-- dump date 20111121_010342 -- class Genbank::misc_feature -- table misc_feature_note -- id note 322098000001 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 322098000002 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 322098000003 Walker A motif; other site 322098000004 ATP binding site [chemical binding]; other site 322098000005 Walker B motif; other site 322098000006 arginine finger; other site 322098000007 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 322098000008 DnaA box-binding interface [nucleotide binding]; other site 322098000009 DNA polymerase III subunit beta; Provisional; Region: PRK14944 322098000010 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 322098000011 putative DNA binding surface [nucleotide binding]; other site 322098000012 dimer interface [polypeptide binding]; other site 322098000013 beta-clamp/clamp loader binding surface; other site 322098000014 beta-clamp/translesion DNA polymerase binding surface; other site 322098000015 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 322098000016 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 322098000017 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 322098000018 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional; Region: PRK14538 322098000019 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 322098000020 DHH family; Region: DHH; pfam01368 322098000021 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 322098000022 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 322098000023 replicative DNA helicase; Region: DnaB; TIGR00665 322098000024 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 322098000025 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 322098000026 Walker A motif; other site 322098000027 ATP binding site [chemical binding]; other site 322098000028 Walker B motif; other site 322098000029 DNA binding loops [nucleotide binding] 322098000030 peptide chain release factor 1; Region: prfA; TIGR00019 322098000031 RF-1 domain; Region: RF-1; cl02875 322098000032 RF-1 domain; Region: RF-1; cl02875 322098000033 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 322098000034 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 322098000035 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 322098000036 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 322098000037 G1 box; other site 322098000038 GTP/Mg2+ binding site [chemical binding]; other site 322098000039 Switch I region; other site 322098000040 G2 box; other site 322098000041 G3 box; other site 322098000042 Switch II region; other site 322098000043 G4 box; other site 322098000044 G5 box; other site 322098000045 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 322098000046 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098000047 active site 322098000048 HIGH motif; other site 322098000049 nucleotide binding site [chemical binding]; other site 322098000050 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098000051 active site 322098000052 KMSKS motif; other site 322098000053 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 322098000054 tRNA binding surface [nucleotide binding]; other site 322098000055 anticodon binding site; other site 322098000056 Protein of unknown function (DUF1393); Region: DUF1393; cl01942 322098000057 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 322098000058 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 322098000059 Walker A/P-loop; other site 322098000060 ATP binding site [chemical binding]; other site 322098000061 Q-loop/lid; other site 322098000062 ABC transporter signature motif; other site 322098000063 Walker B; other site 322098000064 D-loop; other site 322098000065 H-loop/switch region; other site 322098000066 ATP-binding cassette cobalt transporter; Region: DUF3744; pfam12558 322098000067 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 322098000068 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 322098000069 Walker A/P-loop; other site 322098000070 ATP binding site [chemical binding]; other site 322098000071 Q-loop/lid; other site 322098000072 ABC transporter signature motif; other site 322098000073 Walker B; other site 322098000074 D-loop; other site 322098000075 H-loop/switch region; other site 322098000076 Cobalt transport protein; Region: CbiQ; cl00463 322098000077 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 322098000078 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 322098000079 putative dimer interface [polypeptide binding]; other site 322098000080 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 322098000081 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 322098000082 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 322098000083 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 322098000084 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 322098000085 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 322098000086 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07632 322098000087 Ribonucleotide reductase N-terminal; Region: RNR_N; pfam08343 322098000088 Class I ribonucleotide reductase; Region: RNR_I; cd01679 322098000089 active site 322098000090 dimer interface [polypeptide binding]; other site 322098000091 catalytic residues [active] 322098000092 effector binding site; other site 322098000093 R2 peptide binding site; other site 322098000094 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 322098000095 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 322098000096 dimer interface [polypeptide binding]; other site 322098000097 putative radical transfer pathway; other site 322098000098 diiron center [ion binding]; other site 322098000099 tyrosyl radical; other site 322098000100 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 322098000101 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 322098000102 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 322098000103 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000104 Walker A/P-loop; other site 322098000105 ATP binding site [chemical binding]; other site 322098000106 Q-loop/lid; other site 322098000107 ABC transporter signature motif; other site 322098000108 Walker B; other site 322098000109 D-loop; other site 322098000110 H-loop/switch region; other site 322098000111 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 322098000112 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 322098000113 Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide...; Region: ABCC_Glucan_exporter_like; cd03254 322098000114 Walker A/P-loop; other site 322098000115 ATP binding site [chemical binding]; other site 322098000116 Q-loop/lid; other site 322098000117 ABC transporter signature motif; other site 322098000118 Walker B; other site 322098000119 D-loop; other site 322098000120 H-loop/switch region; other site 322098000121 putative transposase OrfB; Reviewed; Region: PHA02517 322098000122 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000123 exodeoxyribonuclease V, alpha subunit; Region: recD; TIGR01447 322098000124 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 322098000125 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000126 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 322098000127 active site 322098000128 metal binding site [ion binding]; metal-binding site 322098000129 interdomain interaction site; other site 322098000130 Integrase core domain; Region: rve; cl01316 322098000131 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 322098000132 Malic enzyme, N-terminal domain; Region: malic; pfam00390 322098000133 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 322098000134 putative NAD(P) binding site [chemical binding]; other site 322098000135 2-hydroxycarboxylate transporter family; Region: 2HCT; cl01386 322098000136 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 322098000137 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (...; Region: DEADc; cd00268 322098000138 DEAD-like helicases superfamily; Region: DEXDc; smart00487 322098000139 ATP binding site [chemical binding]; other site 322098000140 Mg++ binding site [ion binding]; other site 322098000141 motif III; other site 322098000142 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 322098000143 nucleotide binding region [chemical binding]; other site 322098000144 ATP-binding site [chemical binding]; other site 322098000145 heat shock gene repressor HrcA; Region: hrcA; TIGR00331 322098000146 HrcA protein C terminal domain; Region: HrcA; pfam01628 322098000147 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 322098000148 dimer interface [polypeptide binding]; other site 322098000149 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 322098000150 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 322098000151 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 322098000152 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 322098000153 HSP70 interaction site [polypeptide binding]; other site 322098000154 DnaJ central domain; Region: DnaJ_CXXCXGXG; cl14908 322098000155 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 322098000156 DnaJ C terminal domain; Region: DnaJ_C; pfam01556 322098000157 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 322098000158 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 322098000159 P loop; other site 322098000160 GTP binding site [chemical binding]; other site 322098000161 signal recognition particle protein; Provisional; Region: PRK10867 322098000162 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 322098000163 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 322098000164 P loop; other site 322098000165 GTP binding site [chemical binding]; other site 322098000166 Signal peptide binding domain; Region: SRP_SPB; pfam02978 322098000167 5'-3' exonuclease; Provisional; Region: PRK14976 322098000168 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 322098000169 active site 322098000170 metal binding site 1 [ion binding]; metal-binding site 322098000171 putative 5' ssDNA interaction site; other site 322098000172 metal binding site 3; metal-binding site 322098000173 metal binding site 2 [ion binding]; metal-binding site 322098000174 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 322098000175 putative DNA binding site [nucleotide binding]; other site 322098000176 putative metal binding site [ion binding]; other site 322098000177 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 322098000178 active site 322098000179 substrate binding site [chemical binding]; other site 322098000180 catalytic site [active] 322098000181 DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]; Region: PolA; COG0749 322098000182 Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A; cl02626 322098000183 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 322098000184 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 322098000185 DNA binding site [nucleotide binding] 322098000186 catalytic residue [active] 322098000187 H2TH interface [polypeptide binding]; other site 322098000188 putative catalytic residues [active] 322098000189 turnover-facilitating residue; other site 322098000190 intercalation triad [nucleotide binding]; other site 322098000191 8OG recognition residue [nucleotide binding]; other site 322098000192 putative reading head residues; other site 322098000193 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 322098000194 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 322098000195 Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]; Region: DnaB; COG3611 322098000196 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000197 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein...; Region: CSP_CDS; cd04458 322098000198 DNA-binding site [nucleotide binding]; DNA binding site 322098000199 RNA-binding motif; other site 322098000200 Thymidylate kinase [Nucleotide transport and metabolism]; Region: Tmk; COG0125 322098000201 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 322098000202 TMP-binding site; other site 322098000203 ATP-binding site [chemical binding]; other site 322098000204 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000205 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000206 Walker B motif; other site 322098000207 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000208 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000209 UvrD/REP helicase; Region: UvrD-helicase; cl14126 322098000210 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 322098000211 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 322098000212 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 322098000213 active site 322098000214 metal binding site [ion binding]; metal-binding site 322098000215 interdomain interaction site; other site 322098000216 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 322098000217 DAK2 domain; Region: Dak2; cl03685 322098000218 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 322098000219 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 322098000220 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 322098000221 dimer interface [polypeptide binding]; other site 322098000222 conserved gate region; other site 322098000223 putative PBP binding loops; other site 322098000224 ABC-ATPase subunit interface; other site 322098000225 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 322098000226 dimer interface [polypeptide binding]; other site 322098000227 conserved gate region; other site 322098000228 putative PBP binding loops; other site 322098000229 ABC-ATPase subunit interface; other site 322098000230 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000231 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 322098000232 Walker A/P-loop; other site 322098000233 ATP binding site [chemical binding]; other site 322098000234 Q-loop/lid; other site 322098000235 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000236 ABC transporter signature motif; other site 322098000237 Walker B; other site 322098000238 D-loop; other site 322098000239 H-loop/switch region; other site 322098000240 TOBE domain; Region: TOBE_2; cl01440 322098000241 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 322098000242 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 322098000243 Walker A motif; other site 322098000244 ATP binding site [chemical binding]; other site 322098000245 Walker B motif; other site 322098000246 arginine finger; other site 322098000247 Peptidase family M41; Region: Peptidase_M41; pfam01434 322098000248 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 322098000249 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 322098000250 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 322098000251 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 322098000252 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 322098000253 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 322098000254 active site 322098000255 motif I; other site 322098000256 motif II; other site 322098000257 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 322098000258 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 322098000259 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 322098000260 ribonuclease HIII; Provisional; Region: PRK00996 322098000261 Domain of unknown function (DUF3378); Region: DUF3378; pfam11858 322098000262 bacterial Ribonuclease HIII-like; Region: RNase_HII_bacteria_HIII_like; cd06590 322098000263 RNA/DNA hybrid binding site [nucleotide binding]; other site 322098000264 active site 322098000265 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 322098000266 HIT family signature motif; other site 322098000267 catalytic residue [active] 322098000268 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 322098000269 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 322098000270 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 322098000271 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000272 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 322098000273 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 322098000274 DNA binding residues [nucleotide binding] 322098000275 DNA primase, catalytic core; Region: dnaG; TIGR01391 322098000276 CHC2 zinc finger; Region: zf-CHC2; cl02597 322098000277 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 322098000278 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 322098000279 active site 322098000280 metal binding site [ion binding]; metal-binding site 322098000281 interdomain interaction site; other site 322098000282 glycyl-tRNA synthetase; Provisional; Region: PRK04173 322098000283 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 322098000284 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 322098000285 active site 322098000286 motif 2; other site 322098000287 motif 3; other site 322098000288 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 322098000289 anticodon binding site; other site 322098000290 GTPase Era; Reviewed; Region: era; PRK00089 322098000291 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 322098000292 G1 box; other site 322098000293 GTP/Mg2+ binding site [chemical binding]; other site 322098000294 Switch I region; other site 322098000295 G2 box; other site 322098000296 Switch II region; other site 322098000297 G3 box; other site 322098000298 G4 box; other site 322098000299 G5 box; other site 322098000300 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 322098000301 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 322098000302 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 322098000303 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000304 UvrD/REP helicase; Region: UvrD-helicase; cl14126 322098000305 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 322098000306 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 322098000307 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098000308 active site 322098000309 HIGH motif; other site 322098000310 nucleotide binding site [chemical binding]; other site 322098000311 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098000312 active site 322098000313 KMSKS motif; other site 322098000314 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 322098000315 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 322098000316 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 322098000317 Walker A motif; other site 322098000318 ATP binding site [chemical binding]; other site 322098000319 Walker B motif; other site 322098000320 arginine finger; other site 322098000321 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 322098000322 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 322098000323 DNA-directed RNA polymerase delta subunit; Region: RNA_pol_delta; cl01319 322098000324 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 322098000325 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 322098000326 CTP synthetase; Validated; Region: pyrG; PRK05380 322098000327 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 322098000328 Catalytic site [active] 322098000329 Active site [active] 322098000330 UTP binding site [chemical binding]; other site 322098000331 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 322098000332 active site 322098000333 putative oxyanion hole; other site 322098000334 catalytic triad [active] 322098000335 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 322098000336 substrate binding pocket [chemical binding]; other site 322098000337 membrane-bound complex binding site; other site 322098000338 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 322098000339 dimer interface [polypeptide binding]; other site 322098000340 conserved gate region; other site 322098000341 putative PBP binding loops; other site 322098000342 ABC-ATPase subunit interface; other site 322098000343 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 322098000344 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 322098000345 dimer interface [polypeptide binding]; other site 322098000346 putative anticodon binding site; other site 322098000347 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 322098000348 motif 1; other site 322098000349 active site 322098000350 motif 2; other site 322098000351 motif 3; other site 322098000352 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 322098000353 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 322098000354 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 322098000355 DNA polymerase III subunit alpha; Reviewed; Region: PRK07373 322098000356 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 322098000357 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 322098000358 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 322098000359 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 322098000360 dimer interface [polypeptide binding]; other site 322098000361 motif 1; other site 322098000362 active site 322098000363 motif 2; other site 322098000364 motif 3; other site 322098000365 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 322098000366 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 322098000367 putative tRNA-binding site [nucleotide binding]; other site 322098000368 B3/4 domain; Region: B3_4; cl11458 322098000369 tRNA synthetase B5 domain; Region: B5; cl08394 322098000370 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 322098000371 dimer interface [polypeptide binding]; other site 322098000372 motif 1; other site 322098000373 motif 3; other site 322098000374 motif 2; other site 322098000375 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 322098000376 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 322098000377 cell division ATP-binding protein FtsE; Region: FtsE; TIGR02673 322098000378 Walker A/P-loop; other site 322098000379 ATP binding site [chemical binding]; other site 322098000380 Q-loop/lid; other site 322098000381 ABC transporter signature motif; other site 322098000382 Walker B; other site 322098000383 D-loop; other site 322098000384 H-loop/switch region; other site 322098000385 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 322098000386 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 322098000387 TPP-binding site [chemical binding]; other site 322098000388 tetramer interface [polypeptide binding]; other site 322098000389 heterodimer interface [polypeptide binding]; other site 322098000390 phosphorylation loop region [posttranslational modification] 322098000391 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 322098000392 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 322098000393 alpha subunit interface [polypeptide binding]; other site 322098000394 TPP binding site [chemical binding]; other site 322098000395 heterodimer interface [polypeptide binding]; other site 322098000396 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 322098000397 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 322098000398 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 322098000399 E3 interaction surface; other site 322098000400 lipoyl attachment site [posttranslational modification]; other site 322098000401 e3 binding domain; Region: E3_binding; pfam02817 322098000402 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 322098000403 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 322098000404 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 322098000405 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 322098000406 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 322098000407 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 322098000408 putative deoxyribonuclease YjjV; Provisional; Region: PRK11449 322098000409 active site 322098000410 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 322098000411 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 322098000412 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 322098000413 dimerization interface [polypeptide binding]; other site 322098000414 active site 322098000415 metal binding site [ion binding]; metal-binding site 322098000416 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 322098000417 Putative primosome component and related proteins [DNA replication, recombination, and repair]; Region: DnaD; COG3935 322098000418 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000419 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000420 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000421 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 322098000422 dimer interface [polypeptide binding]; other site 322098000423 ssDNA binding site [nucleotide binding]; other site 322098000424 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098000425 Geminivirus Rep catalytic domain; Region: Gemini_AL1; pfam00799 322098000426 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000427 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000428 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000429 Integrase core domain; Region: rve; cl01316 322098000430 Integrase core domain; Region: rve; cl01316 322098000431 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000432 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000433 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000434 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 322098000435 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 322098000436 active site 322098000437 metal binding site [ion binding]; metal-binding site 322098000438 interdomain interaction site; other site 322098000439 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000440 Walker A motif; other site 322098000441 ATP binding site [chemical binding]; other site 322098000442 Walker B motif; other site 322098000443 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 322098000444 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 322098000445 Thymidylate kinase; Region: Thymidylate_kin; pfam02223 322098000446 TMP-binding site; other site 322098000447 ATP-binding site [chemical binding]; other site 322098000448 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000449 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 322098000450 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 322098000451 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 322098000452 Walker A motif; other site 322098000453 ATP binding site [chemical binding]; other site 322098000454 Walker B motif; other site 322098000455 arginine finger; other site 322098000456 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; cl00257 322098000457 IHF - DNA interface [nucleotide binding]; other site 322098000458 IHF dimer interface [polypeptide binding]; other site 322098000459 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 322098000460 dimer interface [polypeptide binding]; other site 322098000461 ssDNA binding site [nucleotide binding]; other site 322098000462 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098000463 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 322098000464 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000465 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000466 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000467 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000468 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000469 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 322098000470 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 322098000471 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 322098000472 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 322098000473 IHF dimer interface [polypeptide binding]; other site 322098000474 IHF - DNA interface [nucleotide binding]; other site 322098000475 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 322098000476 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 322098000477 Walker A motif; other site 322098000478 ATP binding site [chemical binding]; other site 322098000479 Walker B motif; other site 322098000480 arginine finger; other site 322098000481 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 322098000482 putative transposase OrfB; Reviewed; Region: PHA02517 322098000483 Integrase core domain; Region: rve; cl01316 322098000484 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 322098000485 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 322098000486 active site 322098000487 metal binding site [ion binding]; metal-binding site 322098000488 interdomain interaction site; other site 322098000489 Replicative DNA helicase [DNA replication, recombination, and repair]; Region: DnaB; COG0305 322098000490 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000491 Walker A motif; other site 322098000492 ATP binding site [chemical binding]; other site 322098000493 Walker B motif; other site 322098000494 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 322098000495 Thymidylate kinase; Region: Thymidylate_kin; pfam02223 322098000496 TMP-binding site; other site 322098000497 ATP-binding site [chemical binding]; other site 322098000498 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000499 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 322098000500 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 322098000501 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 322098000502 Walker A motif; other site 322098000503 ATP binding site [chemical binding]; other site 322098000504 Walker B motif; other site 322098000505 arginine finger; other site 322098000506 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 322098000507 IHF dimer interface [polypeptide binding]; other site 322098000508 IHF - DNA interface [nucleotide binding]; other site 322098000509 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 322098000510 dimer interface [polypeptide binding]; other site 322098000511 ssDNA binding site [nucleotide binding]; other site 322098000512 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098000513 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 322098000514 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000515 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 322098000516 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000517 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 322098000518 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 322098000519 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 322098000520 RNA binding surface [nucleotide binding]; other site 322098000521 magnesium-transporting ATPase; Provisional; Region: PRK15122 322098000522 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 322098000523 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 322098000524 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 322098000525 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 322098000526 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 322098000527 Uncharacterised protein, DegV family COG1307; Region: DegV; cl00577 322098000528 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 322098000529 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cl00233 322098000530 ATP binding site [chemical binding]; other site 322098000531 UGMP family protein; Validated; Region: PRK09604 322098000532 UGMP family protein; Validated; Region: PRK09604 322098000533 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 322098000534 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 322098000535 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 322098000536 DNA gyrase subunit A; Validated; Region: PRK05560 322098000537 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 322098000538 CAP-like domain; other site 322098000539 Active site [active] 322098000540 primary dimer interface [polypeptide binding]; other site 322098000541 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 322098000542 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 322098000543 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 322098000544 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 322098000545 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 322098000546 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 322098000547 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 322098000548 ATP binding site [chemical binding]; other site 322098000549 Mg2+ binding site [ion binding]; other site 322098000550 G-X-G motif; other site 322098000551 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 322098000552 anchoring element; other site 322098000553 dimer interface [polypeptide binding]; other site 322098000554 ATP binding site [chemical binding]; other site 322098000555 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 322098000556 active site 322098000557 metal binding site [ion binding]; metal-binding site 322098000558 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 322098000559 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 322098000560 dimer interface [polypeptide binding]; other site 322098000561 conserved gate region; other site 322098000562 putative PBP binding loops; other site 322098000563 ABC-ATPase subunit interface; other site 322098000564 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 322098000565 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 322098000566 substrate binding pocket [chemical binding]; other site 322098000567 membrane-bound complex binding site; other site 322098000568 hinge residues; other site 322098000569 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 322098000570 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 322098000571 Walker A/P-loop; other site 322098000572 ATP binding site [chemical binding]; other site 322098000573 Q-loop/lid; other site 322098000574 ABC transporter signature motif; other site 322098000575 Walker B; other site 322098000576 D-loop; other site 322098000577 H-loop/switch region; other site 322098000578 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 322098000579 dimer interface [polypeptide binding]; other site 322098000580 conserved gate region; other site 322098000581 putative PBP binding loops; other site 322098000582 ABC-ATPase subunit interface; other site 322098000583 Geminivirus Rep catalytic domain; Region: Gemini_AL1; pfam00799 322098000584 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000585 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000586 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 322098000587 dimer interface [polypeptide binding]; other site 322098000588 ssDNA binding site [nucleotide binding]; other site 322098000589 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098000590 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; cl00257 322098000591 IHF - DNA interface [nucleotide binding]; other site 322098000592 IHF dimer interface [polypeptide binding]; other site 322098000593 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 322098000594 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 322098000595 Walker A motif; other site 322098000596 ATP binding site [chemical binding]; other site 322098000597 Walker B motif; other site 322098000598 arginine finger; other site 322098000599 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 322098000600 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 322098000601 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 322098000602 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000603 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000604 thymidylate kinase; Validated; Region: tmk; PRK00698 322098000605 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 322098000606 TMP-binding site; other site 322098000607 ATP-binding site [chemical binding]; other site 322098000608 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000609 Walker A motif; other site 322098000610 ATP binding site [chemical binding]; other site 322098000611 Walker B motif; other site 322098000612 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 322098000613 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 322098000614 active site 322098000615 metal binding site [ion binding]; metal-binding site 322098000616 interdomain interaction site; other site 322098000617 putative transposase OrfB; Reviewed; Region: PHA02517 322098000618 Integrase core domain; Region: rve; cl01316 322098000619 recombination factor protein RarA; Reviewed; Region: PRK13342 322098000620 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 322098000621 Walker A motif; other site 322098000622 ATP binding site [chemical binding]; other site 322098000623 Walker B motif; other site 322098000624 arginine finger; other site 322098000625 MgsA AAA+ ATPase C terminal; Region: MgsA_C; cl13440 322098000626 putative transposase OrfB; Reviewed; Region: PHA02517 322098000627 Integrase core domain; Region: rve; cl01316 322098000628 UvrD/REP helicase; Region: UvrD-helicase; cl14126 322098000629 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000630 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000631 putative transposase OrfB; Reviewed; Region: PHA02517 322098000632 Integrase core domain; Region: rve; cl01316 322098000633 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_18; cd04677 322098000634 nudix motif; other site 322098000635 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 322098000636 SecA preprotein cross-linking domain; Region: SecA_PP_bind; pfam01043 322098000637 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 322098000638 nucleotide binding region [chemical binding]; other site 322098000639 ATP-binding site [chemical binding]; other site 322098000640 peptide chain release factor 2; Validated; Region: prfB; PRK00578 322098000641 RF-1 domain; Region: RF-1; cl02875 322098000642 RF-1 domain; Region: RF-1; cl02875 322098000643 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 322098000644 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 322098000645 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 322098000646 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 322098000647 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 322098000648 active site 322098000649 HIGH motif; other site 322098000650 dimer interface [polypeptide binding]; other site 322098000651 KMSKS motif; other site 322098000652 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 322098000653 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 322098000654 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 322098000655 catalytic residue [active] 322098000656 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 322098000657 trimerization site [polypeptide binding]; other site 322098000658 active site 322098000659 tryptophanyl-tRNA synthetase; Region: trpS; TIGR00233 322098000660 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 322098000661 active site 322098000662 HIGH motif; other site 322098000663 dimer interface [polypeptide binding]; other site 322098000664 KMSKS motif; other site 322098000665 DNA polymerase III PolC; Validated; Region: polC; PRK00448 322098000666 Gram-positive type; Region: polC_Gram_pos; TIGR01405 322098000667 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 322098000668 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 322098000669 active site 322098000670 substrate binding site [chemical binding]; other site 322098000671 catalytic site [active] 322098000672 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 322098000673 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 322098000674 dimer interface [polypeptide binding]; other site 322098000675 conserved gate region; other site 322098000676 putative PBP binding loops; other site 322098000677 ABC-ATPase subunit interface; other site 322098000678 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 322098000679 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 322098000680 substrate binding pocket [chemical binding]; other site 322098000681 membrane-bound complex binding site; other site 322098000682 hinge residues; other site 322098000683 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 322098000684 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 322098000685 dimer interface [polypeptide binding]; other site 322098000686 conserved gate region; other site 322098000687 putative PBP binding loops; other site 322098000688 ABC-ATPase subunit interface; other site 322098000689 arginyl-tRNA synthetase; Reviewed; Region: PRK12451 322098000690 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 322098000691 active site 322098000692 HIGH motif; other site 322098000693 KMSK motif region; other site 322098000694 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 322098000695 tRNA binding surface [nucleotide binding]; other site 322098000696 anticodon binding site; other site 322098000697 endonuclease IV; Provisional; Region: PRK01060 322098000698 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 322098000699 AP (apurinic/apyrimidinic) site pocket; other site 322098000700 DNA interaction; other site 322098000701 Metal-binding active site; metal-binding site 322098000702 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 322098000703 DEAD-like helicases superfamily; Region: DEXDc; smart00487 322098000704 ATP binding site [chemical binding]; other site 322098000705 putative Mg++ binding site [ion binding]; other site 322098000706 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 322098000707 nucleotide binding region [chemical binding]; other site 322098000708 ATP-binding site [chemical binding]; other site 322098000709 Domain of unknown function (DUF205); Region: DUF205; cl00410 322098000710 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 322098000711 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 322098000712 nucleotide binding pocket [chemical binding]; other site 322098000713 K-X-D-G motif; other site 322098000714 catalytic site [active] 322098000715 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 322098000716 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 322098000717 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 322098000718 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 322098000719 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 322098000720 Sporulation Regulator WhiA C terminal domain; Region: HTH_WhiA; pfam02650 322098000721 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 322098000722 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 322098000723 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; cl14644 322098000724 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 322098000725 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 322098000726 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 322098000727 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 322098000728 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 322098000729 GTP-binding protein LepA; Provisional; Region: PRK05433 322098000730 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 322098000731 G1 box; other site 322098000732 putative GEF interaction site [polypeptide binding]; other site 322098000733 GTP/Mg2+ binding site [chemical binding]; other site 322098000734 Switch I region; other site 322098000735 G2 box; other site 322098000736 G3 box; other site 322098000737 Switch II region; other site 322098000738 G4 box; other site 322098000739 G5 box; other site 322098000740 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 322098000741 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 322098000742 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 322098000743 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 322098000744 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 322098000745 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 322098000746 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 322098000747 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 322098000748 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 322098000749 Walker A motif; other site 322098000750 ATP binding site [chemical binding]; other site 322098000751 Walker B motif; other site 322098000752 arginine finger; other site 322098000753 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 322098000754 trigger factor; Region: tig; TIGR00115 322098000755 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 322098000756 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 322098000757 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 322098000758 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 322098000759 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 322098000760 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 322098000761 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000762 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000763 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 322098000764 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 322098000765 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000766 cell division protein; Validated; Region: ftsH; CHL00176 322098000767 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000768 Walker A motif; other site 322098000769 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000770 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000771 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098000772 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 322098000773 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000774 putative transposase OrfB; Reviewed; Region: PHA02517 322098000775 Integrase core domain; Region: rve; cl01316 322098000776 Integrase core domain; Region: rve; cl01316 322098000777 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000778 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000779 chromosome segregation protein; Provisional; Region: PRK03918 322098000780 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 322098000781 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000782 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 322098000783 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 322098000784 Walker A motif; other site 322098000785 ATP binding site [chemical binding]; other site 322098000786 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 322098000787 IHF dimer interface [polypeptide binding]; other site 322098000788 IHF - DNA interface [nucleotide binding]; other site 322098000789 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 322098000790 dimer interface [polypeptide binding]; other site 322098000791 ssDNA binding site [nucleotide binding]; other site 322098000792 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098000793 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl00408 322098000794 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 322098000795 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 322098000796 ssDNA binding site [nucleotide binding]; other site 322098000797 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098000798 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; cl00257 322098000799 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 322098000800 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098000801 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 322098000802 FMN binding site [chemical binding]; other site 322098000803 dimer interface [polypeptide binding]; other site 322098000804 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 322098000805 GIY-YIG catalytic domain; Region: GIY-YIG; cl01061 322098000806 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 322098000807 excinuclease ABC subunit B; Provisional; Region: PRK05298 322098000808 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 322098000809 ATP binding site [chemical binding]; other site 322098000810 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 322098000811 nucleotide binding region [chemical binding]; other site 322098000812 ATP-binding site [chemical binding]; other site 322098000813 Ultra-violet resistance protein B; Region: UvrB; pfam12344 322098000814 UvrB/uvrC motif; Region: UVR; pfam02151 322098000815 SVM protein signal sequence; Region: SVM_signal; pfam12113 322098000816 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 322098000817 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 322098000818 Walker A motif; other site 322098000819 ATP binding site [chemical binding]; other site 322098000820 Walker B motif; other site 322098000821 arginine finger; other site 322098000822 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 322098000823 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 322098000824 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 322098000825 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 322098000826 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 322098000827 Walker A motif; other site 322098000828 ATP binding site [chemical binding]; other site 322098000829 Walker B motif; other site 322098000830 arginine finger; other site 322098000831 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 322098000832 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 322098000833 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 322098000834 motif 1; other site 322098000835 active site 322098000836 motif 2; other site 322098000837 motif 3; other site 322098000838 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 322098000839 Uncharacterised protein family (UPF0081); Region: UPF0081; cl00525 322098000840 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 322098000841 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 322098000842 domain; Region: GreA_GreB_N; pfam03449 322098000843 C-term; Region: GreA_GreB; pfam01272 322098000844 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 322098000845 active site 322098000846 motif I; other site 322098000847 motif II; other site 322098000848 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 322098000849 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 322098000850 S-adenosylmethionine binding site [chemical binding]; other site 322098000851 Uncharacterised protein family (UPF0154); Region: UPF0154; cl01536 322098000852 OsmC-like protein; Region: OsmC; cl00767 322098000853 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 322098000854 putative acyl-acceptor binding pocket; other site 322098000855 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 322098000856 folate binding site [chemical binding]; other site 322098000857 NADP+ binding site [chemical binding]; other site 322098000858 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 322098000859 dimerization interface [polypeptide binding]; other site 322098000860 active site 322098000861 dipeptidase PepV; Reviewed; Region: PRK07318 322098000862 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 322098000863 active site 322098000864 metal binding site [ion binding]; metal-binding site 322098000865 pyruvate kinase; Provisional; Region: PRK05826 322098000866 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 322098000867 domain interfaces; other site 322098000868 active site 322098000869 2-hydroxycarboxylate transporter family; Region: 2HCT; cl01386 322098000870 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 322098000871 Sulfatase; Region: Sulfatase; cl10460 322098000872 enolase; Provisional; Region: eno; PRK00077 322098000873 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 322098000874 dimer interface [polypeptide binding]; other site 322098000875 metal binding site [ion binding]; metal-binding site 322098000876 substrate binding pocket [chemical binding]; other site 322098000877 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 322098000878 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 322098000879 active site 322098000880 dimer interface [polypeptide binding]; other site 322098000881 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 322098000882 dimer interface [polypeptide binding]; other site 322098000883 active site 322098000884 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 322098000885 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 322098000886 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 322098000887 active site 322098000888 ADP/pyrophosphate binding site [chemical binding]; other site 322098000889 dimerization interface [polypeptide binding]; other site 322098000890 allosteric effector site; other site 322098000891 fructose-1,6-bisphosphate binding site; other site 322098000892 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 322098000893 DNA topoisomerase I; Validated; Region: PRK05582 322098000894 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 322098000895 active site 322098000896 interdomain interaction site; other site 322098000897 putative metal-binding site [ion binding]; other site 322098000898 nucleotide binding site [chemical binding]; other site 322098000899 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 322098000900 domain I; other site 322098000901 DNA binding groove [nucleotide binding] 322098000902 phosphate binding site [ion binding]; other site 322098000903 domain II; other site 322098000904 domain III; other site 322098000905 nucleotide binding site [chemical binding]; other site 322098000906 catalytic site [active] 322098000907 domain IV; other site 322098000908 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 322098000909 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; cl11977 322098000910 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 322098000911 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 322098000912 GTP/Mg2+ binding site [chemical binding]; other site 322098000913 G4 box; other site 322098000914 G5 box; other site 322098000915 G1 box; other site 322098000916 Switch I region; other site 322098000917 G2 box; other site 322098000918 G3 box; other site 322098000919 Switch II region; other site 322098000920 elongation factor P; Validated; Region: PRK00529 322098000921 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 322098000922 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 322098000923 RNA binding site [nucleotide binding]; other site 322098000924 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 322098000925 RNA binding site [nucleotide binding]; other site 322098000926 IPP transferase; Region: IPPT; cl00403 322098000927 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 322098000928 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 322098000929 putative active site [active] 322098000930 metal binding site [ion binding]; metal-binding site 322098000931 homodimer binding site [polypeptide binding]; other site 322098000932 conserved hypothetical protein YmdA/YtgF; Region: YmdA_YtgF; TIGR03319 322098000933 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 322098000934 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 322098000935 Zn2+ binding site [ion binding]; other site 322098000936 Mg2+ binding site [ion binding]; other site 322098000937 RmuC family; Region: RmuC; pfam02646 322098000938 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; cl11520 322098000939 glucose-inhibited division protein A; Region: gidA; TIGR00136 322098000940 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 322098000941 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 322098000942 S-adenosylmethionine binding site [chemical binding]; other site 322098000943 BAX inhibitor (BI)-1 like protein family. Mammalian members of this family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well characterized oncogene, or...; Region: BI-1-like; cl00473 322098000944 elongation factor Tu; Reviewed; Region: PRK00049 322098000945 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 322098000946 G1 box; other site 322098000947 GEF interaction site [polypeptide binding]; other site 322098000948 GTP/Mg2+ binding site [chemical binding]; other site 322098000949 Switch I region; other site 322098000950 G2 box; other site 322098000951 G3 box; other site 322098000952 Switch II region; other site 322098000953 G4 box; other site 322098000954 G5 box; other site 322098000955 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 322098000956 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 322098000957 Antibiotic Binding Site [chemical binding]; other site 322098000958 elongation factor G; Reviewed; Region: PRK00007 322098000959 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 322098000960 G1 box; other site 322098000961 putative GEF interaction site [polypeptide binding]; other site 322098000962 GTP/Mg2+ binding site [chemical binding]; other site 322098000963 Switch I region; other site 322098000964 G2 box; other site 322098000965 G3 box; other site 322098000966 Switch II region; other site 322098000967 G4 box; other site 322098000968 G5 box; other site 322098000969 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 322098000970 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 322098000971 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 322098000972 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 322098000973 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 322098000974 16S rRNA interaction site [nucleotide binding]; other site 322098000975 streptomycin interaction site [chemical binding]; other site 322098000976 23S rRNA interaction site [nucleotide binding]; other site 322098000977 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 322098000978 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 322098000979 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 322098000980 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 322098000981 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 322098000982 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 322098000983 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 322098000984 Rpb1 (beta') - Rpb6 (omega) interaction site [polypeptide binding]; other site 322098000985 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 322098000986 G-loop; other site 322098000987 DNA binding site [nucleotide binding] 322098000988 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 322098000989 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 322098000990 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 322098000991 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 322098000992 RPB10 interaction site [polypeptide binding]; other site 322098000993 RPB1 interaction site [polypeptide binding]; other site 322098000994 RPB11 interaction site [polypeptide binding]; other site 322098000995 RPB3 interaction site [polypeptide binding]; other site 322098000996 RPB12 interaction site [polypeptide binding]; other site 322098000997 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 322098000998 core dimer interface [polypeptide binding]; other site 322098000999 peripheral dimer interface [polypeptide binding]; other site 322098001000 L10 interface [polypeptide binding]; other site 322098001001 L11 interface [polypeptide binding]; other site 322098001002 putative EF-Tu interaction site [polypeptide binding]; other site 322098001003 putative EF-G interaction site [polypeptide binding]; other site 322098001004 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 322098001005 23S rRNA interface [nucleotide binding]; other site 322098001006 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 322098001007 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 322098001008 mRNA/rRNA interface [nucleotide binding]; other site 322098001009 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 322098001010 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 322098001011 23S rRNA interface [nucleotide binding]; other site 322098001012 L7/L12 interface [polypeptide binding]; other site 322098001013 putative thiostrepton binding site; other site 322098001014 L25 interface [polypeptide binding]; other site 322098001015 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 322098001016 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 322098001017 putative homodimer interface [polypeptide binding]; other site 322098001018 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 322098001019 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 322098001020 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 322098001021 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 322098001022 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 322098001023 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 322098001024 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 322098001025 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 322098001026 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 322098001027 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 322098001028 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 322098001029 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 322098001030 putative nucleic acid binding region [nucleotide binding]; other site 322098001031 G-X-X-G motif; other site 322098001032 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 322098001033 RNA binding site [nucleotide binding]; other site 322098001034 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 322098001035 Ribonuclease P; Region: Ribonuclease_P; cl00457 322098001036 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 322098001037 prolyl-tRNA synthetase; Provisional; Region: PRK08661 322098001038 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 322098001039 dimer interface [polypeptide binding]; other site 322098001040 motif 1; other site 322098001041 active site 322098001042 motif 2; other site 322098001043 motif 3; other site 322098001044 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity...; Region: ProRS_anticodon_zinc; cd00862 322098001045 anticodon binding site; other site 322098001046 zinc-binding site [ion binding]; other site 322098001047 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 322098001048 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 322098001049 IHF - DNA interface [nucleotide binding]; other site 322098001050 IHF dimer interface [polypeptide binding]; other site 322098001051 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 322098001052 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 322098001053 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 322098001054 GTP-binding protein Der; Reviewed; Region: PRK00093 322098001055 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 322098001056 G1 box; other site 322098001057 GTP/Mg2+ binding site [chemical binding]; other site 322098001058 Switch I region; other site 322098001059 G2 box; other site 322098001060 Switch II region; other site 322098001061 G3 box; other site 322098001062 G4 box; other site 322098001063 G5 box; other site 322098001064 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 322098001065 G1 box; other site 322098001066 GTP/Mg2+ binding site [chemical binding]; other site 322098001067 Switch I region; other site 322098001068 G2 box; other site 322098001069 G3 box; other site 322098001070 Switch II region; other site 322098001071 G4 box; other site 322098001072 G5 box; other site 322098001073 cytidylate kinase; Provisional; Region: cmk; PRK00023 322098001074 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 322098001075 CMP-binding site; other site 322098001076 The sites determining sugar specificity; other site 322098001077 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 322098001078 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 322098001079 RNA binding surface [nucleotide binding]; other site 322098001080 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 322098001081 active site 322098001082 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 322098001083 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 322098001084 RNA binding site [nucleotide binding]; other site 322098001085 active site 322098001086 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 322098001087 catalytic residues [active] 322098001088 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001089 cell division protein; Validated; Region: ftsH; CHL00176 322098001090 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 322098001091 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 322098001092 active site 322098001093 HIGH motif; other site 322098001094 KMSKS motif; other site 322098001095 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 322098001096 tRNA binding surface [nucleotide binding]; other site 322098001097 anticodon binding site; other site 322098001098 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; cl00304 322098001099 Predicted methyltransferases [General function prediction only]; Region: COG0313 322098001100 DNA polymerase III subunit delta'; Validated; Region: PRK08058 322098001101 thymidylate kinase; Validated; Region: tmk; PRK00698 322098001102 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 322098001103 TMP-binding site; other site 322098001104 ATP-binding site [chemical binding]; other site 322098001105 pseudouridylate synthase I; Region: hisT_truA; TIGR00071 322098001106 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 322098001107 dimerization interface 3.5A [polypeptide binding]; other site 322098001108 active site 322098001109 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 322098001110 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 322098001111 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 322098001112 alphaNTD homodimer interface [polypeptide binding]; other site 322098001113 alphaNTD - beta interaction site [polypeptide binding]; other site 322098001114 alphaNTD - beta' interaction site [polypeptide binding]; other site 322098001115 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 322098001116 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 322098001117 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 322098001118 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 322098001119 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 322098001120 rRNA binding site [nucleotide binding]; other site 322098001121 predicted 30S ribosome binding site; other site 322098001122 methionine aminopeptidase; Reviewed; Region: PRK07281 322098001123 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 322098001124 active site 322098001125 adenylate kinase; Reviewed; Region: adk; PRK00279 322098001126 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 322098001127 AMP-binding site [chemical binding]; other site 322098001128 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 322098001129 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 322098001130 SecY translocase; Region: SecY; pfam00344 322098001131 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 322098001132 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins...; Region: Ribosomal_L30; cd01658 322098001133 23S rRNA binding site [nucleotide binding]; other site 322098001134 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 322098001135 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 322098001136 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 322098001137 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 322098001138 23S rRNA interface [nucleotide binding]; other site 322098001139 5S rRNA interface [nucleotide binding]; other site 322098001140 L27 interface [polypeptide binding]; other site 322098001141 L5 interface [polypeptide binding]; other site 322098001142 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 322098001143 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 322098001144 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 322098001145 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 322098001146 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 322098001147 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 322098001148 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 322098001149 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 322098001150 KOW motif; Region: KOW; cl00354 322098001151 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 322098001152 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 322098001153 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 322098001154 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 322098001155 23S rRNA interface [nucleotide binding]; other site 322098001156 5S rRNA interface [nucleotide binding]; other site 322098001157 putative antibiotic binding site [chemical binding]; other site 322098001158 L25 interface [polypeptide binding]; other site 322098001159 L27 interface [polypeptide binding]; other site 322098001160 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 322098001161 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 322098001162 G-X-X-G motif; other site 322098001163 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 322098001164 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 322098001165 putative translocon binding site; other site 322098001166 protein-rRNA interface [nucleotide binding]; other site 322098001167 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 322098001168 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 322098001169 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 322098001170 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 322098001171 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 322098001172 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 322098001173 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 322098001174 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 322098001175 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 322098001176 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 322098001177 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 322098001178 Walker A/P-loop; other site 322098001179 ATP binding site [chemical binding]; other site 322098001180 Q-loop/lid; other site 322098001181 ABC transporter signature motif; other site 322098001182 Walker B; other site 322098001183 D-loop; other site 322098001184 H-loop/switch region; other site 322098001185 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 322098001186 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 322098001187 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 322098001188 Walker A/P-loop; other site 322098001189 ATP binding site [chemical binding]; other site 322098001190 Q-loop/lid; other site 322098001191 ABC transporter signature motif; other site 322098001192 Walker B; other site 322098001193 D-loop; other site 322098001194 H-loop/switch region; other site 322098001195 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 322098001196 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 322098001197 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cd00995 322098001198 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 322098001199 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 322098001200 dimer interface [polypeptide binding]; other site 322098001201 conserved gate region; other site 322098001202 putative PBP binding loops; other site 322098001203 ABC-ATPase subunit interface; other site 322098001204 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 322098001205 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 322098001206 dimer interface [polypeptide binding]; other site 322098001207 conserved gate region; other site 322098001208 ABC-ATPase subunit interface; other site 322098001209 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 322098001210 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 322098001211 active site 322098001212 Zn binding site [ion binding]; other site 322098001213 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 322098001214 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 322098001215 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 322098001216 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 322098001217 Uncharacterized conserved protein [Function unknown]; Region: COG1284 322098001218 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 322098001219 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098001220 active site 322098001221 HIGH motif; other site 322098001222 nucleotide binding site [chemical binding]; other site 322098001223 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 322098001224 active site 322098001225 KMSKS motif; other site 322098001226 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 322098001227 tRNA binding surface [nucleotide binding]; other site 322098001228 anticodon binding site; other site 322098001229 GTP-binding protein YchF; Reviewed; Region: PRK09601 322098001230 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 322098001231 G1 box; other site 322098001232 GTP/Mg2+ binding site [chemical binding]; other site 322098001233 Switch I region; other site 322098001234 G2 box; other site 322098001235 Switch II region; other site 322098001236 G3 box; other site 322098001237 G4 box; other site 322098001238 G5 box; other site 322098001239 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 322098001240 GTPase RsgA; Reviewed; Region: PRK00098 322098001241 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 322098001242 GTPase/OB domain interface [polypeptide binding]; other site 322098001243 GTPase/Zn-binding domain interface [polypeptide binding]; other site 322098001244 GTP/Mg2+ binding site [chemical binding]; other site 322098001245 G4 box; other site 322098001246 G5 box; other site 322098001247 G1 box; other site 322098001248 Switch I region; other site 322098001249 G2 box; other site 322098001250 G3 box; other site 322098001251 Switch II region; other site 322098001252 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of...; Region: SHMT; cd00378 322098001253 dimer interface [polypeptide binding]; other site 322098001254 glycine-pyridoxal phosphate binding site [chemical binding]; other site 322098001255 active site 322098001256 folate binding site [chemical binding]; other site 322098001257 Cobalt transport protein; Region: CbiQ; cl00463 322098001258 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13634 322098001259 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 322098001260 Walker A/P-loop; other site 322098001261 ATP binding site [chemical binding]; other site 322098001262 Q-loop/lid; other site 322098001263 ABC transporter signature motif; other site 322098001264 Walker B; other site 322098001265 D-loop; other site 322098001266 H-loop/switch region; other site 322098001267 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13632 322098001268 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 322098001269 Walker A/P-loop; other site 322098001270 ATP binding site [chemical binding]; other site 322098001271 Q-loop/lid; other site 322098001272 ABC transporter signature motif; other site 322098001273 Walker B; other site 322098001274 D-loop; other site 322098001275 H-loop/switch region; other site 322098001276 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_1; cd09606 322098001277 oligoendopeptidase, M3 family; Region: M3_not_pepF; TIGR02289 322098001278 active site 322098001279 Zn binding site [ion binding]; other site 322098001280 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 322098001281 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 322098001282 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 322098001283 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 322098001284 substrate binding site [chemical binding]; other site 322098001285 hinge regions; other site 322098001286 ADP binding site [chemical binding]; other site 322098001287 catalytic site [active] 322098001288 hypothetical protein; Provisional; Region: PRK08185 322098001289 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 322098001290 intersubunit interface [polypeptide binding]; other site 322098001291 active site 322098001292 zinc binding site [ion binding]; other site 322098001293 Na+ binding site [ion binding]; other site 322098001294 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 322098001295 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 322098001296 active site 322098001297 motif I; other site 322098001298 motif II; other site 322098001299 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 322098001300 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 322098001301 substrate binding site [chemical binding]; other site 322098001302 dimer interface [polypeptide binding]; other site 322098001303 catalytic triad [active] 322098001304 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 322098001305 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 322098001306 hinge region; other site 322098001307 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 322098001308 putative nucleotide binding site [chemical binding]; other site 322098001309 uridine monophosphate binding site [chemical binding]; other site 322098001310 homohexameric interface [polypeptide binding]; other site 322098001311 elongation factor Ts; Provisional; Region: tsf; PRK09377 322098001312 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 322098001313 Elongation factor TS; Region: EF_TS; pfam00889 322098001314 Elongation factor TS; Region: EF_TS; pfam00889 322098001315 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 322098001316 rRNA interaction site [nucleotide binding]; other site 322098001317 S8 interaction site; other site 322098001318 putative laminin-1 binding site; other site 322098001319 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 322098001320 trimer interface [polypeptide binding]; other site 322098001321 active site 322098001322 Uracil DNA glycosylase superfamily; Region: UDG; cl00483 322098001323 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 322098001324 Catalytic site [active] 322098001325 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001326 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001327 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001328 Acetokinase family; Region: Acetate_kinase; cl01029 322098001329 Haemolysin-III related; Region: HlyIII; cl03831 322098001330 DNA polymerase III PolC; Validated; Region: polC; PRK00448 322098001331 primosome assembly protein PriA; Validated; Region: PRK05580 322098001332 primosome assembly protein PriA; Validated; Region: PRK05580 322098001333 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 322098001334 ATP binding site [chemical binding]; other site 322098001335 putative Mg++ binding site [ion binding]; other site 322098001336 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 322098001337 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 322098001338 Domain of unknown function DUF21; Region: DUF21; pfam01595 322098001339 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 322098001340 Transporter associated domain; Region: CorC_HlyC; pfam03471 322098001341 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 322098001342 putative active site [active] 322098001343 catalytic residue [active] 322098001344 Ribosome-binding factor A; Region: RBFA; cl00542 322098001345 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 322098001346 translation initiation factor IF-2; Region: IF-2; TIGR00487 322098001347 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 322098001348 G1 box; other site 322098001349 putative GEF interaction site [polypeptide binding]; other site 322098001350 GTP/Mg2+ binding site [chemical binding]; other site 322098001351 Switch I region; other site 322098001352 G2 box; other site 322098001353 G3 box; other site 322098001354 Switch II region; other site 322098001355 G4 box; other site 322098001356 G5 box; other site 322098001357 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 322098001358 Translation-initiation factor 2; Region: IF-2; pfam11987 322098001359 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 322098001360 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 322098001361 putative RNA binding cleft [nucleotide binding]; other site 322098001362 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 322098001363 NusA N-terminal domain; Region: NusA_N; pfam08529 322098001364 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and...; Region: S1_NusA; cd04455 322098001365 RNA binding site [nucleotide binding]; other site 322098001366 homodimer interface [polypeptide binding]; other site 322098001367 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 322098001368 G-X-X-G motif; other site 322098001369 Domain of unknown function(DUF2779); Region: DUF2779; pfam11074 322098001370 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 322098001371 SmpB-tmRNA interface; other site 322098001372 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 322098001373 dimer interface [polypeptide binding]; other site 322098001374 substrate binding site [chemical binding]; other site 322098001375 metal binding sites [ion binding]; metal-binding site 322098001376 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 322098001377 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 322098001378 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 322098001379 THUMP domain; Region: THUMP; cl12076 322098001380 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 322098001381 Ligand Binding Site [chemical binding]; other site 322098001382 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 322098001383 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 322098001384 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 322098001385 Active site [active] 322098001386 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 322098001387 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098001388 active site 322098001389 HIGH motif; other site 322098001390 nucleotide binding site [chemical binding]; other site 322098001391 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098001392 active site 322098001393 KMSKS motif; other site 322098001394 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 322098001395 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 322098001396 active site 322098001397 HIGH motif; other site 322098001398 KMSKS motif; other site 322098001399 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 322098001400 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 322098001401 23S rRNA interface [nucleotide binding]; other site 322098001402 L3 interface [polypeptide binding]; other site 322098001403 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1; Region: GATase1_DJ-1; cd03135 322098001404 conserved cys residue [active] 322098001405 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 322098001406 16S/18S rRNA binding site [nucleotide binding]; other site 322098001407 S13e-L30e interaction site [polypeptide binding]; other site 322098001408 25S rRNA binding site [nucleotide binding]; other site 322098001409 Nitrogen regulatory protein P-II; Region: P-II; cl00412 322098001410 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits...; Region: TM_PBP2; cl00427 322098001411 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 322098001412 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 322098001413 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001414 Walker A/P-loop; other site 322098001415 ATP binding site [chemical binding]; other site 322098001416 Q-loop/lid; other site 322098001417 ABC transporter signature motif; other site 322098001418 Walker B; other site 322098001419 D-loop; other site 322098001420 H-loop/switch region; other site 322098001421 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 322098001422 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 322098001423 RNA binding surface [nucleotide binding]; other site 322098001424 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 322098001425 active site 322098001426 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 322098001427 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 322098001428 Walker A motif; other site 322098001429 ATP binding site [chemical binding]; other site 322098001430 Walker B motif; other site 322098001431 arginine finger; other site 322098001432 Peptidase family M41; Region: Peptidase_M41; pfam01434 322098001433 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 322098001434 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 322098001435 Ligand Binding Site [chemical binding]; other site 322098001436 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 322098001437 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 322098001438 dimer interface [polypeptide binding]; other site 322098001439 anticodon binding site; other site 322098001440 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 322098001441 homodimer interface [polypeptide binding]; other site 322098001442 motif 1; other site 322098001443 active site 322098001444 motif 2; other site 322098001445 GAD domain; Region: GAD; pfam02938 322098001446 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 322098001447 active site 322098001448 motif 3; other site 322098001449 histidyl-tRNA synthetase; Region: hisS; TIGR00442 322098001450 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 322098001451 dimer interface [polypeptide binding]; other site 322098001452 motif 1; other site 322098001453 active site 322098001454 motif 2; other site 322098001455 motif 3; other site 322098001456 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 322098001457 anticodon binding site; other site 322098001458 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 322098001459 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 322098001460 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 322098001461 synthetase active site [active] 322098001462 NTP binding site [chemical binding]; other site 322098001463 metal binding site [ion binding]; metal-binding site 322098001464 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named...; Region: TGS_RelA_SpoT; cd01668 322098001465 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 322098001466 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 322098001467 Ligand Binding Site [chemical binding]; other site 322098001468 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 322098001469 multimer interface [polypeptide binding]; other site 322098001470 active site 322098001471 catalytic triad [active] 322098001472 protein interface 1 [polypeptide binding]; other site 322098001473 NAD synthetase; Reviewed; Region: nadE; PRK02628 322098001474 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 322098001475 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 322098001476 ring oligomerisation interface [polypeptide binding]; other site 322098001477 ATP/Mg binding site [chemical binding]; other site 322098001478 stacking interactions; other site 322098001479 hinge regions; other site 322098001480 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts...; Region: cpn10; cd00320 322098001481 oligomerisation interface [polypeptide binding]; other site 322098001482 mobile loop; other site 322098001483 roof hairpin; other site 322098001484 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 322098001485 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 322098001486 Thymidine kinase; Region: TK; cl00631 322098001487 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 322098001488 nucleoside/Zn binding site; other site 322098001489 dimer interface [polypeptide binding]; other site 322098001490 catalytic motif [active] 322098001491 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13299 322098001492 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 322098001493 active site 322098001494 NTP binding site [chemical binding]; other site 322098001495 metal binding triad [ion binding]; metal-binding site 322098001496 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 322098001497 3'-5' exoribonuclease YhaM; Provisional; Region: PRK13480 322098001498 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 322098001499 Integrase core domain; Region: rve; cl01316 322098001500 DNA topoisomerase IV subunit A; Provisional; Region: PRK13979 322098001501 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001502 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001503 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001504 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 322098001505 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 322098001506 active site 322098001507 metal binding site [ion binding]; metal-binding site 322098001508 interdomain interaction site; other site 322098001509 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001510 Walker A motif; other site 322098001511 ATP binding site [chemical binding]; other site 322098001512 Walker B motif; other site 322098001513 RNA polymerase sigma factor SigF; Reviewed; Region: PRK07408 322098001514 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 322098001515 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 322098001516 Walker A/P-loop; other site 322098001517 ATP binding site [chemical binding]; other site 322098001518 Q-loop/lid; other site 322098001519 ABC transporter signature motif; other site 322098001520 Walker B; other site 322098001521 D-loop; other site 322098001522 H-loop/switch region; other site 322098001523 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 322098001524 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 322098001525 ABC-ATPase subunit interface; other site 322098001526 dimer interface [polypeptide binding]; other site 322098001527 putative PBP binding regions; other site 322098001528 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 322098001529 ABC-ATPase subunit interface; other site 322098001530 dimer interface [polypeptide binding]; other site 322098001531 putative PBP binding regions; other site 322098001532 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 322098001533 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-...; Region: ABC_Metallic_Cations; cd03235 322098001534 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface...; Region: TroA-like; cl00262 322098001535 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 322098001536 intersubunit interface [polypeptide binding]; other site 322098001537 GTPase CgtA; Reviewed; Region: obgE; PRK12297 322098001538 GTP1/OBG; Region: GTP1_OBG; pfam01018 322098001539 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 322098001540 G1 box; other site 322098001541 GTP/Mg2+ binding site [chemical binding]; other site 322098001542 Switch I region; other site 322098001543 G2 box; other site 322098001544 G3 box; other site 322098001545 Switch II region; other site 322098001546 G4 box; other site 322098001547 G5 box; other site 322098001548 Domain of unknown function (DUF1967); Region: DUF1967; cl07779 322098001549 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 322098001550 Protein of unknown function (DUF464); Region: DUF464; cl01080 322098001551 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 322098001552 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 322098001553 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 322098001554 active site residue [active] 322098001555 seryl-tRNA synthetase; Provisional; Region: PRK05431 322098001556 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 322098001557 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 322098001558 dimer interface [polypeptide binding]; other site 322098001559 active site 322098001560 motif 1; other site 322098001561 motif 2; other site 322098001562 motif 3; other site 322098001563 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 322098001564 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 322098001565 HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP; Region: ABC_HisP_GlnQ_permeases; cd03262 322098001566 Walker A/P-loop; other site 322098001567 ATP binding site [chemical binding]; other site 322098001568 Q-loop/lid; other site 322098001569 ABC transporter signature motif; other site 322098001570 Walker B; other site 322098001571 D-loop; other site 322098001572 H-loop/switch region; other site 322098001573 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 322098001574 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; Region: PBPb; cd00134 322098001575 substrate binding pocket [chemical binding]; other site 322098001576 membrane-bound complex binding site; other site 322098001577 hinge residues; other site 322098001578 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 322098001579 dimer interface [polypeptide binding]; other site 322098001580 conserved gate region; other site 322098001581 putative PBP binding loops; other site 322098001582 ABC-ATPase subunit interface; other site 322098001583 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001584 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001585 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 322098001586 Propanediol utilisation protein PduL; Region: PduL; pfam06130 322098001587 Propanediol utilisation protein PduL; Region: PduL; pfam06130 322098001588 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 322098001589 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 322098001590 Zn2+ binding site [ion binding]; other site 322098001591 Mg2+ binding site [ion binding]; other site 322098001592 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 322098001593 SpoVG; Region: SpoVG; cl00915 322098001594 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 322098001595 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 322098001596 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 322098001597 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 322098001598 MatE; Region: MatE; pfam01554 322098001599 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 322098001600 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 322098001601 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 322098001602 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 322098001603 catalytic site [active] 322098001604 G-X2-G-X-G-K; other site 322098001605 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 322098001606 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 322098001607 HIGH motif; other site 322098001608 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 322098001609 active site 322098001610 KMSKS motif; other site 322098001611 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 322098001612 tRNA binding surface [nucleotide binding]; other site 322098001613 Phosphopantetheine attachment site; Region: PP-binding; cl09936 322098001614 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 322098001615 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 322098001616 oligomer interface [polypeptide binding]; other site 322098001617 active site 322098001618 metal binding site [ion binding]; metal-binding site 322098001619 50S ribosomal protein L20/unknown domain fusion protein; Provisional; Region: PRK14537 322098001620 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 322098001621 23S rRNA binding site [nucleotide binding]; other site 322098001622 L21 binding site [polypeptide binding]; other site 322098001623 L13 binding site [polypeptide binding]; other site 322098001624 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 322098001625 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 322098001626 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 322098001627 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 322098001628 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 322098001629 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase...; Region: TGS_ThrRS_N; cd01667 322098001630 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 322098001631 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 322098001632 active site 322098001633 dimer interface [polypeptide binding]; other site 322098001634 motif 1; other site 322098001635 motif 2; other site 322098001636 motif 3; other site 322098001637 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 322098001638 anticodon binding site; other site 322098001639 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 322098001640 DHH family; Region: DHH; pfam01368 322098001641 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 322098001642 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 322098001643 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 322098001644 G1 box; other site 322098001645 GTP/Mg2+ binding site [chemical binding]; other site 322098001646 Switch I region; other site 322098001647 G2 box; other site 322098001648 Switch II region; other site 322098001649 G3 box; other site 322098001650 G4 box; other site 322098001651 G5 box; other site 322098001652 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 322098001653 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 322098001654 DHH family; Region: DHH; pfam01368 322098001655 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 322098001656 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 322098001657 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 322098001658 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 322098001659 dimer interface [polypeptide binding]; other site 322098001660 conserved gate region; other site 322098001661 putative PBP binding loops; other site 322098001662 ABC-ATPase subunit interface; other site 322098001663 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 322098001664 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 322098001665 dimer interface [polypeptide binding]; other site 322098001666 conserved gate region; other site 322098001667 putative PBP binding loops; other site 322098001668 ABC-ATPase subunit interface; other site 322098001669 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 322098001670 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001671 Walker A/P-loop; other site 322098001672 ATP binding site [chemical binding]; other site 322098001673 Q-loop/lid; other site 322098001674 ABC transporter signature motif; other site 322098001675 Walker B; other site 322098001676 D-loop; other site 322098001677 H-loop/switch region; other site 322098001678 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 322098001679 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 322098001680 putative dimer interface [polypeptide binding]; other site 322098001681 putative anticodon binding site; other site 322098001682 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 322098001683 homodimer interface [polypeptide binding]; other site 322098001684 motif 1; other site 322098001685 motif 2; other site 322098001686 active site 322098001687 motif 3; other site 322098001688 Sequencing Center: Integrated Genomics, Inc., 2201 W. Campbell Park Dr., Chicago IL 60612 322098001689 Geminivirus Rep catalytic domain; Region: Gemini_AL1; pfam00799 322098001690 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001691 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 322098001692 dimer interface [polypeptide binding]; other site 322098001693 ssDNA binding site [nucleotide binding]; other site 322098001694 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098001695 Sequencing Center: Integrated Genomics, Inc., 2201 W. Campbell Park Dr., Chicago IL 60612 322098001696 Plasmid replication protein; Region: Rep_2; pfam01719 322098001697 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001698 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001699 Walker A/P-loop; other site 322098001700 ATP binding site [chemical binding]; other site 322098001701 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001702 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 322098001703 dimer interface [polypeptide binding]; other site 322098001704 ssDNA binding site [nucleotide binding]; other site 322098001705 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098001706 Sequencing Center: Integrated Genomics, Inc., 2201 W. Campbell Park Dr., Chicago IL 60612 322098001707 Geminivirus Rep catalytic domain; Region: Gemini_AL1; pfam00799 322098001708 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001709 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 322098001710 dimer interface [polypeptide binding]; other site 322098001711 ssDNA binding site [nucleotide binding]; other site 322098001712 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098001713 Sequencing Center: Integrated Genomics, Inc., 2201 W. Campbell Park Dr., Chicago IL 60612 322098001714 Plasmid replication protein; Region: Rep_2; pfam01719 322098001715 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop NTPase; cl09099 322098001716 Protein of unknown function (DUF2963); Region: DUF2963; pfam11178 322098001717 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 322098001718 dimer interface [polypeptide binding]; other site 322098001719 ssDNA binding site [nucleotide binding]; other site 322098001720 tetramer (dimer of dimers) interface [polypeptide binding]; other site 322098001721 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261