide binding]; other site 505682001154 beta-gamma subunit interface [polypeptide binding]; other site 505682001155 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 505682001156 ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC...; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 505682001157 Walker A/P-loop; other site 505682001158 ATP binding site [chemical binding]; other site 505682001159 Q-loop/lid; other site 505682001160 ABC transporter signature motif; other site 505682001161 Walker B; other site 505682001162 D-loop; other site 505682001163 H-loop/switch region; other site 505682001164 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 505682001165 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 505682001166 RNA binding surface [nucleotide binding]; other site 505682001167 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 505682001168 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 505682001169 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 505682001170 active site 505682001171 DNA binding site [nucleotide binding] 505682001172 Holliday junction DNA helicase ruvB N-terminus; Region: RuvB_N; pfam05496 505682001173 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 505682001174 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 505682001175 active site 505682001176 catalytic residues [active] 505682001177 Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]; Region: RuvB; COG2255 505682001178 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 505682001179 Walker A motif; other site 505682001180 ATP binding site [chemical binding]; other site 505682001181 Walker B motif; other site 505682001182 arginine finger; other site 505682001183 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 505682001184 Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]; Region: RuvA; COG0632 505682001185 Predicted integral membrane protein [Function unknown]; Region: COG0392 505682001186 prolyl-tRNA synthetase; Provisional; Region: PRK08661 505682001187 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 505682001188 dimer interface [polypeptide binding]; other site 505682001189 motif 1; other site 505682001190 active site 505682001191 motif 2; other site 505682001192 motif 3; other site 505682001193 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible...; Region: HGTP_anticodon; cl00266 505682001194 anticodon binding site; other site 505682001195 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 505682001196 trimerization site [polypeptide binding]; other site 505682001197 active site 505682001198 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 505682001199 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 505682001200 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 505682001201 catalytic residue [active] 505682001202 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 505682001203 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 505682001204 substrate binding site [chemical binding]; other site 505682001205 hexamer interface [polypeptide binding]; other site 505682001206 metal binding site [ion binding]; metal-binding site 505682001207 phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial; Region: pheT_bact; TIGR00472 505682001208 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 505682001209 putative tRNA-binding site [nucleotide binding]; other site 505682001210 B3/4 domain; Region: B3_4; cl11458 505682001211 tRNA synthetase B5 domain; Region: B5; cl08394 505682001212 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 505682001213 dimer interface [polypeptide binding]; other site 505682001214 motif 1; other site 505682001215 motif 3; other site 505682001216 motif 2; other site 505682001217 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 505682001218 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 505682001219 dimer interface [polypeptide binding]; other site 505682001220 motif 1; other site 505682001221 active site 505682001222 motif 2; other site 505682001223 motif 3; other site 505682001224 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 505682001225 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 505682001226 homodimer interface [polypeptide binding]; other site 505682001227 NAD binding pocket [chemical binding]; other site 505682001228 ATP binding pocket [chemical binding]; other site 505682001229 Mg binding site [ion binding]; other site 505682001230 active-site loop [active] 505682001231 GTPase CgtA; Reviewed; Region: obgE; PRK12297 505682001232 GTP1/OBG; Region: GTP1_OBG; pfam01018 505682001233 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 505682001234 G1 box; other site 505682001235 GTP/Mg2+ binding site [chemical binding]; other site 505682001236 Switch I region; other site 505682001237 G2 box; other site 505682001238 G3 box; other site 505682001239 Switch II region; other site 505682001240 G4 box; other site 505682001241 G5 box; other site 505682001242 Domain of unknown function (DUF1967); Region: DUF1967; cl07779 505682001243 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 505682001244 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 505682001245 putative active site [active] 505682001246 substrate binding site [chemical binding]; other site 505682001247 putative cosubstrate binding site; other site 505682001248 catalytic site [active] 505682001249 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 505682001250 substrate binding site [chemical binding]; other site 505682001251 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 505682001252 active site 505682001253 catalytic residues [active] 505682001254 metal binding site [ion binding]; metal-binding site 505682001255 Gram-positive; Region: parE_Gpos; TIGR01058 505682001256 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 505682001257 ATP binding site [chemical binding]; other site 505682001258 Mg2+ binding site [ion binding]; other site 505682001259 G-X-G motif; other site 505682001260 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 505682001261 anchoring element; other site 505682001262 dimer interface [polypeptide binding]; other site 505682001263 ATP binding site [chemical binding]; other site 505682001264 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 505682001265 active site 505682001266 putative metal-binding site [ion binding]; other site 505682001267 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 505682001268 Gram-positive; Region: parC_Gpos; TIGR01061 505682001269 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 505682001270 CAP-like domain; other site 505682001271 Active site [active] 505682001272 primary dimer interface [polypeptide binding]; other site 505682001273 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682001274 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 505682001275 ribosome biogenesis GTPase YqeH; Region: GTPase_YqeH; TIGR03597 505682001276 YqeH. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically...; Region: YqeH; cd01855 505682001277 GTP/Mg2+ binding site [chemical binding]; other site 505682001278 G4 box; other site 505682001279 G5 box; other site 505682001280 G1 box; other site 505682001281 Switch I region; other site 505682001282 G2 box; other site 505682001283 G3 box; other site 505682001284 Switch II region; other site 505682001285 putative nicotinate-nucleotide adenylyltransferase; Validated; Region: nadD; PRK07152 505682001286 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 505682001287 active site 505682001288 (T/H)XGH motif; other site 505682001289 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 505682001290 Zn2+ binding site [ion binding]; other site 505682001291 Mg2+ binding site [ion binding]; other site 505682001292 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 505682001293 DUF1410 domain; Region: DUF1410; pfam07198 505682001294 DUF1410 domain; Region: DUF1410; pfam07198 505682001295 DUF1410 domain; Region: DUF1410; pfam07198 505682001296 DUF1410 domain; Region: DUF1410; pfam07198 505682001297 DNA polymerase III PolC; Validated; Region: polC; PRK00448 505682001298 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 505682001299 DUF1410 domain; Region: DUF1410; pfam07198 505682001300 DUF1410 domain; Region: DUF1410; pfam07198 505682001301 DUF1410 domain; Region: DUF1410; pfam07198 505682001302 DUF1410 domain; Region: DUF1410; pfam07198 505682001303 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 505682001304 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 505682001305 DUF1410 domain; Region: DUF1410; pfam07198 505682001306 DUF1410 domain; Region: DUF1410; pfam07198 505682001307 DUF1410 domain; Region: DUF1410; pfam07198 505682001308 DUF1410 domain; Region: DUF1410; pfam07198 505682001309 Acetokinase family; Region: Acetate_kinase; cl01029 505682001310 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 505682001311 putative active site [active] 505682001312 putative catalytic site [active] 505682001313 putative Mg binding site IVb [ion binding]; other site 505682001314 putative phosphate binding site [ion binding]; other site 505682001315 putative DNA binding site [nucleotide binding]; other site 505682001316 putative Mg binding site IVa [ion binding]; other site 505682001317 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 505682001318 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 505682001319 GTPase [General function prediction only]; Region: Era; COG1159 505682001320 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 505682001321 G1 box; other site 505682001322 GTP/Mg2+ binding site [chemical binding]; other site 505682001323 Switch I region; other site 505682001324 G2 box; other site 505682001325 Switch II region; other site 505682001326 G3 box; other site 505682001327 G4 box; other site 505682001328 G5 box; other site 505682001329 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 505682001330 Recombination protein O N terminal; Region: RecO_N; pfam11967 505682001331 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecO; COG1381 505682001332 Recombination protein O C terminal; Region: RecO_C; pfam02565 505682001333 glycyl-tRNA synthetase; Provisional; Region: PRK04173 505682001334 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 505682001335 motif 1; other site 505682001336 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 505682001337 active site 505682001338 motif 2; other site 505682001339 motif 3; other site 505682001340 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 505682001341 anticodon binding site; other site 505682001342 DNA primase, catalytic core; Region: dnaG; TIGR01391 505682001343 CHC2 zinc finger; Region: zf-CHC2; cl02597 505682001344 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 505682001345 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 505682001346 active site 505682001347 metal binding site [ion binding]; metal-binding site 505682001348 interdomain interaction site; other site 505682001349 DUF1410 domain; Region: DUF1410; pfam07198 505682001350 DUF1410 domain; Region: DUF1410; pfam07198 505682001351 DUF1410 domain; Region: DUF1410; pfam07198 505682001352 DUF1410 domain; Region: DUF1410; pfam07198 505682001353 DUF1410 domain; Region: DUF1410; pfam07198 505682001354 DUF1410 domain; Region: DUF1410; pfam07198 505682001355 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 505682001356 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 505682001357 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 505682001358 RNA binding surface [nucleotide binding]; other site 505682001359 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 505682001360 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 505682001361 putative active site [active] 505682001362 metal binding site [ion binding]; metal-binding site 505682001363 homodimer binding site [polypeptide binding]; other site 505682001364 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 505682001365 UvrD/REP helicase; Region: UvrD-helicase; cl14126 505682001366 RDD family; Region: RDD; cl00746 505682001367 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 505682001368 active site 505682001369 Phosphopantetheine attachment site; Region: PP-binding; cl09936 505682001370 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 505682001371 multifunctional aminopeptidase A; Provisional; Region: PRK00913 505682001372 interface (dimer of trimers) [polypeptide binding]; other site 505682001373 Substrate-binding/catalytic site; other site 505682001374 Zn-binding sites [ion binding]; other site 505682001375 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 505682001376 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682001377 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 505682001378 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 505682001379 A sub-family of peptidase family C39. 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...; Region: Peptidase_C39E; cd02424 505682001380 putative active site [active] 505682001381 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682001382 ABC transporter signature motif; other site 505682001383 Walker B; other site 505682001384 D-loop; other site 505682001385 H-loop/switch region; other site 505682001386 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 505682001387 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are 'recycled' and ready for another round of...; Region: RRF; cd00520 505682001388 hinge region; other site 505682001389 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 505682001390 putative nucleotide binding site [chemical binding]; other site 505682001391 uridine monophosphate binding site [chemical binding]; other site 505682001392 homohexameric interface [polypeptide binding]; other site 505682001393 elongation factor Ts; Provisional; Region: tsf; PRK09377 505682001394 Elongation factor TS; Region: EF_TS; pfam00889 505682001395 Elongation factor TS; Region: EF_TS; pfam00889 505682001396 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cl00462 505682001397 ABC-ATPase subunit interface; other site 505682001398 dimer interface [polypeptide binding]; other site 505682001399 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist...; Region: TM_ABC_iron-siderophores_like; cd06550 505682001400 ABC-ATPase subunit interface; other site 505682001401 dimer interface [polypeptide binding]; other site 505682001402 putative PBP binding regions; other site 505682001403 Domain of unknown function DUF31; Region: DUF31; pfam01732 505682001404 Peptidase S7, Flavivirus NS3 serine protease; Region: Peptidase_S7; pfam00949 505682001405 Uncharacterized protein conserved in bacteria (DUF2188); Region: DUF2188; cl11557 505682001406 oligoendopeptidase F; Region: pepF; TIGR00181 505682001407 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 505682001408 active site 505682001409 Zn binding site [ion binding]; other site 505682001410 elongation factor Tu; Reviewed; Region: PRK00049 505682001411 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 505682001412 G1 box; other site 505682001413 GEF interaction site [polypeptide binding]; other site 505682001414 GTP/Mg2+ binding site [chemical binding]; other site 505682001415 Switch I region; other site 505682001416 G2 box; other site 505682001417 G3 box; other site 505682001418 Switch II region; other site 505682001419 G4 box; other site 505682001420 G5 box; other site 505682001421 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 505682001422 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 505682001423 Antibiotic Binding Site [chemical binding]; other site 505682001424 elongation factor G; Reviewed; Region: PRK00007 505682001425 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 505682001426 G1 box; other site 505682001427 putative GEF interaction site [polypeptide binding]; other site 505682001428 GTP/Mg2+ binding site [chemical binding]; other site 505682001429 Switch I region; other site 505682001430 G2 box; other site 505682001431 G3 box; other site 505682001432 Switch II region; other site 505682001433 G4 box; other site 505682001434 G5 box; other site 505682001435 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 505682001436 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 505682001437 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 505682001438 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 505682001439 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 505682001440 S17 interaction site [polypeptide binding]; other site 505682001441 S8 interaction site; other site 505682001442 16S rRNA interaction site [nucleotide binding]; other site 505682001443 streptomycin interaction site [chemical binding]; other site 505682001444 23S rRNA interaction site [nucleotide binding]; other site 505682001445 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 505682001446 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 505682001447 Protein of unknown function DUF262; Region: DUF262; cl14890 505682001448 Protein of unknown function DUF262; Region: DUF262; cl14890 505682001449 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 505682001450 DNA binding site [nucleotide binding] 505682001451 substrate interaction site [chemical binding]; other site 505682001452 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 505682001453 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 505682001454 DNA binding site [nucleotide binding] 505682001455 Int/Topo IB signature motif; other site 505682001456 active site 505682001457 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 505682001458 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-...; Region: PGM2; cd05799 505682001459 active site 505682001460 substrate binding site [chemical binding]; other site 505682001461 metal binding site [ion binding]; metal-binding site 505682001462 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 505682001463 active site 505682001464 catalytic motif [active] 505682001465 Zn binding site [ion binding]; other site 505682001466 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 505682001467 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 505682001468 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 505682001469 active site 505682001470 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 505682001471 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 505682001472 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 505682001473 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 505682001474 active site 505682001475 dimer interface [polypeptide binding]; other site 505682001476 motif 1; other site 505682001477 motif 2; other site 505682001478 motif 3; other site 505682001479 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 505682001480 anticodon binding site; other site 505682001481 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 505682001482 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 505682001483 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1)...; Region: PseudoU_synth_EcTruA; cd02570 505682001484 dimerization interface 3.5A [polypeptide binding]; other site 505682001485 active site 505682001486 Cobalt transport protein; Region: CbiQ; cl00463 505682001487 Cobalt transport protein; Region: CbiQ; cl00463 505682001488 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682001489 Walker A/P-loop; other site 505682001490 ATP binding site [chemical binding]; other site 505682001491 Q-loop/lid; other site 505682001492 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 505682001493 Q-loop/lid; other site 505682001494 ABC transporter signature motif; other site 505682001495 Walker B; other site 505682001496 D-loop; other site 505682001497 H-loop/switch region; other site 505682001498 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13632 505682001499 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 505682001500 Walker A/P-loop; other site 505682001501 ATP binding site [chemical binding]; other site 505682001502 Q-loop/lid; other site 505682001503 ABC transporter signature motif; other site 505682001504 Walker B; other site 505682001505 D-loop; other site 505682001506 H-loop/switch region; other site 505682001507 Cobalt ATP-binding cassette C terminal; Region: CoABC_C; pfam12370 505682001508 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 505682001509 mRNA/rRNA interface [nucleotide binding]; other site 505682001510 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 505682001511 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 505682001512 23S rRNA interface [nucleotide binding]; other site 505682001513 L7/L12 interface [polypeptide binding]; other site 505682001514 putative thiostrepton binding site; other site 505682001515 L25 interface [polypeptide binding]; other site 505682001516 FtsX-like permease family; Region: FtsX; pfam02687 505682001517 DUF1410 domain; Region: DUF1410; pfam07198 505682001518 DUF1410 domain; Region: DUF1410; pfam07198 505682001519 FtsX-like permease family; Region: FtsX; pfam02687 505682001520 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 505682001521 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 505682001522 GatB domain; Region: GatB_Yqey; cl11497 505682001523 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 505682001524 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 505682001525 hypothetical protein; Provisional; Region: PRK09609 505682001526 hypothetical protein; Provisional; Region: PRK09609 505682001527 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 505682001528 replicative DNA helicase; Region: DnaB; TIGR00665 505682001529 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 505682001530 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 505682001531 Walker A motif; other site 505682001532 ATP binding site [chemical binding]; other site 505682001533 Walker B motif; other site 505682001534 DNA binding loops [nucleotide binding] 505682001535 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 505682001536 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 505682001537 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 505682001538 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 505682001539 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 505682001540 dimer interface [polypeptide binding]; other site 505682001541 ssDNA binding site [nucleotide binding]; other site 505682001542 tetramer (dimer of dimers) interface [polypeptide binding]; other site 505682001543 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 505682001544 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 505682001545 Coenzyme A binding pocket [chemical binding]; other site 505682001546 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 505682001547 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 505682001548 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 505682001549 Membrane fusion protein Use1; Region: Use1; pfam09753 505682001550 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 505682001551 Walker A/P-loop; other site 505682001552 ATP binding site [chemical binding]; other site 505682001553 Q-loop/lid; other site 505682001554 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SapF; COG4167 505682001555 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 505682001556 ABC transporter signature motif; other site 505682001557 Walker B; other site 505682001558 D-loop; other site 505682001559 H-loop/switch region; other site 505682001560 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 505682001561 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 505682001562 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 505682001563 Walker A/P-loop; other site 505682001564 ATP binding site [chemical binding]; other site 505682001565 Q-loop/lid; other site 505682001566 ABC transporter signature motif; other site 505682001567 Walker B; other site 505682001568 D-loop; other site 505682001569 H-loop/switch region; other site 505682001570 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 505682001571 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 505682001572 dimer interface [polypeptide binding]; other site 505682001573 conserved gate region; other site 505682001574 putative PBP binding loops; other site 505682001575 ABC-ATPase subunit interface; other site 505682001576 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 505682001577 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 505682001578 dimer interface [polypeptide binding]; other site 505682001579 conserved gate region; other site 505682001580 putative PBP binding loops; other site 505682001581 ABC-ATPase subunit interface; other site 505682001582 Uncharacterized conserved protein [Function unknown]; Region: COG1284 505682001583 Uncharacterized conserved protein [Function unknown]; Region: COG1284 505682001584 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 505682001585 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 505682001586 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 505682001587 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 505682001588 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; Region: Cof-subfamily; TIGR00099 505682001589 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 505682001590 active site 505682001591 motif I; other site 505682001592 motif II; other site 505682001593 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 505682001594 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 505682001595 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 505682001596 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 505682001597 DNA helicase, putative; Region: TIGR00376 505682001598 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 505682001599 Ion channel; Region: Ion_trans_2; cl11596 505682001600 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 505682001601 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 505682001602 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 505682001603 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 505682001604 23S rRNA interface [nucleotide binding]; other site 505682001605 L3 interface [polypeptide binding]; other site 505682001606 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 505682001607 NusG family protein; Region: NusG_myco; TIGR01956 505682001608 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 505682001609 putative homodimer interface [polypeptide binding]; other site 505682001610 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 505682001611 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 505682001612 ATP binding site [chemical binding]; other site 505682001613 putative Mg++ binding site [ion binding]; other site 505682001614 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 505682001615 nucleotide binding region [chemical binding]; other site 505682001616 ATP-binding site [chemical binding]; other site 505682001617 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 505682001618 MatE; Region: MatE; pfam01554 505682001619 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 505682001620 MatE; Region: MatE; pfam01554 505682001621 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 505682001622 intersubunit interface [polypeptide binding]; other site 505682001623 active site 505682001624 catalytic residue [active] 505682001625 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 505682001626 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 505682001627 TPP-binding site [chemical binding]; other site 505682001628 dimer interface [polypeptide binding]; other site 505682001629 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 505682001630 PYR/PP interface [polypeptide binding]; other site 505682001631 dimer interface [polypeptide binding]; other site 505682001632 TPP binding site [chemical binding]; other site 505682001633 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 505682001634 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 505682001635 dimerization domain swap beta strand [polypeptide binding]; other site 505682001636 regulatory protein interface [polypeptide binding]; other site 505682001637 active site 505682001638 regulatory phosphorylation site [posttranslational modification]; other site 505682001639 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 505682001640 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 505682001641 putative active site [active] 505682001642 catalytic site [active] 505682001643 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_2; cd09112 505682001644 putative active site [active] 505682001645 catalytic site [active] 505682001646 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 505682001647 catalytic residues [active] 505682001648 DNA topoisomerase I; Validated; Region: PRK05582 505682001649 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 505682001650 active site 505682001651 interdomain interaction site; other site 505682001652 putative metal-binding site [ion binding]; other site 505682001653 nucleotide binding site [chemical binding]; other site 505682001654 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 505682001655 domain I; other site 505682001656 DNA binding groove [nucleotide binding] 505682001657 phosphate binding site [ion binding]; other site 505682001658 domain II; other site 505682001659 domain III; other site 505682001660 nucleotide binding site [chemical binding]; other site 505682001661 catalytic site [active] 505682001662 domain IV; other site 505682001663 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 505682001664 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 505682001665 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 505682001666 DNA recombination-mediator protein A; Region: DNA_processg_A; cl00695 505682001667 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 505682001668 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 505682001669 GTP/Mg2+ binding site [chemical binding]; other site 505682001670 G4 box; other site 505682001671 G5 box; other site 505682001672 G1 box; other site 505682001673 Switch I region; other site 505682001674 G2 box; other site 505682001675 G3 box; other site 505682001676 Switch II region; other site 505682001677 Thymidine kinase; Region: TK; cl00631 505682001678 GTP-binding protein YchF; Reviewed; Region: PRK09601 505682001679 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 505682001680 G1 box; other site 505682001681 GTP/Mg2+ binding site [chemical binding]; other site 505682001682 Switch I region; other site 505682001683 G2 box; other site 505682001684 Switch II region; other site 505682001685 G3 box; other site 505682001686 G4 box; other site 505682001687 G5 box; other site 505682001688 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 505682001689 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 505682001690 hypothetical protein; Provisional; Region: PRK08185 505682001691 intersubunit interface [polypeptide binding]; other site 505682001692 active site 505682001693 zinc binding site [ion binding]; other site 505682001694 Na+ binding site [ion binding]; other site 505682001695 DNA-directed RNA polymerase delta subunit; Region: RNA_pol_delta; cl01319 505682001696 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 505682001697 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 505682001698 Zn2+ binding site [ion binding]; other site 505682001699 Mg2+ binding site [ion binding]; other site 505682001700 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 505682001701 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 505682001702 HIGH motif; other site 505682001703 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 505682001704 active site 505682001705 KMSKS motif; other site 505682001706 hypothetical protein; Provisional; Region: PRK05905 505682001707 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 505682001708 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 505682001709 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 505682001710 Ribonuclease P; Region: Ribonuclease_P; cl00457 505682001711 Ribosomal protein L34; Region: Ribosomal_L34; cl00370